Merge pull request #28834 from geneontology/issue-28819-2

aligned defs with RHEA, fix xref types for #28819
geneontology · Sep 4, 2024 · e878634 · e878634
2 parents 69ebe22 + d6b74bd
commit e878634
Showing 1 changed file with 18 additions and 13 deletions.
diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo
@@ -36599,7 +36599,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 id: GO:0004161
 name: dimethylallyltranstransferase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate." [EC:2.5.1.1]
+def: "Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = (2E)-geranyl diphosphate + diphosphate." [RHEA:22408]
 comment: Note that this is the first step in the formation of farnesyl diphosphate. The second step is 'geranyltranstransferase activity ; GO:0004337'. Consider also annotating to the biological process term 'farnesyl diphosphate biosynthetic process ; GO:0045337'.
 synonym: "(2E,6E)-farnesyl diphosphate synthetase activity" RELATED [EC:2.5.1.1]
 synonym: "dimethylallyl-diphosphate:isopentenyl-diphosphate dimethylallyltranstransferase activity" RELATED [EC:2.5.1.1]
@@ -36611,10 +36611,11 @@ synonym: "geranyl pyrophosphate synthase activity" RELATED [EC:2.5.1.1]
 synonym: "geranyl pyrophosphate synthetase activity" RELATED [EC:2.5.1.1]
 synonym: "geranyl-diphosphate synthase activity" RELATED [EC:2.5.1.1]
 synonym: "trans-farnesyl pyrophosphate synthetase activity" RELATED [EC:2.5.1.1]
-xref: EC:2.5.1.1
+xref: EC:2.5.1.1 {source="skos:exactMatch"}
 xref: MetaCyc:GPPSYN-RXN
-xref: RHEA:22408
+xref: RHEA:22408 {source="skos:exactMatch"}
 is_a: GO:0004659 ! prenyltransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28819" xsd:anyURI
 
 [Term]
 id: GO:0004162
@@ -39154,7 +39155,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 id: GO:0004337
 name: geranyltranstransferase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate." [EC:2.5.1.10, RHEA:19361]
+def: "Catalysis of the reaction: (2E)-geranyl diphosphate + isopentenyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate." [RHEA:19361]
 comment: Note that this is the second step in the formation of farnesyl diphosphate. The first step is 'dimethylallyltransferase activity ; GO:0004161'. Consider also annotating to the biological process term 'farnesyl diphosphate biosynthetic process ; GO:0045337'.
 synonym: "farnesyl diphosphate synthetase activity" RELATED [EC:2.5.1.10]
 synonym: "farnesyl pyrophosphate synthetase activity" EXACT []
@@ -39164,11 +39165,12 @@ synonym: "FPP synthetase activity" RELATED [EC:2.5.1.10]
 synonym: "geranyl transferase I" RELATED [EC:2.5.1.10]
 synonym: "geranyl-diphosphate:isopentenyl-diphosphate geranyltranstransferase activity" RELATED [EC:2.5.1.10]
 synonym: "geranyltransferase activity" RELATED [EC:2.5.1.10]
-xref: EC:2.5.1.10
+xref: EC:2.5.1.10 {source="skos:exactMatch"}
 xref: KEGG_REACTION:R02003
 xref: MetaCyc:FPPSYN-RXN
-xref: RHEA:19361
+xref: RHEA:19361 {source="skos:exactMatch"}
 is_a: GO:0004659 ! prenyltransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28819" xsd:anyURI
 
 [Term]
 id: GO:0004338
@@ -436981,11 +436983,12 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
 id: GO:0102878
 name: (+)-alpha-barbatene synthase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = (+)-alpha-barbatene + diphosphoric acid." [EC:4.2.3.69, GOC:pz]
-xref: EC:4.2.3.69
+def: "Catalysis of the reaction: (2E,6E)-farnesyl diphosphate = (+)-alpha-barbatene + diphosphate." [RHEA:29499]
+xref: EC:4.2.3.69 {source="skos:exactMatch"}
 xref: MetaCyc:RXN-8417
-xref: RHEA:29499
+xref: RHEA:29499 {source="skos:exactMatch"}
 is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28819#issuecomment-2328362565" xsd:anyURI
 
 [Term]
 id: GO:0102879
@@ -437009,9 +437012,11 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
 id: GO:0102881
 name: (+)-beta-barbatene synthase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = (+)-beta-barbatene + diphosphoric acid." [GOC:pz, PMID:15918888, PMID:16297850]
+def: "Catalysis of the reaction: (2E,6E)-farnesyl diphosphate = (-)-beta-barbatene + diphosphate." [PMID:15918888, PMID:16297850, RHEA:73983]
 xref: MetaCyc:RXN-8421
+xref: RHEA:73983 {source="skos:exactMatch"}
 is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28819" xsd:anyURI
 
 [Term]
 id: GO:0102882
@@ -437027,10 +437032,10 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 id: GO:0102883
 name: (+)-beta-chamigrene synthase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = (+)-beta-chamigrene + diphosphoric acid." [EC:4.2.3.78, GOC:pz]
-xref: EC:4.2.3.78
+def: "Catalysis of the reaction: (2E,6E)-farnesyl diphosphate = (+)-beta-chamigrene + diphosphate." [RHEA:30379]
+xref: EC:4.2.3.78 {source="skos:exactMatch"}
 xref: MetaCyc:RXN-8424
-xref: RHEA:30379
+xref: RHEA:30379 {source="skos:exactMatch"}
 is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
 
 [Term]