Adding MetaCyc def xrefs as db xrefs. #28523

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Here's a diff of how these changes impact the classified ontology:

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-15/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-master.owl/reasoned.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-15/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

1,5-anhydro-D-fructose catabolic process http://purl.obolibrary.org/obo/GO_1901802

Added

• 1,5-anhydro-D-fructose catabolic process database_cross_reference "MetaCyc:PWY-6992"

• 1,5-anhydro-D-fructose catabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

3-(2,3-dihydroxyphenyl)propanoate catabolic process http://purl.obolibrary.org/obo/GO_1901791

Added

• 3-(2,3-dihydroxyphenyl)propanoate catabolic process database_cross_reference "MetaCyc:HCAMHPDEG-PWY"

  • source "skos:broadMatch"

• 3-(2,3-dihydroxyphenyl)propanoate catabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

3-(3-hydroxyphenyl)propanoate catabolic process http://purl.obolibrary.org/obo/GO_1901794

Added

• 3-(3-hydroxyphenyl)propanoate catabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• 3-(3-hydroxyphenyl)propanoate catabolic process database_cross_reference "MetaCyc:PWY0-1277"

  • source "skos:broadMatch"

4-aminobenzoate biosynthetic process http://purl.obolibrary.org/obo/GO_0008153

Removed

• 4-aminobenzoate biosynthetic process definition "The chemical reactions and pathways resulting in the formation of para-aminobenzoic acid, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins."

  • database_cross_reference "PMID:11377864"

  • database_cross_reference "MetaCyc:PWY-6543"

  • database_cross_reference "PMID:11960743"

  • database_cross_reference "ISBN:0198506732"

• 4-aminobenzoate biosynthetic process label "para-aminobenzoic acid biosynthetic process"

Added

• 4-aminobenzoate biosynthetic process database_cross_reference "MetaCyc:PWY-8281"

  • source "skos:narrowMatch"

• 4-aminobenzoate biosynthetic process has_exact_synonym "para-aminobenzoic acid biosynthetic process"

• 4-aminobenzoate biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• 4-aminobenzoate biosynthetic process label "4-aminobenzoate biosynthetic process"

• 4-aminobenzoate biosynthetic process database_cross_reference "MetaCyc:PWY-6543"

  • source "skos:narrowMatch"

• 4-aminobenzoate biosynthetic process definition "The chemical reactions and pathways resulting in the formation of 4-aminobenzoate, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins."

  • database_cross_reference "PMID:11377864"

  • database_cross_reference "MetaCyc:PWY-6543"

  • database_cross_reference "PMID:11960743"

  • database_cross_reference "ISBN:0198506732"

• 4-aminobenzoate biosynthetic process database_cross_reference "MetaCyc:PWY-8276"

  • source "skos:narrowMatch"

9'-cis-neoxanthin http://purl.obolibrary.org/obo/CHEBI_35306

Added

• Class: 9'-cis-neoxanthin

alpha-carotene http://purl.obolibrary.org/obo/CHEBI_28425

Added

• Class: alpha-carotene

alpha-carotene biosynthetic process http://purl.obolibrary.org/obo/GO_1901824

Removed

• alpha-carotene biosynthetic process label "delta-carotene biosynthetic process"

• alpha-carotene biosynthetic process definition "The chemical reactions and pathways resulting in the formation of delta-carotene."

  • database_cross_reference "GOC:yaf"

  • database_cross_reference "GOC:TermGenie"

  • database_cross_reference "MetaCyc:PWY-5946"

  • database_cross_reference "PMID:8837512"

  • database_cross_reference "UniPathway:UPA00801"

• alpha-carotene biosynthetic process EquivalentTo biosynthetic process and (has primary output some delta-carotene)

• alpha-carotene biosynthetic process SubClassOf delta-carotene metabolic process

• alpha-carotene biosynthetic process SubClassOf has primary output some delta-carotene

Added

• alpha-carotene biosynthetic process definition "The chemical reactions and pathways resulting in the formation of alpha-carotene."

  • database_cross_reference "GOC:yaf"

  • database_cross_reference "GOC:TermGenie"

  • database_cross_reference "MetaCyc:PWY-5946"

  • database_cross_reference "PMID:8837512"

  • database_cross_reference "UniPathway:UPA00801"

• alpha-carotene biosynthetic process label "alpha-carotene biosynthetic process"

• alpha-carotene biosynthetic process has_exact_synonym "delta-carotene biosynthetic process"

• alpha-carotene biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• alpha-carotene biosynthetic process database_cross_reference "MetaCyc:PWY-5946"

• alpha-carotene biosynthetic process EquivalentTo biosynthetic process and (has primary output some alpha-carotene)

• alpha-carotene biosynthetic process SubClassOf has primary output some alpha-carotene

anaerobic benzoate metabolic process http://purl.obolibrary.org/obo/GO_0018875

Removed

• anaerobic benzoate metabolic process database_cross_reference "MetaCyc:CENTBENZCOA-PWY"

Added

• anaerobic benzoate metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

astaxanthin biosynthetic process http://purl.obolibrary.org/obo/GO_1901815

Added

• astaxanthin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• astaxanthin biosynthetic process database_cross_reference "MetaCyc:PWY-5288"

benzoate metabolic process http://purl.obolibrary.org/obo/GO_0018874

Removed

• benzoate metabolic process database_cross_reference "MetaCyc:P321-PWY"

Added

• benzoate metabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

benzoyl-CoA catabolic process http://purl.obolibrary.org/obo/GO_1901788

Added

• benzoyl-CoA catabolic process database_cross_reference "MetaCyc:PWY-1361"

  • source "skos:narrowMatch"

• benzoyl-CoA catabolic process database_cross_reference "MetaCyc:P321-PWY"

  • source "skos:narrowMatch"

• benzoyl-CoA catabolic process database_cross_reference "MetaCyc:CENTBENZCOA-PWY"

  • source "skos:narrowMatch"

• benzoyl-CoA catabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

beta-carotene biosynthetic process http://purl.obolibrary.org/obo/GO_1901812

Added

• beta-carotene biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• beta-carotene biosynthetic process database_cross_reference "MetaCyc:PWY-5943"

capsanthin biosynthetic process http://purl.obolibrary.org/obo/GO_1901809

Added

• capsanthin biosynthetic process database_cross_reference "MetaCyc:PWY-5174"

  • source "skos:broadMatch"

• capsanthin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

capsorubin biosynthetic process http://purl.obolibrary.org/obo/GO_1901866

Added

• capsorubin biosynthetic process database_cross_reference "MetaCyc:PWY-5174"

  • source "skos:broadMatch"

• capsorubin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

creatine biosynthetic process http://purl.obolibrary.org/obo/GO_0006601

Added

• creatine biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• creatine biosynthetic process database_cross_reference "MetaCyc:GLYCGREAT-PWY"

farnesyl diphosphate biosynthetic process, mevalonate pathway http://purl.obolibrary.org/obo/GO_0010142

Removed

• farnesyl diphosphate biosynthetic process, mevalonate pathway database_cross_reference "MetaCyc:PWY-922"

fermentation http://purl.obolibrary.org/obo/GO_0006113

Removed

• fermentation database_cross_reference "MetaCyc:FERMENTATION-PWY"

Added

• fermentation database_cross_reference "MetaCyc:Fermentation"

• fermentation term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

glycine catabolic process to creatine http://purl.obolibrary.org/obo/GO_0019463

Removed

• glycine catabolic process to creatine database_cross_reference "MetaCyc:GLYCGREAT-PWY"

Added

• glycine catabolic process to creatine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

isopentenyl diphosphate biosynthetic process, mevalonate pathway http://purl.obolibrary.org/obo/GO_0019287

Added

• isopentenyl diphosphate biosynthetic process, mevalonate pathway database_cross_reference "MetaCyc:PWY-922"

• isopentenyl diphosphate biosynthetic process, mevalonate pathway term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

lincomycin biosynthetic process http://purl.obolibrary.org/obo/GO_1901774

Added

• lincomycin biosynthetic process database_cross_reference "MetaCyc:PWY-6955"

• lincomycin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

mixed acid fermentation http://purl.obolibrary.org/obo/GO_0019664

Added

• mixed acid fermentation database_cross_reference "MetaCyc:FERMENTATION-PWY"

• mixed acid fermentation term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

neomycin biosynthetic process http://purl.obolibrary.org/obo/GO_1901158

Added

• neomycin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• neomycin biosynthetic process database_cross_reference "MetaCyc:PWY-7016"

neoxanthin biosynthetic process http://purl.obolibrary.org/obo/GO_1901833

Removed

• neoxanthin biosynthetic process label "all-trans-neoxanthin biosynthetic process"

• neoxanthin biosynthetic process has_exact_synonym "neoxanthin biosynthetic process"

  • database_cross_reference "GOC:yaf"

• neoxanthin biosynthetic process definition "The chemical reactions and pathways resulting in the formation of all-trans-neoxanthin."

  • database_cross_reference "GOC:yaf"

  • database_cross_reference "GOC:TermGenie"

  • database_cross_reference "UniPathway:UPA00388"

  • database_cross_reference "PMID:11029576"

  • database_cross_reference "MetaCyc:PWY-6809"

• neoxanthin biosynthetic process EquivalentTo biosynthetic process and (has primary output some all-trans-neoxanthin)

Added

• neoxanthin biosynthetic process database_cross_reference "MetaCyc:PWY-6809"

• neoxanthin biosynthetic process definition "The chemical reactions and pathways resulting in the formation of trans-neoxanthin and 9'-cis-neoxanthin."

  • database_cross_reference "GOC:yaf"

  • database_cross_reference "GOC:TermGenie"

  • database_cross_reference "UniPathway:UPA00388"

  • database_cross_reference "PMID:11029576"

  • database_cross_reference "MetaCyc:PWY-6809"

• neoxanthin biosynthetic process has_narrow_synonym "all-trans-neoxanthin biosynthetic process"

• neoxanthin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• neoxanthin biosynthetic process label "neoxanthin biosynthetic process"

• neoxanthin biosynthetic process EquivalentTo biosynthetic process and (has primary output some all-trans-neoxanthin) and (has primary output some 9'-cis-neoxanthin)

• neoxanthin biosynthetic process SubClassOf has primary output some 9'-cis-neoxanthin

p-cumate catabolic process http://purl.obolibrary.org/obo/GO_1901782

Added

• p-cumate catabolic process database_cross_reference "MetaCyc:PWY-5273"

• p-cumate catabolic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

pentalenolactone biosynthetic process http://purl.obolibrary.org/obo/GO_1901780

Added

• pentalenolactone biosynthetic process database_cross_reference "MetaCyc:PWY-6915"

• pentalenolactone biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

phenylacetaldehyde synthase activity http://purl.obolibrary.org/obo/GO_1990055

Added

• phenylacetaldehyde synthase activity term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• phenylacetaldehyde synthase activity database_cross_reference "MetaCyc:RXN-8990"

phosphatidylcholine biosynthesis from phosphatidylethanolamine http://purl.obolibrary.org/obo/GO_0090638

Added

• phosphatidylcholine biosynthesis from phosphatidylethanolamine database_cross_reference "MetaCyc:PWY-6825"

• phosphatidylcholine biosynthesis from phosphatidylethanolamine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

phosphatidylcholine biosynthesis from sn-glycero-3-phosphocholine http://purl.obolibrary.org/obo/GO_0090640

Added

• phosphatidylcholine biosynthesis from sn-glycero-3-phosphocholine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• phosphatidylcholine biosynthesis from sn-glycero-3-phosphocholine database_cross_reference "MetaCyc:PWY-7470"

putrescine biosynthetic process from arginine http://purl.obolibrary.org/obo/GO_0033388

Removed

• putrescine biosynthetic process from arginine EquivalentTo biosynthetic process and (has primary output some 1,4-butanediammonium) and (has primary input some argininium(1+))

• putrescine biosynthetic process from arginine SubClassOf has primary input some argininium(1+)

Added

• putrescine biosynthetic process from arginine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• putrescine biosynthetic process from arginine EquivalentTo biosynthetic process and (has primary output some 1,4-butanediammonium) and (has primary input some L-argininium(1+))

• putrescine biosynthetic process from arginine SubClassOf glutamine family amino acid metabolic process

• putrescine biosynthetic process from arginine SubClassOf has primary input some L-argininium(1+)

putrescine biosynthetic process from arginine via N-carbamoylputrescine http://purl.obolibrary.org/obo/GO_0033390

Removed

• putrescine biosynthetic process from arginine via N-carbamoylputrescine EquivalentTo biosynthetic process and (has intermediate some N-carbamoylputrescinium(1+)) and (has primary output some 1,4-butanediammonium) and (has primary input some argininium(1+))

Added

• putrescine biosynthetic process from arginine via N-carbamoylputrescine database_cross_reference "MetaCyc:PWY-43"

• putrescine biosynthetic process from arginine via N-carbamoylputrescine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• putrescine biosynthetic process from arginine via N-carbamoylputrescine EquivalentTo biosynthetic process and (has intermediate some N-carbamoylputrescinium(1+)) and (has primary output some 1,4-butanediammonium) and (has primary input some L-argininium(1+))

putrescine biosynthetic process from arginine, via agmatine http://purl.obolibrary.org/obo/GO_0033389

Removed

• putrescine biosynthetic process from arginine, via agmatine label "putrescine biosynthetic process from arginine, using agmatinase"

• putrescine biosynthetic process from arginine, via agmatine definition "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine; in this pathway, arginine is converted to agmatine, and agmatine is converted to putrescine in a single enzymatic step."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "MetaCyc:PWY-40"

• putrescine biosynthetic process from arginine, via agmatine EquivalentTo biosynthetic process and (has intermediate some agmatinium(2+)) and (has primary output some 1,4-butanediammonium) and (has primary input some argininium(1+))

Added

• putrescine biosynthetic process from arginine, via agmatine definition "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine via agmatine."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "MetaCyc:PWY-40"

• putrescine biosynthetic process from arginine, via agmatine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• putrescine biosynthetic process from arginine, via agmatine has_exact_synonym "putrescine biosynthetic process from arginine, using agmatinase"

• putrescine biosynthetic process from arginine, via agmatine database_cross_reference "MetaCyc:PWY-40"

• putrescine biosynthetic process from arginine, via agmatine label "putrescine biosynthetic process from arginine, via agmatine"

• putrescine biosynthetic process from arginine, via agmatine EquivalentTo biosynthetic process and (has intermediate some agmatinium(2+)) and (has primary output some 1,4-butanediammonium) and (has primary input some L-argininium(1+))

putrescine biosynthetic process from arginine, via ornithine http://purl.obolibrary.org/obo/GO_0033387

Removed

• putrescine biosynthetic process from arginine, via ornithine label "putrescine biosynthetic process from ornithine"

• putrescine biosynthetic process from arginine, via ornithine definition "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane by decarboxylation of ornithine."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "MetaCyc:PWY-46"

• putrescine biosynthetic process from arginine, via ornithine EquivalentTo biosynthetic process and (has primary output some 1,4-butanediammonium) and (has primary input some ornithinium(1+))

• putrescine biosynthetic process from arginine, via ornithine SubClassOf has primary input some ornithinium(1+)

• putrescine biosynthetic process from arginine, via ornithine SubClassOf putrescine biosynthetic process

• putrescine biosynthetic process from arginine, via ornithine SubClassOf ornithine metabolic process

Added

• putrescine biosynthetic process from arginine, via ornithine has_exact_synonym "putrescine biosynthetic process from ornithine"

• putrescine biosynthetic process from arginine, via ornithine label "putrescine biosynthetic process from arginine, via ornithine"

• putrescine biosynthetic process from arginine, via ornithine term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• putrescine biosynthetic process from arginine, via ornithine database_cross_reference "MetaCyc:PWY-46"

• putrescine biosynthetic process from arginine, via ornithine definition "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine, via decarboxylation of ornithine."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "MetaCyc:PWY-46"

• putrescine biosynthetic process from arginine, via ornithine EquivalentTo biosynthetic process and (has intermediate some ornithinium(1+)) and (has primary output some 1,4-butanediammonium) and (has primary input some L-argininium(1+))

• putrescine biosynthetic process from arginine, via ornithine SubClassOf has intermediate some ornithinium(1+)

• putrescine biosynthetic process from arginine, via ornithine SubClassOf putrescine biosynthetic process from arginine

zeaxanthin biosynthetic process http://purl.obolibrary.org/obo/GO_1901827

Added

• zeaxanthin biosynthetic process database_cross_reference "MetaCyc:PWY-5944"

• zeaxanthin biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

zeaxanthin bis(beta-D-glucoside) biosynthetic process http://purl.obolibrary.org/obo/GO_1901830

Added

• zeaxanthin bis(beta-D-glucoside) biosynthetic process database_cross_reference "MetaCyc:PWY-6288"

• zeaxanthin bis(beta-D-glucoside) biosynthetic process term tracker item "https://github.com/geneontology/go-ontology/issues/28523"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)