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Resolving some oxidoreductase term issues. #29701 #29704

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Feb 11, 2025
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Resolving some oxidoreductase term issues. #29701 #29704

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1f219cb
Resolving some oxidoreductase term issues. #29701
sjm41 Feb 11, 2025
3ece9d4
Resolving some oxidoreductase term issues. #29701
sjm41 Feb 11, 2025
a5e6c7d
Merge branch 'master' into issue-29701
sjm41 Feb 11, 2025
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125 changes: 85 additions & 40 deletions src/ontology/go-edit.obo
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Expand Up @@ -46257,7 +46257,7 @@ is_a: GO:0042083 ! 5,10-methylenetetrahydrofolate-dependent methyltransferase ac
id: GO:0004800
name: thyroxine 5'-deiodinase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3,5,3'-L-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + donor-H2." [EC:1.21.99.4]
def: "Catalysis of the reaction: 3,3',5-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + acceptor-H2." [RHEA:19745]
synonym: "acceptor:3,5,3'-triiodo-L-thyronine oxidoreductase (iodinating)" RELATED [EC:1.21.99.4]
synonym: "diiodothyronine 5'-deiodinase activity" RELATED [EC:1.21.99.4]
synonym: "iodothyronine 5'-deiodinase activity" RELATED [EC:1.21.99.4]
Expand All @@ -46271,7 +46271,8 @@ synonym: "type II iodothyronine deiodinase activity" NARROW [EC:1.21.99.4]
xref: EC:1.21.99.4
xref: MetaCyc:THYROXINE-DEIODINASE-RXN
xref: RHEA:19745
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0004801
Expand Down Expand Up @@ -46907,8 +46908,11 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0004836
name: tyramine-beta hydroxylase activity
namespace: molecular_function
def: "Catalysis of the hydroxylation of tyramine to form octopamine." [PMID:10745161]
is_a: GO:0016491 ! oxidoreductase activity
def: "Catalysis of the reaction: tyramine + L-ascorbate + O2 = (R)-octopamine + L-dehydroascorbate + H2O." [PMID:10745161, RHEA:57132]
xref: MetaCyc:RXN-14645
xref: RHEA:57132 {source="skos:exactMatch"}
is_a: GO:0016715 ! 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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0004837
Expand Down Expand Up @@ -83314,7 +83318,6 @@ xref: MetaCyc:RXN-982
xref: RHEA:22016
xref: UM-BBD_reactionID:r0635
is_a: GO:0030611 ! arsenate reductase activity
is_a: GO:0030614 ! oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor

[Term]
id: GO:0008795
Expand Down Expand Up @@ -99620,8 +99623,9 @@ xref: MetaCyc:RXN-8678 {source="skos:narrowMatch"}
xref: MetaCyc:RXN-8683 {source="skos:narrowMatch"}
xref: RHEA:34419 {source="skos:narrowMatch"}
xref: RHEA:34427 {source="skos:narrowMatch"}
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
is_a: GO:0120546 ! oxidoreductase activity, reducing C-O-C group as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0010284
Expand All @@ -99634,8 +99638,9 @@ xref: MetaCyc:RXN-8679 {source="skos:narrowMatch"}
xref: MetaCyc:RXN-8684 {source="skos:narrowMatch"}
xref: RHEA:34423 {source="skos:narrowMatch"}
xref: RHEA:34431 {source="skos:narrowMatch"}
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
is_a: GO:0120546 ! oxidoreductase activity, reducing C-O-C group as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0010285
Expand Down Expand Up @@ -140864,12 +140869,15 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,

[Term]
id: GO:0019168
name: 2-octaprenylphenol hydroxylase activity
name: 2-polyprenylphenol 6-hydroxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-octaprenylphenol + NADPH + O2 + H+ = 2-octaprenyl-6-hydroxyphenol + NADP+ + H2O." [MetaCyc:2-OCTAPRENYLPHENOL-HYDROX-RXN]
xref: MetaCyc:2-OCTAPRENYLPHENOL-HYDROX-RXN
xref: RHEA:27790
is_a: GO:0016491 ! oxidoreductase activity
def: "Catalysis of the reaction: a 2-(all-trans-polyprenyl)phenol + NADPH + O2 + H+ = a 3-(all-trans-polyprenyl)benzene-1,2-diol + NADP+ + H2O." [RHEA:55892]
synonym: "2-octaprenylphenol hydroxylase activity" NARROW []
xref: EC:1.14.13.240 {source="skos:exactMatch"}
xref: MetaCyc:RXN-18459
xref: RHEA:55892 {source="skos:exactMatch"}
is_a: GO:0016709 ! 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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0019170
Expand Down Expand Up @@ -140922,7 +140930,8 @@ name: tetrahydrothiophene 1-oxide reductase activity
namespace: molecular_function
def: "Catalysis of the reaction: tetrahydrothiophene 1-oxide + reduced acceptor = tetrahydrothiophene + acceptor." [MetaCyc:THTOREDUCT-RXN]
xref: MetaCyc:THTOREDUCT-RXN
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0016671 ! oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0019176
Expand Down Expand Up @@ -163163,15 +163172,18 @@ id: GO:0030611
name: arsenate reductase activity
namespace: molecular_function
def: "Catalysis of the interconversion of arsenate and arsenite." [GOC:mah]
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0030614 ! oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor

[Term]
id: GO:0030612
name: arsenate reductase (thioredoxin) activity
namespace: molecular_function
def: "Catalysis of the reaction: arsenate + thioredoxin = arsenite + thioredoxin disulfide. Thioredoxin disulfide is also known as oxidized thioredoxin." [MetaCyc:RXN-10737]
def: "Catalysis of the reaction: arsenate + [thioredoxin]-dithiol + H+ = arsenite + [thioredoxin]-disulfide + H2O." [RHEA:43848]
xref: EC:1.20.4.4 {source="skos:exactMatch"}
xref: MetaCyc:RXN-10737
xref: RHEA:43848 {source="skos:exactMatch"}
is_a: GO:0030611 ! arsenate reductase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0030613
Expand Down Expand Up @@ -197221,7 +197233,8 @@ synonym: "sulphur reductase activity" EXACT []
xref: EC:1.12.98.4
xref: MetaCyc:RXN-8269
xref: RHEA:35591
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0046995 ! oxidoreductase activity, acting on hydrogen as donor, with other known acceptors
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0033797
Expand All @@ -197240,7 +197253,7 @@ is_a: GO:0016491 ! oxidoreductase activity
id: GO:0033798
name: thyroxine 5-deiodinase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3,3',5'-triiodo-L-thyronine + iodide + A + H+ = L-thyroxine + AH2." [EC:1.21.99.3]
def: "Catalysis of the reaction: 3,3',5'-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + acceptor-H2." [RHEA:18897]
synonym: "acceptor:3,3',5'-triiodo-L-thyronine oxidoreductase (iodinating) activity" RELATED [EC:1.21.99.3]
synonym: "diiodothyronine 5'-deiodinase activity" BROAD [EC:1.21.99.3]
synonym: "inner ring-deiodinating pathway" EXACT [PMID:20403357]
Expand All @@ -197250,7 +197263,8 @@ synonym: "type III iodothyronine deiodinase activity" NARROW [EC:1.21.99.3]
xref: EC:1.21.99.3
xref: MetaCyc:1.97.1.11-RXN
xref: RHEA:18897
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0033799
Expand Down Expand Up @@ -225056,13 +225070,16 @@ creation_date: 2012-09-19T11:52:25Z

[Term]
id: GO:0036354
name: 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase activity
name: bacteriochlorophyllide-a dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a = bacteriochlorophyllide a + 2 H+." [GOC:crds, InterPro:IPR005903, MetaCyc:RXN-8787, PMID:8437569]
def: "Catalysis of the reaction: 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a + NAD+ = bacteriochlorophyllide a + NADH + H+." [PMID:8437569, RHEA:19733]
synonym: "2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase activity" EXACT []
xref: EC:1.1.1.396 {source="skos:exactMatch"}
xref: MetaCyc:RXN-8787
xref: RHEA:19733
is_a: GO:0016491 ! oxidoreductase activity
xref: RHEA:19733 {source="skos:exactMatch"}
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
relationship: part_of GO:0030494 ! bacteriochlorophyll biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI
created_by: bf
creation_date: 2012-09-19T14:46:31Z

Expand Down Expand Up @@ -252157,8 +252174,9 @@ synonym: "MleS" RELATED []
xref: EC:4.1.1.101 {source="skos:exactMatch"}
xref: MetaCyc:RXN-16819 {source="skos:exactMatch"}
xref: RHEA:46276 {source="skos:exactMatch"}
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0016831 ! carboxy-lyase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28324" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0043884
Expand Down Expand Up @@ -265600,14 +265618,18 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i

[Term]
id: GO:0045301
name: tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity
name: tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity
namespace: molecular_function
def: "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." [GOC:mlg, PMID:8253666]
def: "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." [PMID:8253666, RHEA:65812]
synonym: "2-methylthio-cis-ribozeatin hydroxylase activity" EXACT []
synonym: "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity" EXACT []
synonym: "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyladenosine)-hydroxylase activity" EXACT []
synonym: "tRNA-(ms2io6A)-hydroxylase activity" EXACT []
is_a: GO:0016491 ! oxidoreductase activity
xref: EC:1.14.99.69 {source="skos:exactMatch"}
xref: RHEA:65812 {source="skos:exactMatch"}
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0045302
Expand Down Expand Up @@ -278000,7 +278022,8 @@ synonym: "VDE" RELATED [EC:1.23.5.1]
synonym: "violaxanthin:ascorbate oxidoreductase activity" RELATED [EC:1.23.5.1]
xref: EC:1.23.5.1
xref: RHEA:32371
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0120546 ! oxidoreductase activity, reducing C-O-C group as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0046423
Expand Down Expand Up @@ -328740,12 +328763,14 @@ is_a: GO:0016636 ! oxidoreductase activity, acting on the CH-CH group of donors,

[Term]
id: GO:0051744
name: 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity
name: 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity
namespace: molecular_function
def: "Catalysis of the reaction: divinyl protochlorophyllide a + NADPH + H+ = monovinyl protochlorophyllide a + NADP+." [MetaCyc:RXN1F-72]
def: "Catalysis of the reaction: protochlorophyllide a + NADP+ = 3,8-divinyl protochlorophyllide a + NADPH + H+." [RHEA:48884]
synonym: "3,8-divinyl protochlorophyllide a 8-vinyl reductase activity" BROAD []
xref: MetaCyc:RXN1F-72
xref: RHEA:48884
is_a: GO:0016491 ! oxidoreductase activity
xref: RHEA:48884 {source="skos:exactMatch"}
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0051745
Expand Down Expand Up @@ -337074,7 +337099,8 @@ synonym: "pyrimidine oxygenase activity" BROAD [MetaCyc:RXN0-6444]
xref: EC:1.14.99.46
xref: MetaCyc:RXN0-6444
xref: RHEA:31587
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI
creation_date: 2010-08-26T10:11:11Z

[Term]
Expand Down Expand Up @@ -338137,7 +338163,8 @@ namespace: molecular_function
def: "Catalysis of the reaction: epoxyqueuosine in tRNA + reductant = queuosine in tRNA + oxidised reductant." [PMID:21502530, RHEA:32159]
xref: EC:1.17.99.6
xref: RHEA:32159
is_a: GO:0016491 ! oxidoreductase activity
is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI

[Term]
id: GO:0052694
Expand Down Expand Up @@ -339024,13 +339051,17 @@ creation_date: 2011-09-22T03:25:30Z

[Term]
id: GO:0052755
name: reduced coenzyme F420:quinone oxidoreductase activity
name: coenzyme F420H2:quinone oxidoreductase activity
namespace: molecular_function
def: "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." [GOC:mengo_curators, PMID:10971593, PMID:8055920]
def: "Catalysis of the reaction: oxidized coenzyme F420-(gamma-L-Glu)(n) + a quinol + H+ = reduced coenzyme F420-(gamma-L-Glu)(n) + a quinone." [PMID:10971593, PMID:8055920, RHEA:39663]
synonym: "F420H2-dependent quinone oxidoreductase activity" EXACT []
synonym: "F420H2:2,3-dimethyl-1,4-naphthoquinone oxidoreductase activity" EXACT []
synonym: "F420H2:quinone oxidoreductase activity" EXACT []
is_a: GO:0016491 ! oxidoreductase activity
synonym: "reduced coenzyme F420:quinone oxidoreductase activity" EXACT []
xref: EC:1.1.98.4 {source="skos:exactMatch"}
xref: RHEA:39663 {source="skos:exactMatch"}
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI
created_by: ai
creation_date: 2011-09-22T04:08:13Z

Expand Down Expand Up @@ -339140,13 +339171,16 @@ creation_date: 2011-09-29T04:05:44Z

[Term]
id: GO:0052765
name: reduced coenzyme F420 oxidase activity
name: coenzyme F420H2 oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 reduced coenzyme F420 + O2 = 2 coenzyme F420 + 2 H2O." [GOC:mengo_curators, PMID:15340796]
synonym: "coenzyme F420H2 oxidase activity" EXACT []
def: "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+." [PMID:15340796, RHEA:39711]
synonym: "F420H2 oxidase activity" EXACT []
synonym: "F420H2:oxygen oxidoreductase activity" EXACT []
is_a: GO:0016491 ! oxidoreductase activity
synonym: "reduced coenzyme F420 oxidase activity" EXACT []
xref: EC:1.5.3.22 {source="skos:exactMatch"}
xref: RHEA:39711 {source="skos:exactMatch"}
is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI
created_by: ai
creation_date: 2011-09-29T04:33:54Z

Expand Down Expand Up @@ -450607,6 +450641,17 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
created_by: sjm
creation_date: 2025-02-11T09:55:25Z

[Term]
id: GO:0120546
name: oxidoreductase activity, reducing C-O-C group as acceptor
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction in which a reducing C-O-C group acts as acceptor." [EC:1.23.-.-]
xref: EC:1.23.-.-
is_a: GO:0016491 ! oxidoreductase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI
created_by: sjm
creation_date: 2025-02-11T18:09:07Z

[Term]
id: GO:0140001
name: morula formation
Expand Down
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