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Merge pull request #29239 from geneontology/issue-28523sm4
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Fixing MetaCyc def xrefs as db xrefs. #28523
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@sjm41
sjm41 authored Nov 15, 2024
2 parents 91035f7 + 30e8ba8 commit 5ee566f
Showing 1 changed file with 23 additions and 12 deletions.
35 changes: 23 additions & 12 deletions src/ontology/go-edit.obo
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Expand Up @@ -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]
Expand All @@ -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
Expand Down Expand Up @@ -57806,7 +57809,6 @@ synonym: "beta-1,4-linked N-acetylglucosamine catabolism" EXACT []
synonym: "chitin breakdown" EXACT []
synonym: "chitin catabolism" EXACT []
synonym: "chitin degradation" EXACT []
xref: MetaCyc:PWY-6855 {source="skos:narrowMatch"}
xref: MetaCyc:PWY-6902 {source="skos:narrowMatch"}
xref: MetaCyc:PWY-7118 {source="skos:narrowMatch"}
xref: MetaCyc:PWY-7822 {source="skos:narrowMatch"}
Expand Down Expand Up @@ -63862,7 +63864,7 @@ 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 []
Expand Down Expand Up @@ -192146,7 +192148,7 @@ 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 []
Expand All @@ -192157,6 +192159,7 @@ 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
Expand Down Expand Up @@ -338885,16 +338888,19 @@ 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
Expand Down Expand Up @@ -408010,10 +408016,11 @@ 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

Expand Down Expand Up @@ -499704,23 +499711,25 @@ 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

[Term]
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

Expand Down Expand Up @@ -500589,23 +500598,25 @@ 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

[Term]
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

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