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Add CO ontologies and gene source dbs to jsonld file so noctua doesn't
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error when adding
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elserj committed Jun 1, 2017
1 parent 8e934b5 commit 868c3e2
Showing 1 changed file with 15 additions and 1 deletion.
16 changes: 15 additions & 1 deletion minerva-core/src/main/resources/amigo_context_gen.jsonld
Original file line number Diff line number Diff line change
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"COG_Pathway" : "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=",
"CORIELL" : "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=",
"CORUM" : "http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=",
"CO_320" : "http://browser.planteome.org/amigo/term/CO_320:",
"CO_321" : "http://browser.planteome.org/amigo/term/CO_321:",
"CO_322" : "http://browser.planteome.org/amigo/term/CO_322:",
"CO_331" : "http://browser.planteome.org/amigo/term/CO_331:",
"CO_334" : "http://browser.planteome.org/amigo/term/CO_334:",
"CO_336" : "http://browser.planteome.org/amigo/term/CO_336:",
"CO_339" : "http://browser.planteome.org/amigo/term/CO_339:",
"CO_341" : "http://browser.planteome.org/amigo/term/CO_341:",
"DDBJ" : "http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=",
"ECK" : "http://www.ecogene.org/geneInfo.php?eck_id=",
"ECOGENE" : "http://www.ecogene.org/geneInfo.php?eg_id=",
"EMBL" : "http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=",
"ENA" : "http://www.ebi.ac.uk/ena/data/view/",
"ENSEMBL_GeneID" : "http://www.ensembl.org/id/",
"EnsemblPlants" : "http://www.ensemblgenomes.org/id/",
"ENZYME" : "http://www.expasy.ch/cgi-bin/nicezyme.pl?",
"EchoBASE" : "http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=",
"EcoCyc" : "http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=",
Expand All @@ -44,6 +53,8 @@
"GR_PROTEIN" : "http://www.gramene.org/db/protein/protein_search?acc=",
"GR_QTL" : "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=",
"GR_REF" : "http://www.gramene.org/db/literature/pub_search?ref_id=",
"GRIN" : "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=",
"GRINDesc" : "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=",
"Gene3D" : "http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=",
"GeneDB" : "http://www.genedb.org/gene/",
"H-invDB_cDNA" : "http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=",
Expand Down Expand Up @@ -89,6 +100,8 @@
"PATRIC" : "http://patric.vbi.vt.edu/gene/overview.php?fid=",
"PIR" : "http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=",
"PIRSF" : "http://pir.georgetown.edu/cgi-bin/ipcSF?id=",
"Planteome_gene" : "http://browser.planteome.org/amigo/gene_product/Planteome_gene:",
"PO" : "http://browser.planteome.org/amigo/term/PO:",
"PO_REF" : "http://wiki.plantontology.org:8080/index.php/PO_REF:",
"PRINTS" : "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=",
"PSI-MOD" : "http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:",
Expand All @@ -99,6 +112,7 @@
"PubChem_BioAssay" : "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=",
"PubChem_Compound" : "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=",
"PubChem_Substance" : "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=",
"RAP-DB" : "http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=",
"REBASE" : "http://rebase.neb.com/rebase/enz/",
"RHEA" : "http://www.ebi.ac.uk/rhea/reaction.xhtml?id=",
"RNAcentral" : "http://rnacentral.org/rna/",
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"dictyBase_REF" : "http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=",
"taxon" : "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="
}
}
}

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