restored changes

[pgaudet]

No description provided.

[github-actions]

Here's a diff of how these changes impact the classified ontology:

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-12-01/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-master.owl/reasoned.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-12-01/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

3-beta-hydroxysteroid 3-dehydrogenase (NADP+) activity http://purl.obolibrary.org/obo/GO_0000253

Removed

• 3-beta-hydroxysteroid 3-dehydrogenase (NADP+) activity definition "Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H+."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "EC:1.1.1.270"

  • database_cross_reference "PMID:9811880"

• 3-beta-hydroxysteroid 3-dehydrogenase (NADP+) activity comment "Note that zymosterol is cholesta-8,24-dien-3-ol."

Added

• 3-beta-hydroxysteroid 3-dehydrogenase (NADP+) activity definition "Catalysis of the reaction: a 3-betahydroxyl sterol + NADP+ = a 3-oxosterol sterol + NADPH + H+."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "EC:1.1.1.270"

  • database_cross_reference "PMID:9811880"

ATP-dependent DNA/DNA annealing activity http://purl.obolibrary.org/obo/GO_0036310

Removed

• ATP-dependent DNA/DNA annealing activity SubClassOf ATP-dependent activity

Added

• ATP-dependent DNA/DNA annealing activity term tracker item "https://github.com/geneontology/go-ontology/issues/29334"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• ATP-dependent DNA/DNA annealing activity SubClassOf ATP-dependent activity, acting on DNA

C-4 methylsterol oxidase activity http://purl.obolibrary.org/obo/GO_0000254

Removed

• C-4 methylsterol oxidase activity comment "Note that zymosterol is cholesta-8,24-dien-3-ol."

H3K27me3 histone reader activity http://purl.obolibrary.org/obo/GO_0061628

Removed

• H3K27me3 histone reader activity created_by "dph"

• H3K27me3 histone reader activity creation_date "2014-05-14T15:36:53Z"

• H3K27me3 histone reader activity has_exact_synonym "H3-K27me3 modified histone binding"

  • database_cross_reference "GOC:dph"

• H3K27me3 histone reader activity label "H3K27me3 modified histone binding"

• H3K27me3 histone reader activity definition "Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "PMID:23948251"

• H3K27me3 histone reader activity SubClassOf methylated histone binding

Added

• H3K27me3 histone reader activity label "H3K27me3 histone reader activity"

• H3K27me3 histone reader activity has_narrow_synonym "H3-K27me3 modified histone binding"

• H3K27me3 histone reader activity has_narrow_synonym "H3K27me3 modified histone binding"

• H3K27me3 histone reader activity term tracker item "https://github.com/geneontology/go-ontology/issues/27427"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• H3K27me3 histone reader activity definition "A histone reader that recognizes a histone H3 trimethylated at lysine 27."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "PMID:23948251"

• H3K27me3 histone reader activity SubClassOf has part some methylated histone binding

• H3K27me3 histone reader activity SubClassOf histone reader activity

H3K36me3 histone reader activity http://purl.obolibrary.org/obo/GO_0140003

Added

• H3K36me3 histone reader activity definition "A histone reader that recognizes a histone H3 trimethylated at lysine 36."

  • database_cross_reference "PMID:16364921"

  • database_cross_reference "PMID:15489290"

• H3K36me3 histone reader activity has_narrow_synonym "H3K36me3 modified histone binding"

• H3K36me3 histone reader activity label "H3K36me3 histone reader activity"

• H3K36me3 histone reader activity has_obo_namespace "molecular_function"

• H3K36me3 histone reader activity id "GO:0140003"

• H3K36me3 histone reader activity creation_date "2024-11-29T14:20:22Z"

• H3K36me3 histone reader activity term tracker item "https://github.com/geneontology/go-ontology/issues/29337"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• H3K36me3 histone reader activity created_by "pg"

• H3K36me3 histone reader activity has_narrow_synonym "H3-K36me3 modified histone binding"

• Class: H3K36me3 histone reader activity

• H3K36me3 histone reader activity SubClassOf histone reader activity

• H3K36me3 histone reader activity SubClassOf has part some methylated histone binding

H3K4me3 histone reader activity http://purl.obolibrary.org/obo/GO_0140002

Added

• H3K4me3 histone reader activity term tracker item "https://github.com/geneontology/go-ontology/issues/29337"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• H3K4me3 histone reader activity has_narrow_synonym "H3-K4me3 modified histone binding"

• H3K4me3 histone reader activity created_by "pg"

• H3K4me3 histone reader activity has_narrow_synonym "H3K4me3 modified histone binding"

• H3K4me3 histone reader activity has_obo_namespace "molecular_function"

• H3K4me3 histone reader activity id "GO:0140002"

• H3K4me3 histone reader activity label "H3K4me3 histone reader activity"

• H3K4me3 histone reader activity definition "A histone reader that recognizes a histone H3 trimethylated at lysine 4."

  • database_cross_reference "PMID:23318260"

  • database_cross_reference "PMID:15647753"

• H3K4me3 histone reader activity creation_date "2024-11-29T14:13:16Z"

• Class: H3K4me3 histone reader activity

• H3K4me3 histone reader activity SubClassOf histone reader activity

• H3K4me3 histone reader activity SubClassOf has part some methylated histone binding

H3K9me3 histone reader activity http://purl.obolibrary.org/obo/GO_0062072

Removed

• H3K9me3 histone reader activity definition "Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation."

  • database_cross_reference "PMID:30110338"

• H3K9me3 histone reader activity creation_date "2018-09-05T12:58:43Z"

• H3K9me3 histone reader activity created_by "dph"

• H3K9me3 histone reader activity label "H3K9me3 modified histone binding"

• H3K9me3 histone reader activity SubClassOf methylated histone binding

Added

• H3K9me3 histone reader activity term tracker item "https://github.com/geneontology/go-ontology/issues/27427"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• H3K9me3 histone reader activity label "H3K9me3 histone reader activity"

• H3K9me3 histone reader activity definition "A histone reader that recognizes a histone H3 trimethylated at lysine 9."

  • database_cross_reference "PMID:30110338"

• H3K9me3 histone reader activity has_narrow_synonym "H3K9me3 modified histone binding"

• H3K9me3 histone reader activity SubClassOf has part some methylated histone binding

• H3K9me3 histone reader activity SubClassOf histone reader activity

H3Q5ser histone reader activity http://purl.obolibrary.org/obo/GO_0140004

Added

• H3Q5ser histone reader activity creation_date "2024-11-29T14:37:52Z"

• H3Q5ser histone reader activity definition "A histone reader that recognizes a histone H3 serotonylated at glutamine 5."

  • database_cross_reference "PMID:34144982"

• H3Q5ser histone reader activity has_exact_synonym "H3Q5-serotonin histone reader activity"

• H3Q5ser histone reader activity label "H3Q5ser histone reader activity"

• H3Q5ser histone reader activity term tracker item "https://github.com/geneontology/go-ontology/issues/29337"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• H3Q5ser histone reader activity has_obo_namespace "molecular_function"

• H3Q5ser histone reader activity has_narrow_synonym "H3Q5-serotonin modified histone binding"

• H3Q5ser histone reader activity created_by "pg"

• H3Q5ser histone reader activity id "GO:0140004"

• Class: H3Q5ser histone reader activity

• H3Q5ser histone reader activity SubClassOf has part some methylated histone binding

• H3Q5ser histone reader activity SubClassOf histone reader activity

H4K20me2 histone reader activity http://purl.obolibrary.org/obo/GO_0140005

Added

• H4K20me2 histone reader activity created_by "pg"

• H4K20me2 histone reader activity has_narrow_synonym "H4K20me2 modified histone binding"

• H4K20me2 histone reader activity id "GO:0140005"

• H4K20me2 histone reader activity definition "A histone reader that recognizes a histone H4 dimethylated at lysine 20."

  • database_cross_reference "PMID:22150589"

• H4K20me2 histone reader activity label "H4K20me2 histone reader activity"

• H4K20me2 histone reader activity has_obo_namespace "molecular_function"

• H4K20me2 histone reader activity creation_date "2024-11-29T15:16:39Z"

• H4K20me2 histone reader activity term tracker item "https://github.com/geneontology/go-ontology/issues/24912"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• Class: H4K20me2 histone reader activity

• H4K20me2 histone reader activity SubClassOf has part some methylated histone binding

• H4K20me2 histone reader activity SubClassOf histone reader activity

H4K20me3 modified histone binding http://purl.obolibrary.org/obo/GO_1990889

Removed

• H4K20me3 modified histone binding definition "Binding to a histone H4 in which the lysine residue at position 20 has been modified by trimethylation."
  • database_cross_reference "PMID:22150589"

Added

• H4K20me3 modified histone binding definition "A histone reader that recognizes a histone H4 trimethylated at lysine 20."
  • database_cross_reference "PMID:22150589"

chromatin-protein adaptor activity http://purl.obolibrary.org/obo/GO_0140463

Removed

• chromatin-protein adaptor activity definition "The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex."
  • database_cross_reference "PMID:32277274"

Added

• chromatin-protein adaptor activity definition "An adaptor activity that brings together a protein and a region of the chromatin, such as a nucleosome, to establish or maintain the chromatin localization of the protein, or the complex to which it belongs."
  • database_cross_reference "PMID:32277274"

histone reader activity http://purl.obolibrary.org/obo/GO_0140566

Removed

• histone reader activity definition "A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery."

  • database_cross_reference "PMID:32260176"

  • database_cross_reference "PMID:31082667"

  • database_cross_reference "PMID:34726351"

  • database_cross_reference "PMID:11498575"

  • database_cross_reference "PMID:25688442"

Added

• histone reader activity definition "A chromatin adaptor activity that brings together a protein and a specific form of histone, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery."

  • database_cross_reference "PMID:32260176"

  • database_cross_reference "PMID:31082667"

  • database_cross_reference "PMID:34726351"

  • database_cross_reference "PMID:11498575"

  • database_cross_reference "PMID:25688442"

obsolete 17-beta-ketosteroid reductase (NADPH) activity http://purl.obolibrary.org/obo/GO_0072555

Removed

• obsolete 17-beta-ketosteroid reductase (NADPH) activity definition "Catalysis of the reaction: a 17-beta-ketosteroid + NADPH + H+ = a 17-beta-hydroxysteroid + NADP+."

  • database_cross_reference "PMID:17074428"

  • database_cross_reference "GOC:kad"

• obsolete 17-beta-ketosteroid reductase (NADPH) activity label "17-beta-ketosteroid reductase (NADPH) activity"

• obsolete 17-beta-ketosteroid reductase (NADPH) activity SubClassOf steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

Added

• obsolete 17-beta-ketosteroid reductase (NADPH) activity term tracker item "https://github.com/geneontology/go-ontology/issues/29329"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete 17-beta-ketosteroid reductase (NADPH) activity consider "GO:0072582"

• obsolete 17-beta-ketosteroid reductase (NADPH) activity definition "OBSOLETE. Catalysis of the reaction: a 17-beta-ketosteroid + NADPH + H+ = a 17-beta-hydroxysteroid + NADP+."

  • database_cross_reference "PMID:17074428"

  • database_cross_reference "GOC:kad"

• obsolete 17-beta-ketosteroid reductase (NADPH) activity label "obsolete 17-beta-ketosteroid reductase (NADPH) activity"

• obsolete 17-beta-ketosteroid reductase (NADPH) activity deprecated true

• obsolete 17-beta-ketosteroid reductase (NADPH) activity comment "This term was obsoleted because it was an unnecessary grouping term."

obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity http://purl.obolibrary.org/obo/GO_0033208

Removed

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity label "UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity"

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity definition "Catalysis of the reaction: UDP-N-acetylgalactosamine + N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide = UDP + N-acetylgalactosaminyl-N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "PMID:16024623"

  • database_cross_reference "PMID:12678917"

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity SubClassOf obsolete beta-1,4-N-acetylgalactosaminyltransferase activity

Added

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity label "obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity"

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity term tracker item "https://github.com/geneontology/go-ontology/issues/18752"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity comment "This term was obsoleted because it represents a specific substrate of N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity ; GO:0033842."

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity term replaced by "GO:0033842"

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity definition "OBSOLETE. Catalysis of the reaction: UDP-N-acetylgalactosamine + N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide = UDP + N-acetylgalactosaminyl-N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "PMID:16024623"

  • database_cross_reference "PMID:12678917"

• obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity deprecated true

obsolete beta-1,4-N-acetylgalactosaminyltransferase activity http://purl.obolibrary.org/obo/GO_0033207

Removed

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity definition "Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming a beta-1,4 linkage."

  • database_cross_reference "GOC:mah"

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity label "beta-1,4-N-acetylgalactosaminyltransferase activity"

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity SubClassOf acetylgalactosaminyltransferase activity

Added

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity definition "OBSOLETE. Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming a beta-1,4 linkage."

  • database_cross_reference "GOC:mah"

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity term tracker item "https://github.com/geneontology/go-ontology/issues/18752"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity term replaced by "GO:0033842"

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity deprecated true

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity label "obsolete beta-1,4-N-acetylgalactosaminyltransferase activity"

• obsolete beta-1,4-N-acetylgalactosaminyltransferase activity comment "This term was obsoleted because it represents the same reaction as N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity ; GO:0033842."

obsolete nucleotide-binding oligomerization domain containing signaling pathway http://purl.obolibrary.org/obo/GO_0070423

Removed

• obsolete nucleotide-binding oligomerization domain containing signaling pathway comment "This term was obsoleted because it is an unnecessary grouoing term."

Added

• obsolete nucleotide-binding oligomerization domain containing signaling pathway comment "This term was obsoleted because it is an unnecessary grouping term."

obsolete vitamin D 25-hydroxylase activity http://purl.obolibrary.org/obo/GO_0070643

Removed

• obsolete vitamin D 25-hydroxylase activity label "vitamin D 25-hydroxylase activity"

• obsolete vitamin D 25-hydroxylase activity definition "Catalysis of the hydroxylation of C-25 of any form of vitamin D."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "GOC:BHF"

• obsolete vitamin D 25-hydroxylase activity SubClassOf steroid hydroxylase activity

Added

• obsolete vitamin D 25-hydroxylase activity comment "This term was obsoleted because it was an unnecessary grouping term."

• obsolete vitamin D 25-hydroxylase activity deprecated true

• obsolete vitamin D 25-hydroxylase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29330"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete vitamin D 25-hydroxylase activity consider "GO:0030343"

• obsolete vitamin D 25-hydroxylase activity label "obsolete vitamin D 25-hydroxylase activity"

• obsolete vitamin D 25-hydroxylase activity definition "OBSOLETE. Catalysis of the hydroxylation of C-25 of any form of vitamin D."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "GOC:BHF"

protein-macromolecule adaptor activity http://purl.obolibrary.org/obo/GO_0030674

Removed

• protein-macromolecule adaptor activity definition "The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "GOC:bf"

  • database_cross_reference "GOC:vw"

Added

• protein-macromolecule adaptor activity definition "An adaptor activity that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "GOC:bf"

  • database_cross_reference "GOC:vw"

sterol 12-alpha-hydroxylase activity http://purl.obolibrary.org/obo/GO_0008397

Removed

• sterol 12-alpha-hydroxylase activity definition "Catalysis of the reaction: a steroid + donor-H2 + O2 = 12-alpha-hydroxysteroid + H2O."

  • database_cross_reference "GOC:mah"

• sterol 12-alpha-hydroxylase activity database_cross_reference "EC:1.14.14.139"

Added

• sterol 12-alpha-hydroxylase activity definition "Catalysis of the reaction: a steroid + reduced [NADPH--hemoprotein reductase] + O2 = a 12-alpha-hydroxysteroid + oxidized [NADPH--hemoprotein reductase]- H2O +H+."

  • database_cross_reference "EC:1.14.14.139"

• sterol 12-alpha-hydroxylase activity database_cross_reference "EC:1.14.14.139"

  • source "skos:exactMatch"

ubiquitin-modified histone reader activity http://purl.obolibrary.org/obo/GO_0061649

Removed

• ubiquitin-modified histone reader activity definition "A molecular adaptor that recognizes and binds a histone protein containing a ubiquitination modification and that brings the target protein into contact with another protein to allow those proteins to function in a coordinated way."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "PMID:24526689"

Added

• ubiquitin-modified histone reader activity definition "A histone reader that recognizes a histone bearing a ubiquinated lysine residue."
  • database_cross_reference "PMID:24526689"

vitamin D3 25-hydroxylase activity http://purl.obolibrary.org/obo/GO_0030343

Removed

• vitamin D3 25-hydroxylase activity database_cross_reference "RHEA:32903"

• vitamin D3 25-hydroxylase activity definition "Catalysis of the reaction: vitamin D3 + NADPH + H+ + O2 = calcidiol + NADP+ + H2O."

  • database_cross_reference "ISBN:0471331309"

  • database_cross_reference "MetaCyc:RXN-9829"

• vitamin D3 25-hydroxylase activity SubClassOf obsolete vitamin D 25-hydroxylase activity

Added

• vitamin D3 25-hydroxylase activity database_cross_reference "RHEA:32903"

  • source "skos:exactMatch"

• vitamin D3 25-hydroxylase activity definition "Catalysis of the reaction: calciol (vitamin D3) + reduced [NADPH--hemoprotein reductase] + O2 = calcidiol + oxidized [NADPH--hemoprotein reductase] + H2O + H+."

  • database_cross_reference "RHEA:32903"

• vitamin D3 25-hydroxylase activity SubClassOf steroid hydroxylase activity