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Removing incorrect MetaCyc xrefs as def xrefs. #28523 #29230

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merged 1 commit into from
Nov 14, 2024
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@sjm41 sjm41 commented Nov 14, 2024

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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/2024-11-14/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/2024-11-14/go.owl
  • Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

'de novo' XMP biosynthetic process http://purl.obolibrary.org/obo/GO_0097294

Removed

Added

3-(2,3-dihydroxyphenyl)propanoate metabolic process http://purl.obolibrary.org/obo/GO_1901790

Removed

Added

L-homomethionine biosynthetic process http://purl.obolibrary.org/obo/GO_0033322

Removed

Added

ammonia oxidation http://purl.obolibrary.org/obo/GO_0019329

Removed

Added

anaerobic amino acid catabolic process http://purl.obolibrary.org/obo/GO_0019665

Removed

Added

butanediol biosynthetic process http://purl.obolibrary.org/obo/GO_0034079

Removed

Added

butanediol catabolic process http://purl.obolibrary.org/obo/GO_0034078

Removed

Added

butanediol metabolic process http://purl.obolibrary.org/obo/GO_0034077

Removed

Added

cysteine-glucosaminylinositol ligase activity http://purl.obolibrary.org/obo/GO_0035446

Removed

Added

  • cysteine-glucosaminylinositol ligase activity definition "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."

ent-kaurene metabolic process http://purl.obolibrary.org/obo/GO_0033331

Removed

Added

galactose catabolic process via UDP-galactose http://purl.obolibrary.org/obo/GO_0033499

Removed

Added

geranyl diphosphate metabolic process http://purl.obolibrary.org/obo/GO_0033383

Removed

Added

geranylgeranyl diphosphate biosynthetic process http://purl.obolibrary.org/obo/GO_0033386

Removed

Added

geranylgeranyl diphosphate metabolic process http://purl.obolibrary.org/obo/GO_0033385

Removed

Added

glycine cleavage complex http://purl.obolibrary.org/obo/GO_0005960

Removed

Added

  • glycine cleavage complex definition "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."

homomethionine metabolic process http://purl.obolibrary.org/obo/GO_0033321

Removed

Added

kaempferol O-glucoside metabolic process http://purl.obolibrary.org/obo/GO_0033329

Removed

Added

mannosyl-inositol phosphorylceramide metabolic process http://purl.obolibrary.org/obo/GO_0006675

Removed

Added

non-glycolytic fermentation http://purl.obolibrary.org/obo/GO_0019662

Removed

Added

poly(ribitol-phosphate) beta-glucosyltransferase activity http://purl.obolibrary.org/obo/GO_0047266

Removed

Added

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

Removed

Added

quercetin O-glucoside metabolic process http://purl.obolibrary.org/obo/GO_0033302

Removed

Added

rhizobactin 1021 metabolic process http://purl.obolibrary.org/obo/GO_0046494

Removed

Added

  • rhizobactin 1021 metabolic process definition "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."

sophorosyloxydocosanoate metabolic process http://purl.obolibrary.org/obo/GO_0019434

Removed

Added

sulfate adenylyltransferase activity http://purl.obolibrary.org/obo/GO_0004779

Removed

Added

sulfur oxidation http://purl.obolibrary.org/obo/GO_0019417

Removed

Added

@sjm41 sjm41 merged commit 445dd04 into master Nov 14, 2024
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@sjm41 sjm41 deleted the issue-28523sm2 branch November 14, 2024 15:05
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