removed do not annotate fixes #29584

[pgaudet]

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[github-actions]

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/2025-01-30/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/2025-01-30/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

2-hydroxy-1,4-benzoquinone reductase activity http://purl.obolibrary.org/obo/GO_0050625

Removed

• 2-hydroxy-1,4-benzoquinone reductase activity database_cross_reference "RHEA:12428"

• 2-hydroxy-1,4-benzoquinone reductase activity database_cross_reference "EC:1.6.5.7"

• 2-hydroxy-1,4-benzoquinone reductase activity definition "Catalysis of the reaction: 2-hydroxy-1,4-benzoquinone + 2 H+ + NADH = benzene-1,2,4-triol + NAD+."

  • database_cross_reference "EC:1.6.5.7"

  • database_cross_reference "RHEA:12428"

Added

• 2-hydroxy-1,4-benzoquinone reductase activity definition "Catalysis of the reaction: 2-hydroxy-1,4-benzoquinone + 2 H+ + NADH = benzene-1,2,4-triol + NAD+."

  • database_cross_reference "RHEA:12428"

• 2-hydroxy-1,4-benzoquinone reductase activity database_cross_reference "EC:1.6.5.7"

  • source "skos:exactMatch"

• 2-hydroxy-1,4-benzoquinone reductase activity database_cross_reference "RHEA:12428"

  • source "skos:exactMatch"

N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity http://purl.obolibrary.org/obo/GO_0047186

Removed

• N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity definition "Catalysis of the reaction: N-acetylneuraminate + acetyl-CoA = N-acetyl-7-O(or 9-O)-acetylneuraminate + CoA."

  • database_cross_reference "EC:2.3.1.45"

  • database_cross_reference "MetaCyc:2.3.1.45-RXN"

Added

• N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity definition "Catalysis of the reaction: N-acetylneuraminate + acetyl-CoA = N-acetyl-7-O(or 9-O)-acetylneuraminate + CoA."
  • database_cross_reference "EC:2.3.1.45"

NAD(P)H dehydrogenase (quinone) activity http://purl.obolibrary.org/obo/GO_0003955

Removed

• NAD(P)H dehydrogenase (quinone) activity database_cross_reference "EC:1.6.5.2"

Added

• NAD(P)H dehydrogenase (quinone) activity database_cross_reference "EC:1.6.5.2"
  • source "skos:exactMatch"

NADH dehydrogenase (ubiquinone) activity http://purl.obolibrary.org/obo/GO_0008137

Removed

• NADH dehydrogenase (ubiquinone) activity SubClassOf has participant some hydron

• NADH dehydrogenase (ubiquinone) activity SubClassOf has participant some NADH(2-)

• NADH dehydrogenase (ubiquinone) activity SubClassOf has participant some NAD(1-)

Added

• NADH dehydrogenase (ubiquinone) activity SubClassOf NADH dehydrogenase activity

NADH:menaquinone oxidoreductase activity http://purl.obolibrary.org/obo/GO_0103036

Removed

• NADH:menaquinone oxidoreductase activity definition "Catalysis of the reaction: 5 H+ + NADH + a menaquinone = 4 H+ + NAD + a menaquinol."
  • database_cross_reference "GOC:pz"

Added

• NADH:menaquinone oxidoreductase activity database_cross_reference "RHEA:29099"

• NADH:menaquinone oxidoreductase activity definition "Catalysis of the reaction: 5 H+ + NADH + a menaquinone = 4 H+ + NAD + a menaquinol."

  • database_cross_reference "GOC:pz"

  • database_cross_reference "RHEA:29099"

• NADH:menaquinone oxidoreductase activity SubClassOf NADH dehydrogenase activity

NADH:ubiquinone reductase (non-electrogenic) activity http://purl.obolibrary.org/obo/GO_0050136

Removed

• NADH:ubiquinone reductase (non-electrogenic) activity database_cross_reference "RHEA:46160"

• NADH:ubiquinone reductase (non-electrogenic) activity definition "Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol."

  • database_cross_reference "RHEA:46160"

  • database_cross_reference "GOC:mah"

  • database_cross_reference "EC:1.6.5.9"

• NADH:ubiquinone reductase (non-electrogenic) activity database_cross_reference "EC:1.6.5.9"

Added

• NADH:ubiquinone reductase (non-electrogenic) activity definition "Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol."

  • database_cross_reference "RHEA:46160"

• NADH:ubiquinone reductase (non-electrogenic) activity database_cross_reference "RHEA:46160"

  • source "skos:exactMatch"

• NADH:ubiquinone reductase (non-electrogenic) activity database_cross_reference "EC:1.6.5.9"

  • source "skos:exactMatch"

NADPH dehydrogenase (quinone) activity http://purl.obolibrary.org/obo/GO_0008753

Removed

• NADPH dehydrogenase (quinone) activity SubClassOf has participant some NADP(3-)

• NADPH dehydrogenase (quinone) activity SubClassOf has participant some NADPH(4-)

• NADPH dehydrogenase (quinone) activity SubClassOf has participant some hydron

Added

• NADPH dehydrogenase (quinone) activity SubClassOf NADPH dehydrogenase activity

NADPH dehydrogenase activity http://purl.obolibrary.org/obo/GO_0003959

Removed

• NADPH dehydrogenase activity database_cross_reference "EC:1.6.99.1"

• NADPH dehydrogenase activity database_cross_reference "RHEA:13149"

Added

• NADPH dehydrogenase activity database_cross_reference "RHEA:13149"

  • source "skos:exactMatch"

• NADPH dehydrogenase activity database_cross_reference "EC:1.6.99.1"

  • source "skos:exactMatch"

NADPH:quinone reductase activity http://purl.obolibrary.org/obo/GO_0003960

Removed

• NADPH:quinone reductase activity database_cross_reference "RHEA:14269"

• NADPH:quinone reductase activity SubClassOf has participant some NADPH(4-)

• NADPH:quinone reductase activity SubClassOf has participant some NADP(3-)

• NADPH:quinone reductase activity SubClassOf has participant some hydron

Added

• NADPH:quinone reductase activity database_cross_reference "RHEA:14269"

  • source "skos:exactMatch"

• NADPH:quinone reductase activity SubClassOf NADPH dehydrogenase activity

molecular carrier activity http://purl.obolibrary.org/obo/GO_0140104

Removed

• molecular carrier activity in_subset gocheck_do_not_annotate

Added

• molecular carrier activity term tracker item "https://github.com/geneontology/go-ontology/issues/29584"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

monodehydroascorbate reductase (NADH) activity http://purl.obolibrary.org/obo/GO_0016656

Removed

• monodehydroascorbate reductase (NADH) activity database_cross_reference "EC:1.6.5.4"

• monodehydroascorbate reductase (NADH) activity database_cross_reference "RHEA:14581"

• monodehydroascorbate reductase (NADH) activity definition "Catalysis of the reaction: NADH + H+ + 2 monodehydroascorbate = NAD+ + 2 ascorbate."

  • database_cross_reference "EC:1.6.5.4"

Added

• monodehydroascorbate reductase (NADH) activity database_cross_reference "RHEA:14581"

  • source "skos:exactMatch"

• monodehydroascorbate reductase (NADH) activity definition "Catalysis of the reaction: 2 monodehydro-L-ascorbate radical + NADH + H+ = 2 L-ascorbate + NAD+."

  • database_cross_reference "RHEA:14581"

• monodehydroascorbate reductase (NADH) activity database_cross_reference "EC:1.6.5.4"

  • source "skos:exactMatch"

obsolete regulation of proteasome core complex assembly http://purl.obolibrary.org/obo/GO_0090363

Removed

• obsolete regulation of proteasome core complex assembly definition "Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of a mature, active 20S proteasome core particle complex that does not contain any regulatory particles."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "GOC:elh"

  • database_cross_reference "GOC:tb"

• obsolete regulation of proteasome core complex assembly label "regulation of proteasome core complex assembly"

• obsolete regulation of proteasome core complex assembly EquivalentTo biological regulation and (regulates some proteasome core complex assembly)

• obsolete regulation of proteasome core complex assembly SubClassOf regulation of proteasome assembly

• obsolete regulation of proteasome core complex assembly SubClassOf regulates some proteasome core complex assembly

Added

• obsolete regulation of proteasome core complex assembly term tracker item "https://github.com/geneontology/go-ontology/issues/20017"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• obsolete regulation of proteasome core complex assembly consider "GO:0043248"

• obsolete regulation of proteasome core complex assembly comment "This term was obsoleted because was too specific."

• obsolete regulation of proteasome core complex assembly label "obsolete regulation of proteasome core complex assembly"

• obsolete regulation of proteasome core complex assembly definition "OBSOLETE. Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of a mature, active 20S proteasome core particle complex that does not contain any regulatory particles."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "GOC:elh"

  • database_cross_reference "GOC:tb"

• obsolete regulation of proteasome core complex assembly deprecated true

p-benzoquinone reductase (NADPH) activity http://purl.obolibrary.org/obo/GO_0018541

Removed

• p-benzoquinone reductase (NADPH) activity database_cross_reference "RHEA:23488"

Added

• p-benzoquinone reductase (NADPH) activity database_cross_reference "RHEA:23488"
  • source "skos:exactMatch"