Issue 28553

[pgaudet]

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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/2024-12-09/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/2024-12-09/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

'de novo' NAD biosynthetic process from tryptophan http://purl.obolibrary.org/obo/GO_0034354

Removed

• 'de novo' NAD biosynthetic process from tryptophan SubClassOf tryptophan metabolic process

negative regulation of 'de novo' NAD biosynthetic process from tryptophan http://purl.obolibrary.org/obo/GO_1905013

Removed

• negative regulation of 'de novo' NAD biosynthetic process from tryptophan SubClassOf negative regulation of amino acid metabolic process

• negative regulation of 'de novo' NAD biosynthetic process from tryptophan SubClassOf negative regulation of amine metabolic process

positive regulation of 'de novo' NAD biosynthetic process from tryptophan http://purl.obolibrary.org/obo/GO_1905014

Removed

• positive regulation of 'de novo' NAD biosynthetic process from tryptophan SubClassOf positive regulation of tryptophan metabolic process

positive regulation of tryptophan metabolic process http://purl.obolibrary.org/obo/GO_0090358

Removed

• positive regulation of tryptophan metabolic process label "positive regulation of tryptophan metabolic process"

Added

• positive regulation of tryptophan metabolic process has_related_synonym "positive regulation of tryptophan metabolic process"

• positive regulation of tryptophan metabolic process label "positive regulation of L-tryptophan metabolic process"

regulation of 'de novo' NAD biosynthetic process from tryptophan http://purl.obolibrary.org/obo/GO_1905012

Removed

• regulation of 'de novo' NAD biosynthetic process from tryptophan SubClassOf regulation of tryptophan metabolic process

regulation of tryptophan metabolic process http://purl.obolibrary.org/obo/GO_0090357

Removed

• regulation of tryptophan metabolic process label "regulation of tryptophan metabolic process"

Added

• regulation of tryptophan metabolic process label "regulation of L-tryptophan metabolic process"

• regulation of tryptophan metabolic process has_related_synonym "regulation of tryptophan metabolic process"

tryptophan biosynthetic process http://purl.obolibrary.org/obo/GO_0000162

Removed

• tryptophan biosynthetic process has_exact_synonym "tryptophan biosynthesis"

• tryptophan biosynthetic process definition "The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "MetaCyc:TRPSYN-PWY"

  • database_cross_reference "ISBN:0471331309"

• tryptophan biosynthetic process has_exact_synonym "tryptophan anabolism"

• tryptophan biosynthetic process has_exact_synonym "tryptophan synthesis"

• tryptophan biosynthetic process label "tryptophan biosynthetic process"

• tryptophan biosynthetic process EquivalentTo biosynthetic process and (has primary output some tryptophan zwitterion)

• tryptophan biosynthetic process SubClassOf has primary output some tryptophan zwitterion

• tryptophan biosynthetic process SubClassOf alpha-amino acid biosynthetic process

Added

• tryptophan biosynthetic process label "L-tryptophan biosynthetic process"

• tryptophan biosynthetic process has_exact_synonym "L-tryptophan biosynthesis"

• tryptophan biosynthetic process has_related_synonym "tryptophan synthesis"

• tryptophan biosynthetic process definition "The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate."

  • database_cross_reference "GOC:mah"

  • database_cross_reference "MetaCyc:TRPSYN-PWY"

  • database_cross_reference "ISBN:0471331309"

• tryptophan biosynthetic process has_exact_synonym "L-tryptophan anabolism"

• tryptophan biosynthetic process has_related_synonym "tryptophan biosynthetic process"

• tryptophan biosynthetic process EquivalentTo biosynthetic process and (has primary output some L-tryptophan zwitterion)

• tryptophan biosynthetic process SubClassOf tryptophan metabolic process

• tryptophan biosynthetic process SubClassOf has primary output some L-tryptophan zwitterion

• tryptophan biosynthetic process SubClassOf erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process

tryptophan catabolic process http://purl.obolibrary.org/obo/GO_0006569

Removed

• tryptophan catabolic process definition "The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid."

  • database_cross_reference "ISBN:0198547684"

• tryptophan catabolic process label "tryptophan catabolic process"

• tryptophan catabolic process EquivalentTo catabolic process and (has primary input some tryptophan zwitterion)

• tryptophan catabolic process SubClassOf indolalkylamine metabolic process

• tryptophan catabolic process SubClassOf has primary input some tryptophan zwitterion

• tryptophan catabolic process SubClassOf alpha-amino acid catabolic process

Added

• tryptophan catabolic process has_related_synonym "tryptophan catabolic process"

• tryptophan catabolic process definition "The chemical reactions and pathways resulting in the breakdown of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid."

  • database_cross_reference "ISBN:0198547684"

• tryptophan catabolic process label "L-tryptophan catabolic process"

• tryptophan catabolic process EquivalentTo catabolic process and (has primary input some L-tryptophan zwitterion)

• tryptophan catabolic process SubClassOf erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process

• tryptophan catabolic process SubClassOf tryptophan metabolic process

• tryptophan catabolic process SubClassOf has primary input some L-tryptophan zwitterion

tryptophan catabolic process to acetyl-CoA http://purl.obolibrary.org/obo/GO_0019442

Removed

• tryptophan catabolic process to acetyl-CoA label "tryptophan catabolic process to acetyl-CoA"

• tryptophan catabolic process to acetyl-CoA definition "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including acetyl-CoA."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to acetyl-CoA EquivalentTo catabolic process and (has primary output some acetyl-CoA(4-)) and (has primary input some tryptophan zwitterion)

Added

• tryptophan catabolic process to acetyl-CoA has_exact_synonym "tryptophan catabolic process to acetyl-CoA"

• tryptophan catabolic process to acetyl-CoA definition "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including acetyl-CoA."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to acetyl-CoA label "L-tryptophan catabolic process to acetyl-CoA"

• tryptophan catabolic process to acetyl-CoA EquivalentTo catabolic process and (has primary output some acetyl-CoA(4-)) and (has primary input some L-tryptophan zwitterion)

tryptophan catabolic process to catechol http://purl.obolibrary.org/obo/GO_0019444

Removed

• tryptophan catabolic process to catechol definition "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including catechol."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to catechol label "tryptophan catabolic process to catechol"

• tryptophan catabolic process to catechol SubClassOf tryptophan catabolic process

Added

• tryptophan catabolic process to catechol has_exact_synonym "tryptophan catabolic process to catechol"

• tryptophan catabolic process to catechol definition "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including catechol."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to catechol label "L-tryptophan catabolic process to catechol"

• tryptophan catabolic process to catechol SubClassOf indolalkylamine metabolic process

• tryptophan catabolic process to catechol SubClassOf has primary input some tryptophan zwitterion

• tryptophan catabolic process to catechol SubClassOf aromatic amino acid family catabolic process

• tryptophan catabolic process to catechol SubClassOf indole-containing compound catabolic process

• tryptophan catabolic process to catechol SubClassOf alpha-amino acid catabolic process

tryptophan catabolic process to indole-3-acetate http://purl.obolibrary.org/obo/GO_0019440

Removed

• tryptophan catabolic process to indole-3-acetate definition "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including indole-3-acetate."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to indole-3-acetate label "tryptophan catabolic process to indole-3-acetate"

• tryptophan catabolic process to indole-3-acetate EquivalentTo catabolic process and (has primary output some indole-3-acetate) and (has primary input some tryptophan zwitterion)

Added

• tryptophan catabolic process to indole-3-acetate has_exact_synonym "tryptophan catabolic process to indole-3-acetate"

• tryptophan catabolic process to indole-3-acetate definition "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including indole-3-acetate."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to indole-3-acetate label "L-tryptophan catabolic process to indole-3-acetate"

• tryptophan catabolic process to indole-3-acetate EquivalentTo catabolic process and (has primary output some indole-3-acetate) and (has primary input some L-tryptophan zwitterion)

tryptophan catabolic process to kynurenine http://purl.obolibrary.org/obo/GO_0019441

Removed

• tryptophan catabolic process to kynurenine definition "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to kynurenine label "tryptophan catabolic process to kynurenine"

• tryptophan catabolic process to kynurenine EquivalentTo catabolic process and (has primary output some kynurenine) and (has primary input some tryptophan zwitterion)

Added

• tryptophan catabolic process to kynurenine label "L-tryptophan catabolic process to kynurenine"

• tryptophan catabolic process to kynurenine has_exact_synonym "tryptophan catabolic process to kynurenine"

• tryptophan catabolic process to kynurenine definition "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including kynurenine."

  • database_cross_reference "GOC:go_curators"

• tryptophan catabolic process to kynurenine EquivalentTo catabolic process and (has primary output some kynurenine) and (has primary input some L-tryptophan zwitterion)

tryptophan metabolic process http://purl.obolibrary.org/obo/GO_0006568

Removed

• tryptophan metabolic process has_exact_synonym "tryptophan metabolism"

• tryptophan metabolic process label "tryptophan metabolic process"

Added

• tryptophan metabolic process label "L-tryptophan metabolic process"

• tryptophan metabolic process has_related_synonym "tryptophan metabolic process"

• tryptophan metabolic process has_related_synonym "tryptophan metabolism"