Parent/def/name/xref edits. #29533

geneontology · Jan 14, 2025 · 2539f61 · 2539f61
1 parent 70720d6
commit 2539f61
Showing 1 changed file with 61 additions and 42 deletions.
diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo
@@ -34188,17 +34188,17 @@ is_a: GO:0016849 ! phosphorus-oxygen lyase activity
 id: GO:0004017
 name: adenylate kinase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: ATP + AMP = 2 ADP." [EC:2.7.4.3]
+def: "Catalysis of the reaction: ATP + AMP = 2 ADP." [RHEA:12973]
 synonym: "5'-AMP-kinase activity" RELATED [EC:2.7.4.3]
 synonym: "adenylic kinase activity" RELATED [EC:2.7.4.3]
 synonym: "adenylokinase activity" RELATED [EC:2.7.4.3]
 synonym: "ATP:AMP phosphotransferase activity" RELATED [EC:2.7.4.3]
 synonym: "myokinase activity" NARROW [EC:2.7.4.3]
-xref: EC:2.7.4.3
-xref: MetaCyc:ADENYL-KIN-RXN
-xref: RHEA:12973
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
+xref: EC:2.7.4.3 {source="skos:exactMatch"}
+xref: MetaCyc:ADENYL-KIN-RXN {source="skos:exactMatch"}
+xref: RHEA:12973 {source="skos:exactMatch"}
 is_a: GO:0050145 ! nucleoside monophosphate kinase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0004018
@@ -36064,8 +36064,9 @@ synonym: "deoxycytidine monophosphokinase activity" RELATED [EC:2.7.4.25]
 synonym: "deoxycytidylate kinase activity" BROAD [EC:2.7.4.25]
 xref: EC:2.7.4.14 {source="skos:broadMatch"}
 xref: EC:2.7.4.25
-is_a: GO:0050145 ! nucleoside monophosphate kinase activity
+is_a: GO:0019205 ! nucleobase-containing compound kinase activity
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25991" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0004128
@@ -40007,21 +40008,21 @@ consider: GO:0050839
 id: GO:0004385
 name: guanylate kinase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: ATP + GMP = ADP + GDP." [EC:2.7.4.8]
+def: "Catalysis of the reaction: ATP + GMP = ADP + GDP." [RHEA:20780]
 synonym: "5'-GMP kinase activity" RELATED [EC:2.7.4.8]
 synonym: "ATP:(d)GMP phosphotransferase activity" RELATED [EC:2.7.4.8]
 synonym: "ATP:GMP phosphotransferase activity" RELATED [EC:2.7.4.8]
 synonym: "deoxyguanylate kinase activity" RELATED [EC:2.7.4.8]
 synonym: "GMP kinase activity" RELATED [EC:2.7.4.8]
 synonym: "guanosine monophosphate kinase activity" RELATED [EC:2.7.4.8]
 synonym: "membrane-associated guanylate kinase" NARROW []
-xref: EC:2.7.4.8
-xref: MetaCyc:GUANYL-KIN-RXN
-xref: RHEA:20780
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
+xref: EC:2.7.4.8 {source="skos:exactMatch"}
+xref: MetaCyc:GUANYL-KIN-RXN {source="skos:exactMatch"}
+xref: RHEA:20780 {source="skos:exactMatch"}
 is_a: GO:0050145 ! nucleoside monophosphate kinase activity
 relationship: part_of GO:0046037 ! GMP metabolic process
 relationship: part_of GO:0046710 ! GDP metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0004386
@@ -46192,23 +46193,24 @@ is_a: GO:0019136 ! deoxynucleoside kinase activity
 
 [Term]
 id: GO:0004798
-name: thymidylate kinase activity
+name: dTMP kinase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate." [EC:2.7.4.9]
+def: "Catalysis of the reaction: dTMP + ATP = dTDP + ADP." [RHEA:13517]
 synonym: "ATP:dTMP phosphotransferase activity" RELATED [EC:2.7.4.9]
 synonym: "deoxythymidine 5'-monophosphate kinase activity" RELATED [EC:2.7.4.9]
-synonym: "dTMP kinase activity" EXACT []
 synonym: "thymidine 5'-monophosphate kinase activity" RELATED [EC:2.7.4.9]
 synonym: "thymidine monophosphate kinase activity" RELATED [EC:2.7.4.9]
+synonym: "thymidylate kinase activity" EXACT []
 synonym: "thymidylate monophosphate kinase activity" RELATED [EC:2.7.4.9]
 synonym: "thymidylic acid kinase activity" RELATED [EC:2.7.4.9]
 synonym: "thymidylic kinase activity" RELATED [EC:2.7.4.9]
 synonym: "TMPK activity" RELATED [EC:2.7.4.9]
-xref: EC:2.7.4.9
-xref: MetaCyc:DTMPKI-RXN
-xref: RHEA:13517
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
-is_a: GO:0050145 ! nucleoside monophosphate kinase activity
+xref: EC:2.7.4.12 {source="skos:broadMatch"}
+xref: EC:2.7.4.9 {source="skos:exactMatch"}
+xref: MetaCyc:DTMPKI-RXN {source="skos:exactMatch"}
+xref: RHEA:13517 {source="skos:exactMatch"}
+is_a: GO:0047507 ! deoxynucleoside-phosphate kinase activity, ATP as phosphate donor
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0004799
@@ -86816,9 +86818,10 @@ id: GO:0009041
 name: UMP/dUMP kinase activity
 namespace: molecular_function
 def: "Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP." [GOC:go_curators]
-is_a: GO:0050145 ! nucleoside monophosphate kinase activity
+is_a: GO:0019205 ! nucleobase-containing compound kinase activity
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24402" xsd:anyURI
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25991" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0009042
@@ -198073,7 +198076,9 @@ xref: EC:2.7.4.22
 xref: MetaCyc:2.7.4.22-RXN
 xref: RHEA:24400
 is_a: GO:0009041 ! UMP/dUMP kinase activity
+is_a: GO:0050145 ! nucleoside monophosphate kinase activity
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25991" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0033863
@@ -225937,10 +225942,14 @@ id: GO:0036430
 name: CMP kinase activity
 namespace: molecular_function
 def: "Catalysis of the reaction: ATP + CMP = ADP + CDP." [RHEA:11600]
+xref: EC:2.7.4.14 {source="skos:broadMatch"}
+xref: EC:2.7.4.25 {source="skos:broadMatch"}
 xref: KEGG_REACTION:R00512
 xref: MetaCyc:RXN-11832
-xref: RHEA:11600
+xref: RHEA:11600 {source="skos:exactMatch"}
 is_a: GO:0004127 ! (d)CMP kinase activity
+is_a: GO:0050145 ! nucleoside monophosphate kinase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 created_by: bf
 creation_date: 2013-09-16T14:11:48Z
 
@@ -225950,10 +225959,14 @@ name: dCMP kinase activity
 namespace: molecular_function
 def: "Catalysis of the reaction: ATP + dCMP = ADP + dCDP." [RHEA:25094]
 synonym: "ATP:dCMP phosphotransferase activity" EXACT [KEGG_REACTION:R01665]
+xref: EC:2.7.4.14 {source="skos:broadMatch"}
+xref: EC:2.7.4.25 {source="skos:broadMatch"}
 xref: KEGG_REACTION:R01665
 xref: MetaCyc:RXN-7913
-xref: RHEA:25094
+xref: RHEA:25094 {source="skos:exactMatch"}
 is_a: GO:0004127 ! (d)CMP kinase activity
+is_a: GO:0047507 ! deoxynucleoside-phosphate kinase activity, ATP as phosphate donor
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 created_by: bf
 creation_date: 2013-09-16T14:11:56Z
 
@@ -291424,30 +291437,32 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
 
 [Term]
 id: GO:0047506
-name: (deoxy)adenylate kinase activity
+name: deoxyadenylate kinase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: ATP + dAMP = ADP + dADP." [EC:2.7.4.11]
+def: "Catalysis of the reaction: dAMP + ATP = dADP + ADP." [RHEA:23100]
 synonym: "ATP:(d)AMP phosphotransferase activity" RELATED [EC:2.7.4.11]
-xref: EC:2.7.4.11
-xref: MetaCyc:DEOXYADENYLATE-KINASE-RXN
-xref: RHEA:23100
-is_a: GO:0016301 ! kinase activity
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
+xref: EC:2.7.4.11 {source="skos:exactMatch"}
+xref: MetaCyc:DEOXYADENYLATE-KINASE-RXN {source="skos:exactMatch"}
+xref: RHEA:23100 {source="skos:exactMatch"}
+is_a: GO:0047507 ! deoxynucleoside-phosphate kinase activity, ATP as phosphate donor
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0047507
-name: (deoxy)nucleoside-phosphate kinase activity
+name: deoxynucleoside-phosphate kinase activity, ATP as phosphate donor
 namespace: molecular_function
-def: "Catalysis of the reaction: ATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate." [EC:2.7.4.13]
+def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + ATP = a 2'-deoxyribonucleoside 5'-diphosphate + ADP." [RHEA:11216]
 synonym: "ATP:deoxynucleoside-phosphate phosphotransferase activity" RELATED [EC:2.7.4.13]
 synonym: "deoxynucleoside monophosphate kinase activity" RELATED [EC:2.7.4.13]
 synonym: "deoxynucleoside-5'-monophosphate kinase activity" RELATED [EC:2.7.4.13]
+synonym: "deoxynucleoside-phosphate kinase activity" BROAD []
 synonym: "deoxyribonucleoside monophosphokinase activity" RELATED [EC:2.7.4.13]
 xref: EC:2.7.4.13
 xref: MetaCyc:DEOXYNUCLEOSIDE-PHOSPHATE-KINASE-RXN
 xref: RHEA:11216
 is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
 is_a: GO:0019205 ! nucleobase-containing compound kinase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0047508
@@ -309247,7 +309262,7 @@ id: GO:0050145
 name: nucleoside monophosphate kinase activity
 namespace: molecular_function
 alt_id: GO:0019201
-def: "Catalysis of the reaction: ATP + nucleoside monophosphate = ADP + nucleoside diphosphate." [GOC:ai, ISBN:0198506732]
+def: "Catalysis of the reaction: a ribonucleoside 5'-phosphate + ATP = a ribonucleoside 5'-diphosphate + ADP." [RHEA:24036]
 synonym: "ATP:nucleoside-phosphate phosphotransferase activity" RELATED [EC:2.7.4.4]
 synonym: "NMP-kinase activity" RELATED [EC:2.7.4.4]
 synonym: "nucleoside-phosphate kinase activity" EXACT []
@@ -309258,6 +309273,7 @@ xref: RHEA:24036
 is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
 is_a: GO:0019205 ! nucleobase-containing compound kinase activity
 relationship: part_of GO:0046940 ! nucleoside monophosphate phosphorylation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0050146
@@ -311682,15 +311698,16 @@ is_a: GO:0016836 ! hydro-lyase activity
 
 [Term]
 id: GO:0050316
-name: T2-induced deoxynucleotide kinase activity
+name: dGMP kinase activity
 namespace: molecular_function
-def: "Catalysis of the reactions: ATP + dGMP = ADP + dGDP, and ATP + dTMP = ADP + dTDP." [EC:2.7.4.12]
+def: "Catalysis of the reaction: dGMP + ATP = dGDP + ADP." [RHEA:12697]
 synonym: "ATP:(d)NMP phosphotransferase activity" RELATED [EC:2.7.4.12]
-xref: EC:2.7.4.12
-xref: MetaCyc:GMKALT-RXN
-xref: RHEA:12697
-is_a: GO:0016301 ! kinase activity
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
+synonym: "T2-induced deoxynucleotide kinase activity" BROAD [EC:2.7.4.12]
+xref: EC:2.7.4.12 {source="skos:broadMatch"}
+xref: MetaCyc:GMKALT-RXN {source="skos:exactMatch"}
+xref: RHEA:12697 {source="skos:exactMatch"}
+is_a: GO:0047507 ! deoxynucleoside-phosphate kinase activity, ATP as phosphate donor
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 
 [Term]
 id: GO:0050317
@@ -443178,7 +443195,7 @@ creation_date: 2021-02-23T21:18:12Z
 
 [Term]
 id: GO:0106367
-name: (deoxy)nucleoside phosphate kinase activity, dGTP as phosphate donor
+name: deoxynucleoside phosphate kinase activity, dGTP as phosphate donor
 namespace: molecular_function
 def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + dGTP = a 2'-deoxyribonucleoside 5'-diphosphate + dGDP." [PMID:20497505, RHEA:62128]
 xref: RHEA:62128
@@ -443189,7 +443206,7 @@ creation_date: 2021-03-11T20:06:53Z
 
 [Term]
 id: GO:0106368
-name: (deoxy)nucleoside phosphate kinase activity, dTTP as phosphate donor
+name: deoxynucleoside phosphate kinase activity, dTTP as phosphate donor
 namespace: molecular_function
 def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + dTTP = a 2'-deoxyribonucleoside 5'-diphosphate + dTDP." [PMID:20497505, RHEA:62132]
 xref: RHEA:62132
@@ -443200,7 +443217,7 @@ creation_date: 2021-03-11T20:09:34Z
 
 [Term]
 id: GO:0106369
-name: (deoxy)nucleoside phosphate kinase activity, GTP as phosphate donor
+name: deoxynucleoside phosphate kinase activity, GTP as phosphate donor
 namespace: molecular_function
 def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + GTP = a 2'-deoxyribonucleoside 5'-diphosphate + GDP." [PMID:20497505, RHEA:62124]
 xref: RHEA:62124
@@ -447112,7 +447129,9 @@ synonym: "deoxyuridine monophosphate kinase activity" EXACT []
 synonym: "dUMP-kinase activity" EXACT []
 xref: RHEA:30655
 is_a: GO:0009041 ! UMP/dUMP kinase activity
+is_a: GO:0047507 ! deoxynucleoside-phosphate kinase activity, ATP as phosphate donor
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15447" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
 created_by: krc
 creation_date: 2018-03-21T21:16:06Z