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Merge pull request #28256 from geneontology/issue-28107
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Issue 28107
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@raymond91125
raymond91125 committed Jun 22, 2024
2 parents 6ce36fb + 4375052 commit 8b3d182
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102 changes: 46 additions & 56 deletions src/ontology/go-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -35078,9 +35078,9 @@ is_a: GO:0016783 ! sulfurtransferase activity

[Term]
id: GO:0004077
name: biotin-[acetyl-CoA-carboxylase] ligase activity
name: biotin--[biotin carboxyl-carrier protein] ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + biotin + apo-(acetyl-CoA:carbon-dioxide ligase (ADP forming)) = AMP + diphosphate + (acetyl-CoA:carbon-dioxide ligase (ADP forming))." [EC:6.3.4.15]
def: "Catalysis of the reaction: ATP + biotin + L-lysyl-[protein] = AMP + diphosphate + H+ + N(6)-biotinyl-L-lysyl-[protein]." [RHEA:11756]
synonym: "acetyl CoA holocarboxylase synthetase activity" RELATED [EC:6.3.4.15]
synonym: "acetyl coenzyme A holocarboxylase synthetase activity" RELATED [EC:6.3.4.15]
synonym: "acetyl-CoA carboxylase biotin holoenzyme synthetase activity" RELATED [EC:6.3.4.15]
Expand All @@ -35090,70 +35090,57 @@ synonym: "biotin--protein ligase activity" RELATED [EC:6.3.4.15]
synonym: "biotin-acetyl coenzyme A carboxylase synthetase activity" RELATED [EC:6.3.4.15]
synonym: "biotin-acetyl-CoA carboxylase synthetase" BROAD [EC:6.3.4.15]
synonym: "biotin-acetyl-CoA-carboxylase ligase activity" RELATED [EC:6.3.4.15]
synonym: "biotin-protein ligase activity" EXACT []
synonym: "biotin:apo-acetyl-CoA:carbon-dioxide ligase (ADP-forming) ligase (AMP-forming)" RELATED [EC:6.3.4.15]
synonym: "biotin:apocarboxylase ligase activity" RELATED [EC:6.3.4.15]
synonym: "HCS" RELATED [EC:6.3.4.15]
xref: EC:6.3.4.10 {source="skos:narrowMatch"}
xref: EC:6.3.4.15
xref: EC:6.3.4.9 {source="skos:narrowMatch"}
xref: MetaCyc:6.3.4.9-RXN {source="skos:narrowMatch"}
xref: MetaCyc:BIOTINLIG-RXN
xref: RHEA:11756
is_a: GO:0018271 ! biotin-protein ligase activity
xref: RHEA:23668 {source="skos:narrowMatch"}
xref: MetaCyc:6.3.4.10-RXN {source="skos:narrowMatch"}
xref: RHEA:11204 {source="skos:narrowMatch"}
xref: EC:6.3.4.11 {source="skos:narrowMatch"}
xref: MetaCyc:6.3.4.11-RXN {source="skos:narrowMatch"}
xref: RHEA:24376 {source="skos:narrowMatch"}
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI

[Term]
id: GO:0004078
name: biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity
name: obsolete biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + biotin + apo-(3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)) = AMP + diphosphate + (3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming))." [EC:6.3.4.11]
synonym: "beta-methylcrotonyl coenzyme A holocarboxylase synthetase activity" RELATED [EC:6.3.4.11]
synonym: "biotin--[methylcrotonoyl-CoA-carboxylase] synthetase activity" RELATED [EC:6.3.4.11]
synonym: "biotin-beta-methylcrotonyl coenzyme A carboxylase synthetase activity" RELATED [EC:6.3.4.11]
synonym: "biotin-methylcrotonoyl-CoA-carboxylase ligase activity" RELATED [EC:6.3.4.11]
synonym: "biotin-methylcrotonoyl-CoA-carboxylase synthetase" BROAD [EC:6.3.4.11]
synonym: "biotin:apo-3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming) ligase (AMP-forming)" RELATED [EC:6.3.4.11]
xref: EC:6.3.4.11
xref: MetaCyc:6.3.4.11-RXN
xref: RHEA:24376
is_a: GO:0018271 ! biotin-protein ligase activity
def: "OBSOLETE. Catalysis of the reaction: ATP + biotin + apo-(3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)) = AMP + diphosphate + (3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming))." [GOC:rynl]
comment: The reason for obsoletion is this term is more specific than the specificity of any known gene product.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004077

[Term]
id: GO:0004079
name: biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity
name: obsolete biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + biotin + apo-(methylmalonyl-CoA:pyruvate carboxytransferase) = AMP + diphosphate + (methylmalonyl-CoA:pyruvate carboxytransferase)." [EC:6.3.4.9]
synonym: "biotin--[methylmalonyl-CoA-carboxyltransferase] ligase activity" RELATED [EC:6.3.4.9]
synonym: "biotin--[methylmalonyl-CoA-carboxyltransferase] synthetase activity" RELATED [EC:6.3.4.9]
synonym: "biotin--[methylmalonyl-CoA-carboxytransferase] synthetase activity" RELATED [EC:6.3.4.9]
def: "OBSOLETE. Catalysis of the reaction: ATP + biotin + apo-(methylmalonyl-CoA:pyruvate carboxytransferase) = AMP + diphosphate + (methylmalonyl-CoA:pyruvate carboxytransferase)." [GOC:rynl]
comment: The reason for obsoletion is this term is more specific than the specificity of any known gene product.
synonym: "biotin-[methylmalonyl-CoA-carboxyltransferase] ligase activity" EXACT []
synonym: "biotin-methylmalonyl coenzyme A carboxyltransferase synthetase activity" RELATED [EC:6.3.4.9]
synonym: "biotin-methylmalonyl-CoA-carboxyltransferase ligase activity" RELATED [EC:6.3.4.9]
synonym: "biotin-methylmalonyl-CoA-carboxyltransferase synthetase" BROAD [EC:6.3.4.9]
synonym: "biotin-methylmalonyl-CoA-carboxytransferase ligase activity" RELATED [EC:6.3.4.9]
synonym: "biotin-methylmalonyl-CoA-carboxytransferase synthetase activity" RELATED [EC:6.3.4.9]
synonym: "biotin-transcarboxylase synthetase activity" RELATED [EC:6.3.4.9]
synonym: "biotin:apomethylmalonyl-CoA:pyruvate carboxyltransferase ligase (AMP-forming)" RELATED [EC:6.3.4.9]
synonym: "biotin:apomethylmalonyl-CoA:pyruvate carboxytransferase ligase (AMP-forming)" RELATED [EC:6.3.4.9]
synonym: "methylmalonyl coenzyme A holotranscarboxylase synthetase activity" RELATED [EC:6.3.4.9]
xref: EC:6.3.4.9
xref: MetaCyc:6.3.4.9-RXN
xref: RHEA:23668
is_a: GO:0018271 ! biotin-protein ligase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004077

[Term]
id: GO:0004080
name: biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + biotin + apo-(propanoyl-CoA:carbon-dioxide ligase (ADP-forming)) = AMP + diphosphate + (propanoyl-CoA:carbon-dioxide ligase (ADP-forming))." [EC:6.3.4.10]
synonym: "biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] synthetase activity" RELATED [EC:6.3.4.10]
synonym: "biotin-propionyl coenzyme A carboxylase synthetase activity" RELATED [EC:6.3.4.10]
synonym: "biotin-propionyl-CoA-carboxylase (ATP-hydrolysing) ligase activity" RELATED [EC:6.3.4.10]
synonym: "biotin-propionyl-CoA-carboxylase (ATP-hydrolysing) synthetase activity" RELATED [EC:6.3.4.10]
synonym: "biotin:apo-propanoyl-CoA:carbon-dioxide ligase (ADP-forming) ligase (AMP-forming)" RELATED [EC:6.3.4.10]
synonym: "holocarboxylase synthetase activity" RELATED [EC:6.3.4.10]
synonym: "propionyl coenzyme A holocarboxylase synthetase activity" RELATED [EC:6.3.4.10]
synonym: "propionyl-CoA holocarboxylase synthetase activity" RELATED [EC:6.3.4.10]
xref: EC:6.3.4.10
xref: MetaCyc:6.3.4.10-RXN
xref: RHEA:11204
is_a: GO:0018271 ! biotin-protein ligase activity
name: obsolete biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: ATP + biotin + apo-(propanoyl-CoA:carbon-dioxide ligase (ADP-forming)) = AMP + diphosphate + (propanoyl-CoA:carbon-dioxide ligase (ADP-forming))." [GOC:rynl]
comment: The reason for obsoletion is this term is more specific than the specificity of any known gene product.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004077

[Term]
id: GO:0004081
Expand Down Expand Up @@ -131040,15 +131027,15 @@ intersection_of: has_primary_output CHEBI:24410 ! glycosylphosphatidylinositol

[Term]
id: GO:0018271
name: biotin-protein ligase activity
name: obsolete biotin-protein ligase activity
namespace: molecular_function
alt_id: GO:0000106
def: "Catalysis of the reaction: ATP + biotin + protein = AMP + diphosphate + biotin-protein." [GOC:mah]
def: "OBSOLETE. Catalysis of the reaction: ATP + biotin + protein = AMP + diphosphate + biotin-protein." [GOC:mah]
comment: The reason for obsoletion is this term is an unnecessary grouping term.
synonym: "biotin-apoprotein ligase activity" EXACT []
xref: EC:6.3.4.-
xref: MetaCyc:BIOTINLIG-RXN
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004077

[Term]
id: GO:0018272
Expand Down Expand Up @@ -383898,16 +383885,19 @@ creation_date: 2010-03-19T02:01:19Z

[Term]
id: GO:0071734
name: biotin-[pyruvate-carboxylase] ligase activity
name: obsolete biotin-[pyruvate-carboxylase] ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + biotin + apo-(pyruvate-carboxylase) = AMP + diphosphate + biotin-(pyruvate-carboxylase)." [GOC:mah, PMID:10551847]
def: "OBSOLETE. Catalysis of the reaction: ATP + biotin + apo-(pyruvate-carboxylase) = AMP + diphosphate + biotin-(pyruvate-carboxylase)." [GOC:mah, PMID:10551847]
comment: The reason for obsoletion is this term is more specific than the specificity of any known gene product.
synonym: "biotin-[pyruvate carboxylase] ligase activity" EXACT [GOC:jp]
synonym: "biotin-[pyruvate carboxylase] synthetase activity" EXACT [GOC:mah]
synonym: "biotin-pyruvate carboxylase synthetase activity" EXACT [GOC:mah]
synonym: "biotin-pyruvate-carboxylase ligase activity" EXACT [GOC:mah]
synonym: "biotin:apo-pyruvate-carboxylase ligase" EXACT [GOC:mah]
xref: EC:6.3.4.-
is_a: GO:0018271 ! biotin-protein ligase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004077
created_by: mah
creation_date: 2010-03-19T02:37:24Z

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135 changes: 3 additions & 132 deletions src/ontology/imports/go-catalytic-activities-participants.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -33716,148 +33716,19 @@

<!-- http:https://purl.obolibrary.org/obo/GO_0004078 -->

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<!-- http:https://purl.obolibrary.org/obo/GO_0004079 -->

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<!-- http:https://purl.obolibrary.org/obo/GO_0004080 -->

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