From 2539f618720e1233f0a0441ac9501fd7e4b3db94 Mon Sep 17 00:00:00 2001 From: sjm41 Date: Tue, 14 Jan 2025 17:51:46 +0000 Subject: [PATCH] Parent/def/name/xref edits. #29533 --- src/ontology/go-edit.obo | 103 +++++++++++++++++++++++---------------- 1 file changed, 61 insertions(+), 42 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 3a2299394..a96e0f6bc 100644 --- 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 @@ -40007,7 +40008,7 @@ 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] @@ -40015,13 +40016,13 @@ 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