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Merge pull request #29230 from geneontology/issue-28523sm2
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Removing incorrect MetaCyc xrefs as def xrefs. #28523
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@sjm41
sjm41 authored Nov 14, 2024
2 parents a89500c + f37385f commit 445dd04
Showing 1 changed file with 29 additions and 27 deletions.
56 changes: 29 additions & 27 deletions src/ontology/go-edit.obo
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Expand Up @@ -45834,7 +45834,7 @@ is_a: GO:0016289 ! acyl-CoA hydrolase activity
id: GO:0004779
name: sulfate adenylyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an adenylyl group from an adenosine nucleotide (ATP or ADP) to sulfate, forming adenylylsulfate." [GOC:mah, MetaCyc:SULFATE-ADENYLYLTRANS-RXN, MetaCyc:SULFATE-ADENYLYLTRANSFERASE-ADP-RXN]
def: "Catalysis of the transfer of an adenylyl group from an adenosine nucleotide (ATP or ADP) to sulfate, forming adenylylsulfate." [GOC:mah]
synonym: "sulphate adenylyltransferase activity" EXACT []
is_a: GO:0070566 ! adenylyltransferase activity

Expand Down Expand Up @@ -56980,7 +56980,7 @@ name: glycine cleavage complex
namespace: cellular_component
alt_id: GO:0005961
alt_id: GO:0070015
def: "A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T." [GOC:mah, MetaCyc:GCVMULTI-CPLX]
def: "A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T." [GOC:mah]
subset: goslim_pir
synonym: "glycine cleavage system" EXACT []
synonym: "glycine decarboxylase complex" EXACT []
Expand Down Expand Up @@ -64679,7 +64679,7 @@ intersection_of: has_primary_input_or_output CHEBI:64916 ! inositol phosphoceram
id: GO:0006675
name: mannosyl-inositol phosphorylceramide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving mannosyl-inositol phosphorylceramide, any lipid with a phosphodiester bridge between an inositol residue and the ceramide group which contains a phosphoryl (-P(O)=) groups and a mannose derivative." [GOC:ai, MetaCyc:MIPC]
def: "The chemical reactions and pathways involving mannosyl-inositol phosphorylceramide, any lipid with a phosphodiester bridge between an inositol residue and the ceramide group which contains a phosphoryl (-P(O)=) groups and a mannose derivative." [GOC:ai]
synonym: "mannose inositol phosphoceramide metabolic process" EXACT []
synonym: "mannose inositol phosphoceramide metabolism" EXACT []
synonym: "mannose-inositol-P-ceramide (MIPC) metabolic process" EXACT []
Expand Down Expand Up @@ -142368,7 +142368,7 @@ is_a: GO:0019396 ! gallate catabolic process
id: GO:0019329
name: ammonia oxidation
namespace: biological_process
def: "The chemical reactions and pathways by which ammonia or ammonium is converted to molecular nitrogen or another nitrogen compound, with accompanying loss of electrons." [GOC:mah, MetaCyc:AMMOXID-PWY, MetaCyc:P303-PWY, MetaCyc:PWY-2242]
def: "The chemical reactions and pathways by which ammonia or ammonium is converted to molecular nitrogen or another nitrogen compound, with accompanying loss of electrons." [GOC:mah]
is_a: GO:0044281 ! small molecule metabolic process

[Term]
Expand Down Expand Up @@ -143367,7 +143367,7 @@ is_a: GO:0006790 ! sulfur compound metabolic process
id: GO:0019417
name: sulfur oxidation
namespace: biological_process
def: "The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur." [GOC:jl, MetaCyc:FESULFOX-PWY, MetaCyc:SULFUROX-PWY]
def: "The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur." [GOC:jl]
synonym: "sulphur oxidation" EXACT []
is_a: GO:0006790 ! sulfur compound metabolic process

Expand Down Expand Up @@ -143563,7 +143563,7 @@ intersection_of: has_primary_input CHEBI:17855 ! triglyceride
id: GO:0019434
name: sophorosyloxydocosanoate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving sophorosyloxydocosanoate, 13-sophorosyloxydocosanoate 6',6''-diacetate, an aromatic hydrocarbon." [MetaCyc:DIGLUCODIACETYL-DOCOSANOATE]
def: "The chemical reactions and pathways involving sophorosyloxydocosanoate, 13-sophorosyloxydocosanoate 6',6''-diacetate, an aromatic hydrocarbon." [GOC:curators]
synonym: "sophorosyloxydocosanoate metabolism" EXACT []
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_primary_input_or_output CHEBI:51078 ! 13-sophorosyloxydocosanoate 6',6''-diacetate
Expand Down Expand Up @@ -146153,7 +146153,7 @@ relationship: ends_with GO:0019246 ! L(+)-lactate biosynthetic process from pyru
id: GO:0019662
name: non-glycolytic fermentation
namespace: biological_process
def: "Fermentation that does not include the anaerobic conversion of glucose to pyruvate via the glycolytic pathway." [GOC:jl, MetaCyc:Fermentation]
def: "Fermentation that does not include the anaerobic conversion of glucose to pyruvate via the glycolytic pathway." [GOC:jl]
is_a: GO:0006113 ! fermentation

[Term]
Expand All @@ -146178,7 +146178,7 @@ intersection_of: has_primary_output CHEBI:30089 ! acetate
id: GO:0019665
name: anaerobic amino acid catabolic process
namespace: biological_process
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids, yielding energy in the form of ATP." [GOC:curators, GOC:jl, MetaCyc:Fermentation]
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids, yielding energy in the form of ATP." [GOC:curators, GOC:jl]
synonym: "amino acid fermentation" EXACT []
is_a: GO:0006113 ! fermentation
is_a: GO:0009063 ! amino acid catabolic process
Expand Down Expand Up @@ -191499,7 +191499,7 @@ is_a: GO:0000278 ! mitotic cell cycle
id: GO:0033302
name: quercetin O-glucoside metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving O-glucosylated derivatives of quercetin." [GOC:mah, MetaCyc:PWY-5321]
def: "The chemical reactions and pathways involving O-glucosylated derivatives of quercetin." [GOC:mah]
synonym: "quercetin O-glucoside metabolism" EXACT []
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_primary_input_or_output CHEBI:64621 ! quercetin O-glucoside
Expand Down Expand Up @@ -191708,23 +191708,25 @@ intersection_of: has_primary_output CHEBI:57632 ! UDP-alpha-D-xylose(2-)
id: GO:0033321
name: homomethionine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving homomethionine, a non-protein amino acid synthesized from methionine via chain elongation." [GOC:mah, MetaCyc:PWY-1186]
def: "The chemical reactions and pathways involving homomethionine, a non-protein amino acid synthesized from methionine via chain elongation." [GOC:mah]
synonym: "homomethionine metabolism" EXACT []
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_primary_input_or_output CHEBI:62936 ! homomethioninate

[Term]
id: GO:0033322
name: homomethionine biosynthetic process
name: L-homomethionine biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of homomethionine, a non-protein amino acid synthesized from methionine via chain elongation." [GOC:mah, MetaCyc:PWY-1186]
def: "The chemical reactions and pathways resulting in the formation of L-homomethionine, a non-protein amino acid synthesized from L-methionine via chain elongation." [GOC:mah, MetaCyc:PWY-1186]
synonym: "homomethionine anabolism" EXACT []
synonym: "homomethionine biosynthesis" EXACT []
synonym: "homomethionine biosynthetic process" EXACT []
synonym: "homomethionine formation" EXACT []
synonym: "homomethionine synthesis" EXACT []
xref: MetaCyc:PWY-1186
intersection_of: GO:0009058 ! biosynthetic process
intersection_of: has_primary_output CHEBI:62936 ! homomethioninate
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI

[Term]
id: GO:0033323
Expand Down Expand Up @@ -191806,7 +191808,7 @@ is_a: GO:0000268 ! peroxisome targeting sequence binding
id: GO:0033329
name: kaempferol O-glucoside metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving O-glucosylated derivatives of kaempferol." [GOC:mah, MetaCyc:PWY-5320]
def: "The chemical reactions and pathways involving O-glucosylated derivatives of kaempferol." [GOC:mah]
synonym: "kaempferol O-glucoside metabolism" EXACT []
is_a: GO:0016137 ! glycoside metabolic process
intersection_of: GO:0008152 ! metabolic process
Expand All @@ -191831,7 +191833,7 @@ intersection_of: has_primary_output CHEBI:169942 ! kaempferol 3-O-beta-D-glucosi
id: GO:0033331
name: ent-kaurene metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving ent-kaur-16-ene. Ent-kaurene is a tetracyclic diterpenoid that is a precursor of several plant isoprenoids, including gibberellins." [GOC:mah, MetaCyc:PWY-5032, PMID:17064690]
def: "The chemical reactions and pathways involving ent-kaur-16-ene. Ent-kaurene is a tetracyclic diterpenoid that is a precursor of several plant isoprenoids, including gibberellins." [GOC:mah, PMID:17064690]
synonym: "ent-kaurene metabolism" EXACT []
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_primary_input_or_output CHEBI:15415 ! ent-kaurene
Expand Down Expand Up @@ -192427,7 +192429,7 @@ relationship: part_of GO:0033380 ! granzyme B localization to T cell secretory g
id: GO:0033383
name: geranyl diphosphate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving geranyl diphosphate, the universal precursor of the monoterpenes." [GOC:mah, MetaCyc:PWY-5122]
def: "The chemical reactions and pathways involving geranyl diphosphate, the universal precursor of the monoterpenes." [GOC:mah]
synonym: "geranyl diphosphate metabolism" EXACT []
synonym: "geranyldiphosphate metabolic process" EXACT []
intersection_of: GO:0008152 ! metabolic process
Expand All @@ -192451,7 +192453,7 @@ intersection_of: has_primary_output CHEBI:58057 ! geranyl diphosphate(3-)
id: GO:0033385
name: geranylgeranyl diphosphate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving geranylgeranyl diphosphate, a polyprenol compound involved in the biosynthesis of a variety of terpenoids including chlorophylls, carotenoids, tocopherols, plastoquinones, and the plant hormones gibberellins." [GOC:mah, MetaCyc:PWY-5120]
def: "The chemical reactions and pathways involving geranylgeranyl diphosphate, a polyprenol compound involved in the biosynthesis of a variety of terpenoids including chlorophylls, carotenoids, tocopherols, plastoquinones, and the plant hormones gibberellins." [GOC:mah]
synonym: "geranylgeranyl diphosphate metabolism" EXACT []
synonym: "geranylgeranyldiphosphate metabolic process" EXACT []
intersection_of: GO:0008152 ! metabolic process
Expand All @@ -192461,7 +192463,7 @@ intersection_of: has_primary_input_or_output CHEBI:57533 ! geranylgeranyl diphos
id: GO:0033386
name: geranylgeranyl diphosphate biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of geranylgeranyl diphosphate." [GOC:mah, MetaCyc:PWY-5120]
def: "The chemical reactions and pathways resulting in the formation of geranylgeranyl diphosphate." [GOC:mah]
synonym: "geranylgeranyl diphosphate anabolism" EXACT []
synonym: "geranylgeranyl diphosphate biosynthesis" EXACT []
synonym: "geranylgeranyl diphosphate formation" EXACT []
Expand Down Expand Up @@ -192489,7 +192491,7 @@ intersection_of: has_primary_output CHEBI:326268 ! 1,4-butanediammonium
id: GO:0033388
name: putrescine biosynthetic process from arginine
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine." [GOC:mah, MetaCyc:PWY-46]
def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine." [GOC:mah]
synonym: "putrescine anabolism from arginine" EXACT []
synonym: "putrescine biosynthesis from arginine" EXACT []
synonym: "putrescine formation from arginine" EXACT []
Expand Down Expand Up @@ -193682,7 +193684,7 @@ intersection_of: has_primary_input CHEBI:28260 ! galactose
id: GO:0033499
name: galactose catabolic process via UDP-galactose
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of galactose, via the intermediate UDP-galactose." [GOC:mah, MetaCyc:PWY-3821]
def: "The chemical reactions and pathways resulting in the breakdown of galactose, via the intermediate UDP-galactose." [GOC:mah]
synonym: "galactose breakdown via UDP-galactose" EXACT []
synonym: "galactose catabolism via UDP-galactose" EXACT []
synonym: "galactose degradation via UDP-galactose" EXACT []
Expand Down Expand Up @@ -200698,7 +200700,7 @@ is_a: GO:0031559 ! oxidosqualene cyclase activity
id: GO:0034077
name: butanediol metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3." [ISBN:0911910123, MetaCyc:BUTANEDIOL]
def: "The chemical reactions and pathways involving butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3." [ISBN:0911910123]
synonym: "butanediol metabolism" EXACT []
synonym: "butylene glycol metabolic process" EXACT []
synonym: "butylene glycol metabolism" EXACT []
Expand All @@ -200710,7 +200712,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
id: GO:0034078
name: butanediol catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3." [GOC:mah, ISBN:0911910123, MetaCyc:BUTANEDIOL]
def: "The chemical reactions and pathways resulting in the breakdown of butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3." [GOC:mah, ISBN:0911910123]
synonym: "butanediol breakdown" EXACT []
synonym: "butanediol catabolism" EXACT []
synonym: "butanediol degradation" EXACT []
Expand All @@ -200724,7 +200726,7 @@ intersection_of: has_primary_input CHEBI:62064 ! butane-2,3-diol
id: GO:0034079
name: butanediol biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3." [GOC:mah, ISBN:0911910123, MetaCyc:BUTANEDIOL, MetaCyc:P125-PWY]
def: "The chemical reactions and pathways resulting in the formation of butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3." [GOC:mah, ISBN:0911910123, MetaCyc:P125-PWY]
synonym: "butanediol anabolism" EXACT []
synonym: "butanediol biosynthesis" EXACT []
synonym: "butanediol formation" EXACT []
Expand Down Expand Up @@ -214082,7 +214084,7 @@ creation_date: 2010-04-13T09:24:23Z
id: GO:0035446
name: cysteine-glucosaminylinositol ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: 1-(2-amino-2-deoxy-alpha-D-glucopyranoside)-1D-myo-inositol + L-cysteine + ATP = 1-D-myo-inosityl-2-L-cysteinylamido-2-deoxy-alpha-D-glucopyranoside + AMP + diphosphate + 2 H+. 1-(2-amino-2-deoxy-alpha-D-glucopyranoside)-1D-myo-inositol is also known as glucosaminyl-inositol or GlcN-Ins, and 1-D-myo-inosityl-2-L-cysteinylamido-2-deoxy-alpha-D-glucopyranoside as desacetylmycothiol or Cys-GlcN-Ins." [EC:6.3.1.13, MetaCyc:RXN1G-4, PMID:12033919]
def: "Catalysis of the reaction: 1-(2-amino-2-deoxy-alpha-D-glucopyranoside)-1D-myo-inositol + L-cysteine + ATP = 1-D-myo-inosityl-2-L-cysteinylamido-2-deoxy-alpha-D-glucopyranoside + AMP + diphosphate + 2 H+. 1-(2-amino-2-deoxy-alpha-D-glucopyranoside)-1D-myo-inositol is also known as glucosaminyl-inositol or GlcN-Ins, and 1-D-myo-inosityl-2-L-cysteinylamido-2-deoxy-alpha-D-glucopyranoside as desacetylmycothiol or Cys-GlcN-Ins." [EC:6.3.1.13, PMID:12033919]
synonym: "desacetylmycothiol synthase" RELATED [PMID:12033919]
synonym: "L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase" RELATED [EC:6.3.1.13]
synonym: "MshC ligase" RELATED [EC:6.3.1.13]
Expand Down Expand Up @@ -278446,7 +278448,7 @@ intersection_of: has_primary_input_or_output CHEBI:47040 ! lipid A
id: GO:0046494
name: rhizobactin 1021 metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving rhizobactin 1021, (E)-4-((3-(acetylhydroxyamino)propyl)-amino)-2-hydroxy-(2-(2-(3-(hydroxy(1-oxo-2-decenyl)amino)propyl)amino)-2-oxoethyl)-4-oxobutanoic acid, a siderophore produced by Sinorhizobium meliloti." [MetaCyc:PWY-761, PMID:11274118]
def: "The chemical reactions and pathways involving rhizobactin 1021, (E)-4-((3-(acetylhydroxyamino)propyl)-amino)-2-hydroxy-(2-(2-(3-(hydroxy(1-oxo-2-decenyl)amino)propyl)amino)-2-oxoethyl)-4-oxobutanoic acid, a siderophore produced by Sinorhizobium meliloti." [PMID:11274118]
synonym: "rhizobactin 1021 metabolism" EXACT []
is_a: GO:0009237 ! siderophore metabolic process
intersection_of: GO:0008152 ! metabolic process
Expand Down Expand Up @@ -287690,7 +287692,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047266
name: poly(ribitol-phosphate) beta-glucosyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: poly(ribitol phosphate) + UDP-D-glucose = beta-D-glucosylpoly(ribitol phosphate) + UDP." [EC:2.4.1.53, MetaCyc:2.4.1.53-RXN]
def: "Catalysis of the reaction: poly(ribitol phosphate) + UDP-D-glucose = beta-D-glucosylpoly(ribitol phosphate) + UDP." [EC:2.4.1.53]
synonym: "UDP glucose-poly(ribitol-phosphate) beta-glucosyltransferase activity" RELATED [EC:2.4.1.53]
synonym: "UDP-D-glucose polyribitol phosphate glucosyl transferase activity" RELATED [EC:2.4.1.53]
synonym: "UDP-D-glucose:polyribitol phosphate glucosyl transferase activity" RELATED [EC:2.4.1.53]
Expand Down Expand Up @@ -414329,7 +414331,7 @@ creation_date: 2012-04-26T09:54:13Z
id: GO:0097294
name: 'de novo' XMP biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of XMP, xanthosine monophosphate, from simpler precursors." [GOC:yaf, MetaCyc:IMP-DEHYDROG-RXN, PMID:27590927]
def: "The chemical reactions and pathways resulting in the formation of XMP, xanthosine monophosphate, from simpler precursors." [GOC:yaf, PMID:27590927]
synonym: "'de novo' XMP anabolism" EXACT []
synonym: "'de novo' XMP biosynthesis" EXACT []
synonym: "'de novo' XMP formation" EXACT []
Expand Down Expand Up @@ -499369,7 +499371,7 @@ creation_date: 2013-01-16T11:14:03Z
id: GO:1901790
name: 3-(2,3-dihydroxyphenyl)propanoate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving 3-(2,3-dihydroxyphenyl)propanoate." [GOC:TermGenie, GOC:yaf, MetaCyc:HCAMHPDEG-PWY]
def: "The chemical reactions and pathways involving 3-(2,3-dihydroxyphenyl)propanoate." [GOC:TermGenie, GOC:yaf]
synonym: "3-(2,3-dihydroxyphenyl)propanoate metabolism" EXACT [GOC:TermGenie]
intersection_of: GO:0008152 ! metabolic process
intersection_of: has_primary_input_or_output CHEBI:46951 ! 3-(2,3-dihydroxyphenyl)propanoate
Expand Down

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