Resolving some oxidoreductase term issues. #29701

[sjm41]

No description provided.

[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/2025-02-11/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/2025-02-11/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

2-polyprenylphenol 6-hydroxylase activity http://purl.obolibrary.org/obo/GO_0019168

Removed

• 2-polyprenylphenol 6-hydroxylase activity label "2-octaprenylphenol hydroxylase activity"

• 2-polyprenylphenol 6-hydroxylase activity definition "Catalysis of the reaction: 2-octaprenylphenol + NADPH + O2 + H+ = 2-octaprenyl-6-hydroxyphenol + NADP+ + H2O."

  • database_cross_reference "MetaCyc:2-OCTAPRENYLPHENOL-HYDROX-RXN"

• 2-polyprenylphenol 6-hydroxylase activity database_cross_reference "RHEA:27790"

• 2-polyprenylphenol 6-hydroxylase activity database_cross_reference "MetaCyc:2-OCTAPRENYLPHENOL-HYDROX-RXN"

• 2-polyprenylphenol 6-hydroxylase activity SubClassOf oxidoreductase activity

Added

• 2-polyprenylphenol 6-hydroxylase activity database_cross_reference "EC:1.14.13.240"

  • source "skos:exactMatch"

• 2-polyprenylphenol 6-hydroxylase activity label "2-polyprenylphenol 6-hydroxylase activity"

• 2-polyprenylphenol 6-hydroxylase activity database_cross_reference "MetaCyc:RXN-18459"

• 2-polyprenylphenol 6-hydroxylase activity has_narrow_synonym "2-octaprenylphenol hydroxylase activity"

• 2-polyprenylphenol 6-hydroxylase activity database_cross_reference "RHEA:55892"

  • source "skos:exactMatch"

• 2-polyprenylphenol 6-hydroxylase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• 2-polyprenylphenol 6-hydroxylase activity definition "Catalysis of the reaction: a 2-(all-trans-polyprenyl)phenol + NADPH + O2 + H+ = a 3-(all-trans-polyprenyl)benzene-1,2-diol + NADP+ + H2O."

  • database_cross_reference "RHEA:55892"

• 2-polyprenylphenol 6-hydroxylase activity SubClassOf oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen

3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity http://purl.obolibrary.org/obo/GO_0051744

Removed

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity definition "Catalysis of the reaction: divinyl protochlorophyllide a + NADPH + H+ = monovinyl protochlorophyllide a + NADP+."

  • database_cross_reference "MetaCyc:RXN1F-72"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity database_cross_reference "RHEA:48884"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity label "3,8-divinyl protochlorophyllide a 8-vinyl reductase activity"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity SubClassOf oxidoreductase activity

Added

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity definition "Catalysis of the reaction: protochlorophyllide a + NADP+ = 3,8-divinyl protochlorophyllide a + NADPH + H+."

  • database_cross_reference "RHEA:48884"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity has_broad_synonym "3,8-divinyl protochlorophyllide a 8-vinyl reductase activity"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity database_cross_reference "RHEA:48884"

  • source "skos:exactMatch"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity label "3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity"

• 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity SubClassOf oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor

arsenate reductase (glutaredoxin) activity http://purl.obolibrary.org/obo/GO_0008794

Removed

• arsenate reductase (glutaredoxin) activity SubClassOf oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor

arsenate reductase (thioredoxin) activity http://purl.obolibrary.org/obo/GO_0030612

Removed

• arsenate reductase (thioredoxin) activity definition "Catalysis of the reaction: arsenate + thioredoxin = arsenite + thioredoxin disulfide. Thioredoxin disulfide is also known as oxidized thioredoxin."
  • database_cross_reference "MetaCyc:RXN-10737"

Added

• arsenate reductase (thioredoxin) activity definition "Catalysis of the reaction: arsenate + [thioredoxin]-dithiol + H+ = arsenite + [thioredoxin]-disulfide + H2O."

  • database_cross_reference "RHEA:43848"

• arsenate reductase (thioredoxin) activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• arsenate reductase (thioredoxin) activity database_cross_reference "RHEA:43848"

  • source "skos:exactMatch"

• arsenate reductase (thioredoxin) activity database_cross_reference "EC:1.20.4.4"

  • source "skos:exactMatch"

arsenate reductase activity http://purl.obolibrary.org/obo/GO_0030611

Removed

• arsenate reductase activity SubClassOf oxidoreductase activity

Added

• arsenate reductase activity SubClassOf oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor

bacteriochlorophyllide-a dehydrogenase activity http://purl.obolibrary.org/obo/GO_0036354

Removed

• bacteriochlorophyllide-a dehydrogenase activity database_cross_reference "RHEA:19733"

• bacteriochlorophyllide-a dehydrogenase activity label "2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase activity"

• bacteriochlorophyllide-a dehydrogenase activity definition "Catalysis of the reaction: 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a = bacteriochlorophyllide a + 2 H+."

  • database_cross_reference "PMID:8437569"

  • database_cross_reference "GOC:crds"

  • database_cross_reference "MetaCyc:RXN-8787"

  • database_cross_reference "InterPro:IPR005903"

• bacteriochlorophyllide-a dehydrogenase activity SubClassOf oxidoreductase activity

Added

• bacteriochlorophyllide-a dehydrogenase activity has_exact_synonym "2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase activity"

• bacteriochlorophyllide-a dehydrogenase activity label "bacteriochlorophyllide-a dehydrogenase activity"

• bacteriochlorophyllide-a dehydrogenase activity database_cross_reference "RHEA:19733"

  • source "skos:exactMatch"

• bacteriochlorophyllide-a dehydrogenase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• bacteriochlorophyllide-a dehydrogenase activity definition "Catalysis of the reaction: 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a + NAD+ = bacteriochlorophyllide a + NADH + H+."

  • database_cross_reference "PMID:8437569"

  • database_cross_reference "RHEA:19733"

• bacteriochlorophyllide-a dehydrogenase activity database_cross_reference "EC:1.1.1.396"

  • source "skos:exactMatch"

• bacteriochlorophyllide-a dehydrogenase activity SubClassOf oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

coenzyme F420H2 oxidase activity http://purl.obolibrary.org/obo/GO_0052765

Removed

• coenzyme F420H2 oxidase activity has_exact_synonym "coenzyme F420H2 oxidase activity"

• coenzyme F420H2 oxidase activity label "reduced coenzyme F420 oxidase activity"

• coenzyme F420H2 oxidase activity definition "Catalysis of the reaction: 2 reduced coenzyme F420 + O2 = 2 coenzyme F420 + 2 H2O."

  • database_cross_reference "PMID:15340796"

  • database_cross_reference "GOC:mengo_curators"

• coenzyme F420H2 oxidase activity SubClassOf oxidoreductase activity

Added

• coenzyme F420H2 oxidase activity label "coenzyme F420H2 oxidase activity"

• coenzyme F420H2 oxidase activity database_cross_reference "RHEA:39711"

  • source "skos:exactMatch"

• coenzyme F420H2 oxidase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• coenzyme F420H2 oxidase activity database_cross_reference "EC:1.5.3.22"

  • source "skos:exactMatch"

• coenzyme F420H2 oxidase activity has_exact_synonym "reduced coenzyme F420 oxidase activity"

• coenzyme F420H2 oxidase activity definition "Catalysis of the reaction: 2 reduced coenzyme F420-(gamma-L-Glu)(n) + O2 = 2 oxidized coenzyme F420-(gamma-L-Glu)(n) + 2 H2O + 2 H+."

  • database_cross_reference "RHEA:39711"

  • database_cross_reference "PMID:15340796"

• coenzyme F420H2 oxidase activity SubClassOf oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor

coenzyme F420H2:quinone oxidoreductase activity http://purl.obolibrary.org/obo/GO_0052755

Removed

• coenzyme F420H2:quinone oxidoreductase activity definition "Catalysis of the reaction: reduced coenzyme F420 + 2,3-dimethyl-1,4-naphthoquinone = coenzyme F420 + reduced 2,3-dimethyl-1,4-naphthoquinone. Reduced 2,3-dimethyl-1,4-naphthoquinone is also known as 2,3-dimethyl-1,4-hydronaphthoquinone."

  • database_cross_reference "PMID:10971593"

  • database_cross_reference "PMID:8055920"

  • database_cross_reference "GOC:mengo_curators"

• coenzyme F420H2:quinone oxidoreductase activity label "reduced coenzyme F420:quinone oxidoreductase activity"

• coenzyme F420H2:quinone oxidoreductase activity SubClassOf oxidoreductase activity

Added

• coenzyme F420H2:quinone oxidoreductase activity definition "Catalysis of the reaction: oxidized coenzyme F420-(gamma-L-Glu)(n) + a quinol + H+ = reduced coenzyme F420-(gamma-L-Glu)(n) + a quinone."

  • database_cross_reference "RHEA:39663"

  • database_cross_reference "PMID:10971593"

  • database_cross_reference "PMID:8055920"

• coenzyme F420H2:quinone oxidoreductase activity has_exact_synonym "reduced coenzyme F420:quinone oxidoreductase activity"

• coenzyme F420H2:quinone oxidoreductase activity database_cross_reference "EC:1.1.98.4"

  • source "skos:exactMatch"

• coenzyme F420H2:quinone oxidoreductase activity database_cross_reference "RHEA:39663"

  • source "skos:exactMatch"

• coenzyme F420H2:quinone oxidoreductase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• coenzyme F420H2:quinone oxidoreductase activity label "coenzyme F420H2:quinone oxidoreductase activity"

• coenzyme F420H2:quinone oxidoreductase activity SubClassOf oxidoreductase activity, acting on CH-OH group of donors

epoxyqueuosine reductase activity http://purl.obolibrary.org/obo/GO_0052693

Removed

• epoxyqueuosine reductase activity SubClassOf oxidoreductase activity

Added

• epoxyqueuosine reductase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• epoxyqueuosine reductase activity SubClassOf oxidoreductase activity, acting on CH or CH2 groups

lariciresinol reductase activity http://purl.obolibrary.org/obo/GO_0010284

Removed

• lariciresinol reductase activity SubClassOf oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor

Added

• lariciresinol reductase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• lariciresinol reductase activity SubClassOf oxidoreductase activity, reducing C-O-C group as acceptor

malolactic enzyme activity http://purl.obolibrary.org/obo/GO_0043883

Removed

• malolactic enzyme activity SubClassOf oxidoreductase activity

Added

• malolactic enzyme activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• malolactic enzyme activity SubClassOf carboxy-lyase activity

oxidoreductase activity, reducing C-O-C group as acceptor http://purl.obolibrary.org/obo/GO_0120546

Added

• oxidoreductase activity, reducing C-O-C group as acceptor definition "Catalysis of an oxidation-reduction (redox) reaction in which a reducing C-O-C group acts as acceptor."

  • database_cross_reference "EC:1.23.-.-"

• oxidoreductase activity, reducing C-O-C group as acceptor creation_date "2025-02-11T18:09:07Z"

• oxidoreductase activity, reducing C-O-C group as acceptor id "GO:0120546"

• oxidoreductase activity, reducing C-O-C group as acceptor created_by "sjm"

• oxidoreductase activity, reducing C-O-C group as acceptor database_cross_reference "EC:1.23.-.-"

• oxidoreductase activity, reducing C-O-C group as acceptor label "oxidoreductase activity, reducing C-O-C group as acceptor"

• oxidoreductase activity, reducing C-O-C group as acceptor has_obo_namespace "molecular_function"

• oxidoreductase activity, reducing C-O-C group as acceptor term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• Class: oxidoreductase activity, reducing C-O-C group as acceptor

• oxidoreductase activity, reducing C-O-C group as acceptor SubClassOf oxidoreductase activity

pinoresinol reductase activity http://purl.obolibrary.org/obo/GO_0010283

Removed

• pinoresinol reductase activity SubClassOf oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor

Added

• pinoresinol reductase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• pinoresinol reductase activity SubClassOf oxidoreductase activity, reducing C-O-C group as acceptor

sulfur reductase activity http://purl.obolibrary.org/obo/GO_0033796

Removed

• sulfur reductase activity SubClassOf oxidoreductase activity

Added

• sulfur reductase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• sulfur reductase activity SubClassOf oxidoreductase activity, acting on hydrogen as donor, with other known acceptors

tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity http://purl.obolibrary.org/obo/GO_0045301

Removed

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity label "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity definition "Catalysis of the reaction: tRNA-(2-methylthio-N-6-isopentenyl adenosine) = tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine) + O2. 2-methylthio-N-6-isopentenyl adenosine is also known as ms2i6A; 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine is also known as ms2io6A and 2-methylthio-cis-ribozeatin."

  • database_cross_reference "PMID:8253666"

  • database_cross_reference "GOC:mlg"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity SubClassOf oxidoreductase activity

Added

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity label "tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity database_cross_reference "RHEA:65812"

  • source "skos:exactMatch"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity database_cross_reference "EC:1.14.99.69"

  • source "skos:exactMatch"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity definition "Catalysis of the reaction: 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + acceptor-H2 + O2 = N(6)-[(2E)-4-hydroxy-3-methylbut-2-en-1-yl]-2-(methylsulfanyl)adenosine(37) in tRNA + acceptor + H2O."

  • database_cross_reference "RHEA:65812"

  • database_cross_reference "PMID:8253666"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity has_exact_synonym "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity"

• tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity SubClassOf oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

tetrahydrothiophene 1-oxide reductase activity http://purl.obolibrary.org/obo/GO_0019174

Removed

• tetrahydrothiophene 1-oxide reductase activity SubClassOf oxidoreductase activity

Added

• tetrahydrothiophene 1-oxide reductase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tetrahydrothiophene 1-oxide reductase activity SubClassOf oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor

thyroxine 5'-deiodinase activity http://purl.obolibrary.org/obo/GO_0004800

Removed

• thyroxine 5'-deiodinase activity definition "Catalysis of the reaction: 3,5,3'-L-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + donor-H2."

  • database_cross_reference "EC:1.21.99.4"

• thyroxine 5'-deiodinase activity SubClassOf oxidoreductase activity

Added

• thyroxine 5'-deiodinase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• thyroxine 5'-deiodinase activity definition "Catalysis of the reaction: 3,3',5-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + acceptor-H2."

  • database_cross_reference "RHEA:19745"

• thyroxine 5'-deiodinase activity SubClassOf oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond

thyroxine 5-deiodinase activity http://purl.obolibrary.org/obo/GO_0033798

Removed

• thyroxine 5-deiodinase activity definition "Catalysis of the reaction: 3,3',5'-triiodo-L-thyronine + iodide + A + H+ = L-thyroxine + AH2."

  • database_cross_reference "EC:1.21.99.3"

• thyroxine 5-deiodinase activity SubClassOf oxidoreductase activity

Added

• thyroxine 5-deiodinase activity definition "Catalysis of the reaction: 3,3',5'-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + acceptor-H2."

  • database_cross_reference "RHEA:18897"

• thyroxine 5-deiodinase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• thyroxine 5-deiodinase activity SubClassOf oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond

tyramine-beta hydroxylase activity http://purl.obolibrary.org/obo/GO_0004836

Removed

• tyramine-beta hydroxylase activity definition "Catalysis of the hydroxylation of tyramine to form octopamine."

  • database_cross_reference "PMID:10745161"

• tyramine-beta hydroxylase activity SubClassOf oxidoreductase activity

Added

• tyramine-beta hydroxylase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• tyramine-beta hydroxylase activity database_cross_reference "MetaCyc:RXN-14645"

• tyramine-beta hydroxylase activity database_cross_reference "RHEA:57132"

  • source "skos:exactMatch"

• tyramine-beta hydroxylase activity definition "Catalysis of the reaction: tyramine + L-ascorbate + O2 = (R)-octopamine + L-dehydroascorbate + H2O."

  • database_cross_reference "RHEA:57132"

  • database_cross_reference "PMID:10745161"

• tyramine-beta hydroxylase activity SubClassOf oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen

uracil oxygenase activity http://purl.obolibrary.org/obo/GO_0052614

Removed

• uracil oxygenase activity SubClassOf oxidoreductase activity

Added

• uracil oxygenase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• uracil oxygenase activity SubClassOf oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

violaxanthin de-epoxidase activity http://purl.obolibrary.org/obo/GO_0046422

Removed

• violaxanthin de-epoxidase activity SubClassOf oxidoreductase activity

Added

• violaxanthin de-epoxidase activity term tracker item "https://github.com/geneontology/go-ontology/issues/29701"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• violaxanthin de-epoxidase activity SubClassOf oxidoreductase activity, reducing C-O-C group as acceptor