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Merge pull request #28818 from geneontology/issue-28070-42
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Issue 28070 42
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@pgaudet
pgaudet authored Sep 2, 2024
2 parents 8fcf4a6 + 4b14dc6 commit ed7e9dd
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102 changes: 50 additions & 52 deletions src/ontology/go-edit.obo
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Expand Up @@ -31485,7 +31485,7 @@ is_a: GO:0016411 ! acylglycerol O-acyltransferase activity
id: GO:0003847
name: 1-alkyl-2-acetylglycerophosphocholine esterase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine + H2O = 1-alkyl-sn-glycero-3-phosphocholine + acetate." [EC:3.1.1.47]
def: "Catalysis of the reaction: a 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H2O = 1-O-alkyl-sn-glycero-3-phosphocholine + acetate + H+." [RHEA:17777]
subset: goslim_chembl
synonym: "1-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetohydrolase activity" RELATED [EC:3.1.1.47]
synonym: "1-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetylhydrolase activity" RELATED [EC:3.1.1.47]
Expand All @@ -31500,7 +31500,7 @@ synonym: "PAF acetylhydrolase activity" RELATED [EC:3.1.1.47]
synonym: "platelet-activating factor acetylhydrolase activity" RELATED [EC:3.1.1.47]
xref: EC:3.1.1.47
xref: MetaCyc:3.1.1.47-RXN
xref: RHEA:17777
xref: RHEA:17777 {source="skos:exactMatch"}
is_a: GO:0052689 ! carboxylic ester hydrolase activity

[Term]
Expand Down Expand Up @@ -35347,6 +35347,7 @@ synonym: "L-branched chain amino acid aminotransferase activity" RELATED [EC:2.6
synonym: "transaminase B activity" RELATED [EC:2.6.1.42]
xref: EC:2.6.1.42 {source="skos:exactMatch"}
is_a: GO:0008483 ! transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI

[Term]
id: GO:0004085
Expand Down Expand Up @@ -46921,7 +46922,7 @@ synonym: "tyrosine-alpha-ketoglutarate aminotransferase activity" BROAD [EC:2.6.
synonym: "tyrosine-alpha-ketoglutarate transaminase activity" BROAD [EC:2.6.1.5]
xref: EC:2.6.1.5 {source="skos:broadMatch"}
xref: MetaCyc:TYROSINE-AMINOTRANSFERASE-RXN
xref: RHEA:15093
xref: RHEA:15093 {source="skos:exactMatch"}
xref: UM-BBD_reactionID:r0297
is_a: GO:0008793 ! aromatic-amino-acid transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
Expand Down Expand Up @@ -87507,7 +87508,7 @@ intersection_of: has_primary_output CHEBI:57762 ! L-valine zwitterion
relationship: has_part GO:0003984 ! acetolactate synthase activity
relationship: has_part GO:0004160 ! dihydroxy-acid dehydratase activity
relationship: has_part GO:0004455 ! ketol-acid reductoisomerase activity
relationship: has_part GO:0052655 ! L-valine transaminase activity
relationship: has_part GO:0052655 ! L-valine-2-oxoglutarate transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28686" xsd:anyURI

[Term]
Expand Down Expand Up @@ -120137,17 +120138,17 @@ relationship: part_of GO:0005783 ! endoplasmic reticulum

[Term]
id: GO:0016223
name: beta-alanine-pyruvate transaminase activity
name: beta-alanine:pyruvate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-alanine + 2-oxopropanoate = pyruvate + beta-alanine." [EC:2.6.1.18]
def: "Catalysis of the reaction: L-alanine + 2-oxopropanoate = pyruvate + beta-alanine." [RHEA:14077]
synonym: "beta-alanine--pyruvate aminotransferase activity" RELATED [EC:2.6.1.18]
synonym: "beta-alanine-alpha-alanine transaminase activity" RELATED [EC:2.6.1.18]
synonym: "beta-alanine-pyruvate aminotransferase activity" EXACT []
synonym: "L-alanine:3-oxopropanoate aminotransferase activity" RELATED [EC:2.6.1.18]
synonym: "omega-amino acid--pyruvate aminotransferase activity" RELATED [EC:2.6.1.18]
xref: EC:2.6.1.18
xref: EC:2.6.1.18 {source="skos:exactMatch"}
xref: MetaCyc:2.6.1.18-RXN
xref: RHEA:14077
xref: RHEA:14077 {source="skos:exactMatch"}
is_a: GO:0008483 ! transaminase activity

[Term]
Expand Down Expand Up @@ -127552,7 +127553,6 @@ comment: This term was made obsolete because the definition does not match the t
synonym: "phosphatidylserine-specific phospholipase A1 activity" EXACT []
is_obsolete: true
consider: GO:0052739
consider: GO:0052740

[Term]
id: GO:0017064
Expand Down Expand Up @@ -197849,15 +197849,15 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0033853
name: aspartate-prephenate aminotransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-arogenate + oxaloacetate = prephenate + L-aspartate." [EC:2.6.1.78]
def: "Catalysis of the reaction: L-arogenate + oxaloacetate = prephenate + L-aspartate." [RHEA:20445]
synonym: "L-arogenate:oxaloacetate aminotransferase activity" RELATED [EC:2.6.1.78]
synonym: "L-aspartate:prephenate aminotransferase activity" RELATED [EC:2.6.1.78]
synonym: "PAT" RELATED [EC:2.6.1.78]
synonym: "prephenate aspartate aminotransferase activity" RELATED [EC:2.6.1.78]
synonym: "prephenate transaminase activity" BROAD [EC:2.6.1.78]
xref: EC:2.6.1.78
xref: MetaCyc:PREPHENATE-ASP-TRANSAMINE-RXN
xref: RHEA:20445
xref: RHEA:20445 {source="skos:exactMatch"}
is_a: GO:0008483 ! transaminase activity

[Term]
Expand Down Expand Up @@ -288156,14 +288156,14 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0047297
name: asparagine-oxo-acid transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: a 2-oxo acid + L-asparagine = an amino acid + 2-oxosuccinamate." [EC:2.6.1.14, MetaCyc:2.6.1.14-RXN]
def: "Catalysis of the reaction: a 2-oxo acid + L-asparagine = an amino acid + 2-oxosuccinamate." [RHEA:19813]
synonym: "asparagine--oxo-acid aminotransferase activity" RELATED [EC:2.6.1.14]
synonym: "asparagine-keto acid aminotransferase activity" RELATED [EC:2.6.1.14]
synonym: "asparagine-oxo-acid aminotransferase activity" EXACT []
synonym: "L-asparagine:2-oxo-acid aminotransferase activity" RELATED [EC:2.6.1.14]
xref: EC:2.6.1.14
xref: EC:2.6.1.14 {source="skos:exactMatch"}
xref: MetaCyc:2.6.1.14-RXN
xref: RHEA:19813
xref: RHEA:19813 {source="skos.exactMatch"}
is_a: GO:0008483 ! transaminase activity

[Term]
Expand Down Expand Up @@ -288423,7 +288423,7 @@ synonym: "phenylalanine (histidine) aminotransferase activity" BROAD [EC:2.6.1.5
synonym: "phenylalanine(histidine) aminotransferase activity" BROAD []
synonym: "phenylalanine(histidine) transaminase activity" BROAD [EC:2.6.1.58]
synonym: "phenylalanine(histidine):pyruvate aminotransferase activity" BROAD [EC:2.6.1.58]
xref: EC:2.6.1.58
xref: EC:2.6.1.58 {source="skos:broadMatch"}
xref: KEGG_REACTION:R00692
xref: MetaCyc:2.6.1.58-RXN
xref: RHEA:13053 {source="skos:exactMatch"}
Expand Down Expand Up @@ -288489,14 +288489,14 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047319
name: aspartate-phenylpyruvate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: keto-phenylpyruvate + L-aspartate = L-phenylalanine + oxaloacetate." [EC:2.6.1.70, RHEA:14097]
def: "Catalysis of the reaction: keto-phenylpyruvate + L-aspartate = L-phenylalanine + oxaloacetate." [RHEA:14097]
synonym: "aspartate--phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.70]
synonym: "aspartate-phenylpyruvate aminotransferase activity" EXACT []
synonym: "aspartate:phenylpyruvate aminotransferase activity" EXACT []
synonym: "L-aspartate:phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.70]
xref: EC:2.6.1.70
xref: EC:2.6.1.70 {source="skos:exactMatch"}
xref: KEGG_REACTION:R00695
xref: MetaCyc:2.6.1.70-RXN
xref: RHEA:14097
xref: RHEA:14097 {source="skos:exactMatch"}
is_a: GO:0008483 ! transaminase activity

[Term]
Expand Down Expand Up @@ -307689,19 +307689,14 @@ is_a: GO:0016869 ! intramolecular aminotransferase activity

[Term]
id: GO:0050048
name: L-leucine:2-oxoglutarate aminotransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate." [EC:2.6.1.6, MetaCyc:LEUCINE-AMINOTRANSFERASE-RXN]
synonym: "L-leucine aminotransferase activity" BROAD [EC:2.6.1.6]
synonym: "leucine 2-oxoglutarate transaminase activity" RELATED [EC:2.6.1.6]
synonym: "leucine aminotransferase activity" BROAD []
synonym: "leucine transaminase activity" BROAD [EC:2.6.1.6]
synonym: "leucine-alpha-ketoglutarate transaminase activity" RELATED [EC:2.6.1.6]
xref: EC:2.6.1.6
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERLEU-RXN {source="skos:broadMatch"}
xref: RHEA:18321
is_a: GO:0008483 ! transaminase activity
name: obsolete L-leucine:2-oxoglutarate aminotransferase activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate." [GOC:curators]
comment: This term was obsoleted because it represents the same activity L-leucine transaminase activity ; GO:0052654.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28817" xsd:anyURI
is_obsolete: true
replaced_by: GO:0052654

[Term]
id: GO:0050049
Expand Down Expand Up @@ -337178,41 +337173,42 @@ creation_date: 2010-09-23T11:16:56Z

[Term]
id: GO:0052654
name: L-leucine transaminase activity
name: L-leucine-2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxoglutarate + L-leucine = 4-methyl-2-oxopentanoate + L-glutamatic acid." [EC:2.6.1.42, MetaCyc:BRANCHED-CHAINAMINOTRANSFERLEU-RXN]
def: "Catalysis of the reaction: 2-oxoglutarate + L-leucine = 4-methyl-2-oxopentanoate + L-glutamatic acid." [RHEA:18321]
subset: goslim_chembl
synonym: "L-leucine aminotransferase activity" EXACT []
xref: KEGG_REACTION:R01090
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERLEU-RXN {source="skos:broadMatch"}
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERLEU-RXN
is_a: GO:0004084 ! branched-chain-amino-acid transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI

[Term]
id: GO:0052655
name: L-valine transaminase activity
name: L-valine-2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxoglutarate + L-valine = 3-methyl-2-oxobutanoic acid + L-glutamatic acid." [EC:2.6.1.42, MetaCyc:BRANCHED-CHAINAMINOTRANSFERVAL-RXN]
def: "Catalysis of the reaction: 2-oxoglutarate + L-valine = 3-methyl-2-oxobutanoic acid + L-glutamatic acid." [RHEA:24813]
subset: goslim_chembl
synonym: "L-valine aminotransferase activity" EXACT []
xref: EC:2.6.1.42
xref: KEGG_REACTION:R01214
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERVAL-RXN
xref: RHEA:24813
xref: RHEA:24813 {source="skos:exactMatch"}
is_a: GO:0004084 ! branched-chain-amino-acid transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI

[Term]
id: GO:0052656
name: L-isoleucine transaminase activity
name: L-isoleucine-2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxoglutarate + L-isoleucine = (S)-3-methyl-2-oxopentanoic acid + L-glutamic acid." [RHEA:24801]
subset: goslim_chembl
synonym: "L-isoleucine aminotransferase activity" EXACT []
xref: EC:2.6.1.42
xref: KEGG_REACTION:R02199
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERILEU-RXN
xref: RHEA:24801 {source="skos:exactMatch"}
is_a: GO:0004084 ! branched-chain-amino-acid transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI

[Term]
id: GO:0052657
Expand Down Expand Up @@ -338410,18 +338406,19 @@ name: phosphatidylserine 1-acylhydrolase activity
namespace: molecular_function
def: "Catalysis of the reaction: phosphatidylserine + H2O = 2-acyl-sn-glycero-3-phosphoserine + fatty acid." [KEGG_REACTION:R04034]
synonym: "phosphatidylserine-specific phospholipase A1 activity" BROAD [EC:3.1.1.32]
xref: EC:3.1.1.32
xref: EC:3.1.1.32 {source="skos:broadMatch"}
xref: KEGG_REACTION:R04034
is_a: GO:0004620 ! phospholipase activity

[Term]
id: GO:0052740
name: 1-acyl-2-lysophosphatidylserine acylhydrolase activity
name: obsolete 1-acyl-2-lysophosphatidylserine acylhydrolase activity
namespace: molecular_function
def: "Catalysis of the reaction: 1-acyl-2-lysophosphatidylserine + H2O = sn-glycerol-phosphoserine + a carboxylate." [EC:3.1.1.32]
synonym: "phosphatidylserine-specific phospholipase A1 activity" BROAD [EC:3.1.1.32]
xref: EC:3.1.1.32
is_a: GO:0004620 ! phospholipase activity
def: "OBSOLETE. Catalysis of the reaction: 1-acyl-2-lysophosphatidylserine + H2O = sn-glycerol-phosphoserine + a carboxylate." [GOC:curators]
comment: This term was obsoleted because it represents the same activity as phospholipase A1 activity ; GO:0008970.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
is_obsolete: true
replaced_by: GO:0008970

[Term]
id: GO:0052741
Expand Down Expand Up @@ -400239,7 +400236,6 @@ id: GO:0080097
name: L-tryptophan:pyruvate aminotransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-tryptophan + pyruvate = 3-(indol-3-yl)pyruvate + L-alanine." [RHEA:27586]
comment: This reaction falls within the larger set of reactions associated with EC:2.6.1.28 (See BRENDA: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.6.1.28; note: 3-indole-2-oxopropanoate = indolepyruvate = 3-(indol-3-yl)pyruvate).
xref: EC:2.6.1.99
xref: MetaCyc:RXN-10139
xref: RHEA:27586
Expand Down Expand Up @@ -400616,7 +400612,7 @@ creation_date: 2009-04-29T03:34:50Z
id: GO:0080130
name: L-phenylalanine-2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = 3-phenylpyruvate + L-glutamate." [PMID:18394996]
def: "Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = 3-phenylpyruvate + L-glutamate." [PMID:18394996, RHEA:25152]
synonym: "L-phenylalanine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "L-phenylalanine:alpha-ketoglutarate aminotransferase activity" EXACT []
xref: EC:2.6.1.57 {source="skos:broadMatch"}
Expand Down Expand Up @@ -431412,11 +431408,13 @@ replaced_by: GO:0033954

[Term]
id: GO:0102257
name: 1-16:0-2-18:2-phosphatidylcholine sn-1 acylhydrolase activity
name: obsolete 1-16:0-2-18:2-phosphatidylcholine sn-1 acylhydrolase activity
namespace: molecular_function
def: "Catalysis of the reaction: 1-palmitoyl-2-linoleoyl-phosphatidylcholine + H2O = 1-linoleoyl-sn-glycero-3-phosphocholine + hexadecanoate + H+." [EC:3.1.1.32, GOC:pz]
xref: MetaCyc:RXN-12430
is_a: GO:0052689 ! carboxylic ester hydrolase activity
def: "OBSOLETE. Catalysis of the reaction: 1-palmitoyl-2-linoleoyl-phosphatidylcholine + H2O = 1-linoleoyl-sn-glycero-3-phosphocholine + hexadecanoate + H+." [GOC:pz]
comment: This term was obsoleted because it represents a specific substrate of phospholipase A1 activity ; GO:0008970.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
is_obsolete: true
replaced_by: GO:0008970

[Term]
id: GO:0102258
Expand Down
27 changes: 1 addition & 26 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 @@ -129914,32 +129914,7 @@

<!-- http://purl.obolibrary.org/obo/GO_0050048 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0050048">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_16810"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_17865"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_29985"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_57427"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0050048"/>



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