Merge pull request #29697 from geneontology/issue-29695

Resolving some isomerase term issues. #29695

src/ontology/go-edit.obo

@@ -82272,12 +82272,13 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 id: GO:0008719
 name: dihydroneopterin triphosphate 2'-epimerase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: dihydroneopterin triphosphate = dihydromonapterin-triphosphate." [MetaCyc:H2NTPEPIM-RXN]
+def: "Catalysis of the reaction: 7,8-dihydroneopterin 3'-triphosphate = 7,8-dihydromonapterin 3'-triphosphate." [RHEA:28346]
 synonym: "D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase activity" EXACT []
 xref: EC:5.1.99.7
 xref: MetaCyc:H2NTPEPIM-RXN
 xref: RHEA:28346
-is_a: GO:0016853 ! isomerase activity
+is_a: GO:0016854 ! racemase and epimerase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
 
 [Term]
 id: GO:0008720
@@ -251142,14 +251143,16 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 
 [Term]
 id: GO:0043800
-name: hexulose-6-phosphate isomerase activity
+name: 6-phospho-3-hexuloisomerase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: D-arabino-3-hexulose 6-phosphate = D-fructose 6-phosphate." [MetaCyc:R12-RXN, PMID:11839305]
+def: "Catalysis of the reaction: D-arabino-hex-3-ulose 6-phosphate = beta-D-fructose 6-phosphate." [PMID:11839305, RHEA:25900]
+synonym: "hexulose-6-phosphate isomerase activity" EXACT []
 synonym: "HUMPI" EXACT []
 xref: EC:5.3.1.27
 xref: MetaCyc:R12-RXN
 xref: RHEA:25900
-is_a: GO:0016853 ! isomerase activity
+is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
 
 [Term]
 id: GO:0043801
@@ -359542,8 +359545,11 @@ creation_date: 2014-02-05T15:27:39Z
 id: GO:0061593
 name: sulfoquinovose isomerase activity
 namespace: molecular_function
-def: "Catalysis of the reaction sulfoquinovose = 6-deoxy-6-sulfofructose." [GOC:dph, PMID:24463506]
-is_a: GO:0016853 ! isomerase activity
+def: "Catalysis of the reaction: 6-sulfo-beta-D-quinovose = 6-deoxy-6-sulfo-D-fructose." [PMID:24463506, RHEA:40439]
+xref: EC:5.3.1.31 {source="skos:exactMatch"}
+xref: RHEA:40439 {source="skos:exactMatch"}
+is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
 created_by: dph
 creation_date: 2014-02-10T09:56:04Z
 
@@ -369044,12 +369050,16 @@ intersection_of: has_primary_input CHEBI:16709 ! pyridoxine
 
 [Term]
 id: GO:0070284
-name: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity
+name: phosphomethylpyrimidine synthase activity
 namespace: molecular_function
-def: "Catalysis of the reaction: 5-aminoimidazole ribonucleotide + S-adenosylmethionine = 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate + 5'deoxyadenosine." [PMID:18953358]
+def: "Catalysis of the reaction: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H+." [PMID:18953358, RHEA:24840]
+synonym: "4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity" EXACT []
 synonym: "HMP-P synthase activity" EXACT [PMID:18953358]
 synonym: "ThiC" RELATED [PMID:18953358]
-is_a: GO:0016853 ! isomerase activity
+xref: EC:4.1.99.17 {source="skos:exactMatch"}
+xref: RHEA:24840 {source="skos:exactMatch"}
+is_a: GO:0016830 ! carbon-carbon lyase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
 
 [Term]
 id: GO:0070285
@@ -452510,8 +452520,9 @@ id: GO:0140226
 name: RNA topoisomerase activity
 namespace: molecular_function
 def: "Catalysis of the transient cleavage and passage of individual RNA strands or double helices through one another, resulting a topological transformation in RNA." [GOC:lnp, PMID:23912945, PMID:27257063]
-is_a: GO:0016853 ! isomerase activity
+is_a: GO:0120545 ! nucleic acid conformation isomerase activity
 is_a: GO:0140098 ! catalytic activity, acting on RNA
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
 created_by: pg
 creation_date: 2018-05-29T11:06:37Z