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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Transferred ECs to update #28647

Closed sjm41 closed 2 months ago

sjm41 commented 2 months ago

From https://github.com/geneontology/go-ontology/pull/28636:

ERROR: http://purl.obolibrary.org/obo/GO_0016844 has a definition xref to an obsolete EC: "EC:4.3.3.2" ERROR: http://purl.obolibrary.org/obo/GO_0016844 has a synonym xref to an obsolete EC: "EC:4.3.3.2" ERROR: http://purl.obolibrary.org/obo/GO_0016844 has an xref to an obsolete EC: "EC:4.3.3.2" ERROR: http://purl.obolibrary.org/obo/GO_0030269 has a definition xref to an obsolete EC: "EC:2.1.1.86" ERROR: http://purl.obolibrary.org/obo/GO_0030269 has a synonym xref to an obsolete EC: "EC:2.1.1.86" ERROR: http://purl.obolibrary.org/obo/GO_0030269 has an xref to an obsolete EC: "EC:2.1.1.86" ERROR: http://purl.obolibrary.org/obo/GO_0050474 has a definition xref to an obsolete EC: "EC:4.2.1.78" ERROR: http://purl.obolibrary.org/obo/GO_0050474 has a synonym xref to an obsolete EC: "EC:4.2.1.78" ERROR: http://purl.obolibrary.org/obo/GO_0050474 has an xref to an obsolete EC: "EC:4.2.1.78" ERROR: http://purl.obolibrary.org/obo/GO_0050556 has a definition xref to an obsolete EC: "EC:4.3.3.3" ERROR: http://purl.obolibrary.org/obo/GO_0050556 has a synonym xref to an obsolete EC: "EC:4.3.3.3" ERROR: http://purl.obolibrary.org/obo/GO_0050556 has an xref to an obsolete EC: "EC:4.3.3.3" ERROR: http://purl.obolibrary.org/obo/GO_0050557 has a definition xref to an obsolete EC: "EC:4.3.3.4" ERROR: http://purl.obolibrary.org/obo/GO_0050557 has a synonym xref to an obsolete EC: "EC:4.3.3.4" ERROR: http://purl.obolibrary.org/obo/GO_0050557 has an xref to an obsolete EC: "EC:4.3.3.4"

EC 4.3.3.2 Transferred entry: 3.5.99.13

EC 2.1.1.86 Transferred entry: 7.2.1.4

EC 4.2.1.78 Transferred entry: 3.5.99.14

EC 4.3.3.3 Transferred entry: 3.5.99.15

EC 4.3.3.4 Transferred entry: 3.5.99.16

So, the good news is that these 5 cases are all 1:1 transfers. But the complication in each cases is the reaction/enzyme has changed its major classification (e.g. lyase to hydrolase), so we will need to review and change the parentage in GO.

sjm41 commented 2 months ago

id: GO:0016844 name: strictosidine synthase activity namespace: molecular_function def: "Catalysis of the reaction: 3alpha(S)-strictosidine + H2O = secologanin + tryptamine." [EC:4.3.3.2, RHEA:15013] synonym: "3-alpha(S)-strictosidine tryptamine-lyase (secologanin-forming)" RELATED [EC:4.3.3.2] synonym: "3-alpha(S)-strictosidine tryptamine-lyase activity" RELATED [EC:4.3.3.2] synonym: "STR activity" RELATED [EC:4.3.3.2] synonym: "strictosidine synthetase activity" RELATED [EC:4.3.3.2] xref: EC:4.3.3.2 xref: KEGG_REACTION:R03738 xref: MetaCyc:STRICTOSIDINE-SYNTHASE-RXN xref: RHEA:15013 is_a: GO:0016843 ! amine-lyase activity

id: GO:0030269 name: tetrahydromethanopterin S-methyltransferase activity namespace: molecular_function alt_id: GO:0018709 def: "Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme M = 5,6,7,8-tetrahydromethanopterin + methyl-coenzyme M. 2-(methylthio)ethanesulfonate is also known as methyl-CoM." [EC:2.1.1.86, RHEA:53492] synonym: "5-methyl-5,6,7,8-tetrahydromethanopterin:2-mercaptoethanesulfonate 2-methyltransferase activity" RELATED [EC:2.1.1.86] synonym: "N(5)-methyltetrahydromethanopterin--coenzyme M methyltransferase activity" RELATED [EC:2.1.1.86] synonym: "N5-methyltetrahydromethanopterin--coenzyme M methyltransferase activity" RELATED [EC:2.1.1.86] synonym: "tetrahydromethanopterin methyltransferase activity" RELATED [EC:2.1.1.86] xref: EC:2.1.1.86 xref: KEGG_REACTION:R04347 xref: MetaCyc:2.1.1.86-RXN xref: RHEA:53492 xref: UM-BBD_reactionID:r0355 is_a: GO:0008172 ! S-methyltransferase activity is_a: GO:0042086 ! 5-methyl-5,6,7,8-tetrahydromethanopterin-dependent methyltransferase activity

id: GO:0050474 name: (S)-norcoclaurine synthase activity namespace: molecular_function alt_id: GO:0050475 def: "Catalysis of the reaction: 4-(2-aminoethyl)benzene-1,2-diol + 4-hydroxyphenylacetaldehyde = (S)-norcoclaurine + H2O." [EC:4.2.1.78] synonym: "(S)-norlaudanosoline synthase activity" RELATED [EC:4.2.1.78] synonym: "4-hydroxyphenylacetaldehyde hydro-lyase (adding dopamine)" RELATED [EC:4.2.1.78] synonym: "4-hydroxyphenylacetaldehyde hydro-lyase [adding dopamine; (S)-norcoclaurine-forming]" RELATED [EC:4.2.1.78] xref: EC:4.2.1.78 xref: MetaCyc:S-NORLAUDANOSOLINE-SYNTHASE-RXN xref: RHEA:16173 is_a: GO:0016836 ! hydro-lyase activity

id: GO:0050556 name: deacetylisoipecoside synthase activity namespace: molecular_function def: "Catalysis of the reaction: deacetylisoipecoside + H2O = dopamine + secologanin." [EC:4.3.3.3, RHEA:21756] synonym: "deacetylisoipecoside dopamine-lyase (secologanin-forming)" RELATED [EC:4.3.3.3] synonym: "deacetylisoipecoside dopamine-lyase activity" RELATED [EC:4.3.3.3] xref: EC:4.3.3.3 xref: KEGG_REACTION:R05750 xref: MetaCyc:4.3.3.3-RXN xref: RHEA:21756 is_a: GO:0016843 ! amine-lyase activity

id: GO:0050557 name: deacetylipecoside synthase activity namespace: molecular_function def: "Catalysis of the reaction: deacetylipecoside + H2O = dopamine + secologanin." [EC:4.3.3.4, RHEA:12296] synonym: "deacetylipecoside dopamine-lyase (secologanin-forming)" RELATED [EC:4.3.3.4] synonym: "deacetylipecoside dopamine-lyase activity" RELATED [EC:4.3.3.4] xref: EC:4.3.3.4 xref: KEGG_REACTION:R05749 xref: MetaCyc:4.3.3.4-RXN xref: RHEA:12296 is_a: GO:0016843 ! amine-lyase activity