From 0b74fbab0aedd14601d2f3127ca6826c888c236f Mon Sep 17 00:00:00 2001 From: sjm41 Date: Fri, 15 Nov 2024 09:22:37 +0000 Subject: [PATCH] Fixing MetaCyc def xrefs as db xrefs. #28523 --- src/ontology/go-edit.obo | 34 +++++++++++++++++++++++----------- 1 file changed, 23 insertions(+), 11 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 49d85cb2d5..d9a884dbd4 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -35795,6 +35795,7 @@ id: GO:0004111 name: creatine kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H+." [EC:2.7.3.2, RHEA:17157] +comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step. synonym: "adenosine triphosphate-creatine transphosphorylase activity" RELATED [EC:2.7.3.2] synonym: "ATP:creatine N-phosphotransferase activity" RELATED [EC:2.7.3.2] synonym: "ATP:creatine phosphotransferase activity" RELATED [EC:2.7.3.2] @@ -35814,9 +35815,11 @@ synonym: "phosphocreatine kinase activity" RELATED [EC:2.7.3.2] xref: EC:2.7.3.2 xref: KEGG_REACTION:R01881 xref: MetaCyc:CREATINE-KINASE-RXN +xref: MetaCyc:PWY-6158 {source="skos:relatedMatch"} xref: RHEA:17157 is_a: GO:0016301 ! kinase activity is_a: GO:0016775 ! phosphotransferase activity, nitrogenous group as acceptor +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI [Term] id: GO:0004112 @@ -63862,7 +63865,7 @@ intersection_of: has_primary_input_or_output CHEBI:57947 ! creatine zwitterion id: GO:0006601 name: creatine biosynthetic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of creatine, N-[amino(imino)methyl]-N-methylglycine. Creatine is formed by a process beginning with amidino group transfer from L-arginine to glycine to form guanidinoacetate, followed by methyl group transfer from S-adenosyl-L-methionine to guanidinoacetate; it is then is phosphorylated to form a pool that stores high energy phosphate for the replenishment of ATP during periods of high, or fluctuating energy demand. In animals, most creatine is transported to and used in muscle." [GOC:mah, MetaCyc:GLYCGREAT-PWY, MetaCyc:PWY-6158] +def: "The chemical reactions and pathways resulting in the formation of creatine, N-[amino(imino)methyl]-N-methylglycine. Creatine is formed by a process beginning with amidino group transfer from L-arginine to glycine to form guanidinoacetate, followed by methyl group transfer from S-adenosyl-L-methionine to guanidinoacetate; it is then is phosphorylated to form a pool that stores high energy phosphate for the replenishment of ATP during periods of high, or fluctuating energy demand. In animals, most creatine is transported to and used in muscle." [GOC:mah, MetaCyc:GLYCGREAT-PWY] synonym: "creatine anabolism" EXACT [] synonym: "creatine biosynthesis" EXACT [] synonym: "creatine formation" EXACT [] @@ -192146,7 +192149,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0033359 name: lysine biosynthetic process via diaminopimelate and N-succinyl-2-amino-6-ketopimelate namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and N-succinyl-2-amino-6-ketopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps." [GOC:mah, MetaCyc:DAPLYSINESYN-PWY-] +def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and N-succinyl-2-amino-6-ketopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps." [GOC:mah, MetaCyc:DAPLYSINESYN-PWY] synonym: "lysine anabolism via diaminopimelate and N-succinyl-2-amino-6-ketopimelate" EXACT [] synonym: "lysine biosynthesis via diaminopimelic acid and N-succinyl-2-amino-6-ketopimelate" EXACT [] synonym: "lysine biosynthetic process via diaminopimelic acid and N-succinyl-2-amino-6-ketopimelate" EXACT [] @@ -192157,6 +192160,7 @@ intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_intermediate CHEBI:15685 ! L-2-succinylamino-6-oxoheptanedioate(3-) intersection_of: has_intermediate CHEBI:57791 ! meso-2,6-diaminopimelic acid dizwitterion intersection_of: has_primary_output CHEBI:32564 ! lysinium(1+) +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI [Term] id: GO:0033360 @@ -338885,16 +338889,19 @@ creation_date: 2011-10-05T03:30:33Z [Term] id: GO:0052776 -name: diacetylchitobiose catabolic process to glucosamine and acetate +name: chitin catabolic process to fructose 6-phosphate via glucosamine namespace: biological_process -def: "The pathway resulting in the breakdown of diacetylchitobiose into simpler products, including glucosamine and glucosamine. The catabolism proceeds by the deacetylation of diacetylchitobiose, producing acetate and GlcN-GlcNAc; the latter is cleaved to produce glucosamine (GlcN) and N-acetylglucosamine (GlcNAc). The N-acetylglucosamine (GlcNAc) is then deacetylated to produce glucosamine (GlcN) and acetate." [GOC:bf, GOC:mengo_curators, MetaCyc:PWY-6855, PMID:15136574, PMID:16232910, PMID:16736587] +def: "The pathway resulting in the breakdown of chitin into fructose 6-phosphate, via glucosamine; acetate is also produced during the process." [GOC:bf, GOC:mengo_curators, MetaCyc:PWY-6855, PMID:15136574, PMID:16232910, PMID:16736587] +synonym: "diacetylchitobiose catabolic process to glucosamine and acetate" EXACT [] +xref: MetaCyc:PWY-6855 intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:28681 ! N,N'-diacetylchitobiose +intersection_of: has_primary_input CHEBI:17029 ! chitin intersection_of: has_primary_output CHEBI:30089 ! acetate -intersection_of: has_primary_output CHEBI:5417 ! glucosamine +intersection_of: has_primary_output CHEBI:57634 ! beta-D-fructofuranose 6-phosphate(2-) relationship: has_part GO:0050119 ! N-acetylglucosamine deacetylase activity relationship: has_part GO:0052761 ! exo-1,4-beta-D-glucosaminidase activity relationship: has_part GO:0052773 ! diacetylchitobiose deacetylase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI [Term] id: GO:0052777 @@ -408010,10 +408017,11 @@ creation_date: 2012-08-08T15:41:45Z id: GO:0090439 name: tetraketide alpha-pyrone synthase activity namespace: molecular_function -def: "Catalyzes the reaction: 7-hydroxylauroyl-CoA + 3 malonyl-CoA + 2 H+ = 2-(8-hydroxy-2-oxotridecyl)-6-oxopyran-4-olate + 3 CO2 + 4 coenzyme A." [MetaCyc:RXN-12183, PMID:21193570] +def: "Catalyzes the reaction: 7-hydroxylauroyl-CoA + 3 malonyl-CoA + 2 H+ = 2-(8-hydroxy-2-oxotridecyl)-6-oxopyran-4-olate + 3 CO2 + 4 coenzyme A." [MetaCyc:RXN-16407, PMID:21193570] xref: MetaCyc:RXN-16407 {source="skos:exactMatch"} is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28324" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI created_by: tb creation_date: 2012-08-09T14:35:06Z @@ -499704,10 +499712,11 @@ creation_date: 2013-01-22T10:10:30Z id: GO:1901807 name: capsanthin metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving capsanthin." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5174, PMID:10995282, UniPathway:UPA00806] +def: "The chemical reactions and pathways involving capsanthin." [GOC:TermGenie, GOC:yaf, PMID:10995282, UniPathway:UPA00806] synonym: "capsanthin metabolism" EXACT [GOC:TermGenie] intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:3375 ! capsanthin +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI created_by: yaf creation_date: 2013-01-22T10:21:39Z @@ -499715,12 +499724,13 @@ creation_date: 2013-01-22T10:21:39Z id: GO:1901808 name: capsanthin catabolic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of capsanthin." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5174, PMID:10995282, UniPathway:UPA00806] +def: "The chemical reactions and pathways resulting in the breakdown of capsanthin." [GOC:TermGenie, GOC:yaf, PMID:10995282, UniPathway:UPA00806] synonym: "capsanthin breakdown" EXACT [GOC:TermGenie] synonym: "capsanthin catabolism" EXACT [GOC:TermGenie] synonym: "capsanthin degradation" EXACT [GOC:TermGenie] intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:3375 ! capsanthin +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI created_by: yaf creation_date: 2013-01-22T10:21:46Z @@ -500589,10 +500599,11 @@ creation_date: 2013-02-01T10:30:57Z id: GO:1901864 name: capsorubin metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving capsorubin." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5174, UniPathway:UPA00807] +def: "The chemical reactions and pathways involving capsorubin." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00807] synonym: "capsorubin metabolism" EXACT [GOC:TermGenie] intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:3378 ! capsorubin +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI created_by: yaf creation_date: 2013-02-04T10:50:13Z @@ -500600,12 +500611,13 @@ creation_date: 2013-02-04T10:50:13Z id: GO:1901865 name: capsorubin catabolic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of capsorubin." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5174, UniPathway:UPA00807] +def: "The chemical reactions and pathways resulting in the breakdown of capsorubin." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00807] synonym: "capsorubin breakdown" EXACT [GOC:TermGenie] synonym: "capsorubin catabolism" EXACT [GOC:TermGenie] synonym: "capsorubin degradation" EXACT [GOC:TermGenie] intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:3378 ! capsorubin +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI created_by: yaf creation_date: 2013-02-04T10:50:17Z