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Duplicate xrefs as definition xrefs on catalytic activity terms #28776

Closed sjm41 closed 1 month ago

sjm41 commented 1 month ago

These are 61 cases of duplicate xrefs as definition xrefs (that are not already on other lists to review/fix). Need to review to see what the underlying issue is and work out how to fix.

See spreadsheet here: https://docs.google.com/spreadsheets/d/1uC4YrTZd5Fri_wkFrOZ-EuYSQZgVPSSrDjWLYs96weY/edit?gid=1296339985#gid=1296339985

Def xref Associated GO Count
EC:1.1.1.287 GO:0033709, GO:0052677 2
EC:1.1.1.331 GO:0102912, GO:0102911 2
EC:1.11.-.- GO:0103003, GO:0016684 2
EC:1.14.13.39 GO:0004517, GO:0051767 2
EC:1.3.-.- GO:0016627, GO:0102725 2
EC:1.3.3.4 GO:0070818, GO:0004729 2
EC:1.5.1.43 GO:0102143, GO:0102144 2
EC:2.1.1.10 GO:0008898, GO:0061627 2
EC:2.1.1.222 GO:0102004, GO:0102208 2
EC:2.1.2.2 GO:0043815, GO:0004644 2
EC:2.2.1.- GO:0102648, GO:0102647 2
EC:2.3.1.26 GO:0004772, GO:0034736 2
EC:2.3.2.- GO:0102272, GO:0102273 2
EC:2.4.1.67 GO:0047268, GO:0102827 2
EC:2.6.1.51 GO:0004760, GO:0005969 2
EC:2.7.4.- GO:0102352, GO:0102763 2
EC:2.7.7.4 GO:0004781, GO:0102297 2
EC:2.8.2.33 GO:0050659, GO:0036443 2
EC:3.1.-.- GO:0102667, GO:0102666 2
EC:3.2.1.68 GO:0102681, GO:0019156 2
EC:3.2.2.21 GO:0052822, GO:0003905 2
EC:3.5.1.- GO:0102281, GO:0102622 2
EC:3.7.1.8 GO:0018774, GO:0102326 2
EC:4.1.1.- GO:0102328, GO:0102765 2
EC:4.2.1.121 GO:0102895, GO:0102896 2
EC:5.1.3.- GO:0102540, GO:0102541 2
EC:5.3.-.- GO:0016860, GO:0102929 2
EC:6.3.2.- GO:0103044, GO:0102650 2
MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN GO:0047545, GO:0051990 2
MetaCyc:CPD-8065 GO:0033534, GO:0033533 2
MetaCyc:CPD-8066 GO:0033535, GO:0033536 2
MetaCyc:RXN-11629 GO:0052671, GO:0052672 2
MetaCyc:RXN-9385 GO:0052754, GO:0043910 2
MetaCyc:RXN0-5061 GO:0008713, GO:0008920 2
MetaCyc:RXN0-5122 GO:0071967, GO:0008920 2
MetaCyc:RXN0-5127 GO:0071968, GO:0008920 2
RHEA:11260 GO:0106294, GO:0016174 2
RHEA:23752 GO:0036432, GO:0009038 2
EC:1.1.1.- GO:0102182, GO:0016616, GO:0102727 3
EC:1.2.1.- GO:0102819, GO:0102006, GO:0102792 3
EC:2.1.1.157 GO:0052730, GO:0033805, GO:0052729 3
EC:2.7.1.- GO:0102731, GO:0102770, GO:0102238 3
EC:3.1.3.- GO:0103026, GO:0102537, GO:0102520 3
MetaCyc:RXN-8505 GO:1901022, GO:1901023, GO:1901024 3
EC:2.5.1.- GO:0102753, GO:0102754, GO:0102298, GO:0102747 4
MetaCyc:1.13.11.16-RXN GO:1901792, GO:1901791, GO:0047070, GO:1901790 4
EC:2.3.3.- GO:0103079, GO:0103082, GO:0103088, GO:0103091, GO:0103085 5
EC:2.7.7.6 GO:0003899, GO:0034062, GO:0003901, GO:0003900, GO:0003902 5
EC:5.4.4.- GO:0103086, GO:0103080, GO:0103083, GO:0103089, GO:0103092 5
EC:2.4.2.- GO:0102562, GO:0102582, GO:0018127, GO:0018071, GO:0018121, GO:1990585 6
EC:2.6.1.- GO:0103105, GO:0036137, GO:0036136, GO:0102658, GO:0102570, GO:0102081 6
EC:3.2.1.- GO:0102224, GO:0035885, GO:0102509, GO:0008843, GO:0102508, GO:0102413 6
EC:3.3.2.- GO:0102546, GO:0102071, GO:0016803, GO:0103005, GO:0102547, GO:0102564 6
EC:2.8.2.- GO:0102142, GO:0080131, GO:0019111, GO:0050698, GO:0001537, GO:0103104, GO:0102141 7
EC:1.14.-.- GO:0102123, GO:0102124, GO:0102730, GO:0016705, GO:0102371, GO:0102760, GO:0102125, GO:0102764 8
EC:6.3.-.- GO:0102052, GO:0102085, GO:0102088, GO:0102950, GO:0102951, GO:0102050, GO:0016879, GO:0102665, GO:0102664, GO:0102051, GO:0102087, GO:0102086 12
EC:4.2.3.- GO:0102889, GO:0102907, GO:0102063, GO:0102385, GO:0102888, GO:0010333, GO:0102065, GO:0010334, GO:0016838, GO:0102880, GO:0102066, GO:0102356, GO:0102886, GO:0102700 14
EC:1.14.11.- GO:0102663, GO:0103055, GO:0102569, GO:0102712, GO:0102495, GO:0102111, GO:0102715, GO:0103008, GO:0102716, GO:0102924, GO:0102496, GO:0102768, GO:0102972, GO:0102713, GO:0103054, GO:0102714, GO:0102652, GO:0103010, GO:0102653, GO:0102711, GO:0102494, GO:0103056, GO:0103057, GO:0102755 24
EC:2.1.1.- GO:0102528, GO:0102941, GO:0102914, GO:0102603, GO:0102708, GO:0102215, GO:0102147, GO:0102820, GO:0102122, GO:0102119, GO:0102438, GO:0102608, GO:0102399, GO:0102631, GO:0016435, GO:0102630, GO:0102398, GO:0102709, GO:0102913, GO:0102990, GO:0102400, GO:0102168, GO:0102942, GO:0102964, GO:0102363, GO:0102939, GO:0102821, GO:0102436, GO:0102940, GO:0102629 30
EC:2.3.1.- GO:0102301, GO:0102583, GO:0102775, GO:0102247, GO:0102922, GO:0102104, GO:0102589, GO:0102817, GO:0102287, GO:0102737, GO:0102989, GO:0102093, GO:0102814, GO:0102594, GO:0102923, GO:0102330, GO:0102595, GO:0102649, GO:0102586, GO:0102774, GO:0102248, GO:0102591, GO:0102806, GO:0102592, GO:0102660, GO:0102812, GO:0102581, GO:0102787, GO:0016747, GO:0102333, GO:0102286, GO:0102788, GO:0102295, GO:0102275, GO:0102331, GO:0102332, GO:0102800 37
EC:1.14.13.- GO:0102898, GO:0102599, GO:0102897, GO:0102181, GO:0102370, GO:0102901, GO:0102368, GO:0102627, GO:0102178, GO:0102902, GO:0102633, GO:0102606, GO:0102781, GO:0102427, GO:0103009, GO:0102639, GO:0102743, GO:0102899, GO:0102620, GO:0102372, GO:0102605, GO:0102780, GO:0102152, GO:0102517, GO:0102469, GO:0102173, GO:0102614, GO:0102171, GO:0102628, GO:0102680, GO:0102677, GO:0103096, GO:0102563, GO:0102376, GO:0102640, GO:0102367, GO:0102602, GO:0103097, GO:0102179, GO:0102292, GO:0102607, GO:0102600, GO:0102615, GO:0103098, GO:0102900, GO:0102472, GO:0102133, GO:0102626, GO:0102621, GO:0102476, GO:0102782, GO:0102466, GO:0102699, GO:0102992, GO:0016709, GO:0102366, GO:0102174, GO:0102759 58
sjm41 commented 1 month ago

id: GO:0033709 name: D-arabinitol dehydrogenase, D-ribulose forming (NADP+) activity def: "Catalysis of the reaction: D-arabinitol + NADP+ = D-ribulose + NADPH + H+." [EC:1.1.1.287] xref: KEGG_REACTION:R07144 xref: MetaCyc:RXN-7972 xref: RHEA:11868 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

id: GO:0052677 name: D-arabinitol dehydrogenase, D-xylulose forming (NADP+) activity def: "Catalysis of the reaction: D-arabinitol + NADP+ = D-xylulose + NADPH + H+." [EC:1.1.1.287] xref: KEGG_REACTION:R07143 xref: MetaCyc:RXN-7971 xref: RHEA:21276 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor created_by: ai creation_date: 2011-04-12T02:33:43Z

id: GO:0102911 name: (-)-secoisolariciresinol dehydrogenase activity def: "Catalysis of the reaction: (-)-secoisolariciresinol + NAD = H+ + (-)-lactol + NADH." [EC:1.1.1.331, GOC:pz] xref: MetaCyc:RXN-8680 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

id: GO:0102912 name: (-)-lactol dehydrogenase activity def: "Catalysis of the reaction: (-)-lactol + NAD = H+ + (-)-matairesinol + NADH." [EC:1.1.1.331, GOC:pz] xref: MetaCyc:RXN-8681 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

MetaCyc:RXN-8680 & MetaCyc:RXN-8681 describe a subreaction of EC:1.1.1.331 (= RHEA:33887) -> not in GO => make new term for EC:1.1.1.331/RHEA:33887 and merge these 2 terms into it

id: GO:0016684 name: oxidoreductase activity, acting on peroxide as acceptor def: "Catalysis of an oxidation-reduction (redox) reaction in which the peroxide group acts as a hydrogen or electron acceptor." [EC:1.11.-.-] xref: EC:1.11.-.- is_a: GO:0016491 ! oxidoreductase activity

id: GO:0103003 name: oleate peroxygenase activity def: "Catalysis of the reaction: oleate + a lipid hydroperoxide = 9,10-epoxystearate + a lipid alcohol." [EC:1.11.-.-, GOC:pz] xref: MetaCyc:RXN-9804 is_a: GO:0016684 ! oxidoreductase activity, acting on peroxide as acceptor

MetaCyc:RXN-9804 says this is EC:1.11.2.3 => merge with GO:1990137 (= EC:1.11.2.3) and add MetaCyc:RXN-9804 as narrowMatch xref, or could just obsolete since 0 annotations to GO:0103003

id: GO:0004517 name: nitric-oxide synthase activity namespace: molecular_function def: "Catalysis of the reaction: L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [EC:1.14.13.39, RHEA:19897] xref: EC:1.14.13.39 xref: MetaCyc:NITRIC-OXIDE-SYNTHASE-RXN xref: RHEA:19897 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

id: GO:0051767 name: nitric-oxide synthase biosynthetic process namespace: biological_process alt_id: GO:0051768 def: "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [EC:1.14.13.39, GOC:ai] is_a: GO:0009059 ! macromolecule biosynthetic process

=> remove EC xref from the BP term (GO:0051767) def. => though GO:0051767 seems an odd GO, and has no annotations => obsolete??

id: GO:0016627 name: oxidoreductase activity, acting on the CH-CH group of donors def: "Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [EC:1.3.-.-] synonym: "oxidoreductase activity, acting on the CH-CH group of donors, other acceptors" NARROW [] xref: EC:1.3.-.- is_a: GO:0016491 ! oxidoreductase activity

id: GO:0102725 name: 24-methyldesmosterol reductase activity def: "Catalysis of the reaction: H+ + 24-methyldesmosterol + NADPH = campesterol + NADP." [EC:1.3.-.-, GOC:pz] xref: MetaCyc:RXN-708 is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors

MetaCyc:RXN-708 says it's a subreaction of "1.3.1.M20" (ie. an EC internal to MetaCyc) => There are 0 annotations to GO:0102725, so suggest we obsolete it.

id: GO:0070818 name: protoporphyrinogen oxidase activity def: "Catalysis of the reaction: protoporphyrinogen IX + acceptor = protoporphyrin IX + reduced acceptor." [EC:1.3.3.4, GOC:mah, PMID:19583219] is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors created_by: mah creation_date: 2009-07-20T02:41:12Z

id: GO:0004729 name: oxygen-dependent protoporphyrinogen oxidase activity def: "Catalysis of the reaction: 3 O2 + protoporphyrinogen IX = 3 H2O2 + protoporphyrin IX." [EC:1.3.3.4, RHEA:25576] xref: EC:1.3.3.4 xref: KEGG_REACTION:R03222 xref: MetaCyc:PROTOPORGENOXI-RXN xref: RHEA:25576 is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor is_a: GO:0070818 ! protoporphyrinogen oxidase activity

id: GO:0070819 name: menaquinone-dependent protoporphyrinogen oxidase activity def: "Catalysis of the reaction: protoporphyrinogen IX + menaquinone = protoporphyrin IX + reduced menaquinone." [GOC:mah, PMID:19583219] xref: EC:1.3.3.4 {source="skos:broadMatch"} is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor is_a: GO:0070818 ! protoporphyrinogen oxidase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24056" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI created_by: mah creation_date: 2009-07-20T02:46:06Z

EC:1.3.3.4 is: 3 O2 + protoporphyrinogen IX = 3 H2O2 + protoporphyrin IX => make exactMatch on GO:0004729 => remove from def of GO:0070818

id: GO:0102143 name: carboxynorspermidine dehydrogenase I activity def: "Catalysis of the reaction: carboxynorspermidine + NADP + H2O = L-aspartic acid 4-semialdehyde betaine + trimethylenediaminium + NADPH + H+." [EC:1.5.1.43, GOC:pz] xref: MetaCyc:RXN-11565 xref: RHEA:34115 is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor

[Term] id: GO:0102144 name: carboxyspermidine dehydrogenase II activity def: "Catalysis of the reaction: carboxyspermidine + H2O + NADP = L-aspartic acid 4-semialdehyde betaine + 1,4-butanediammonium + NADPH + H+." [EC:1.5.1.43, GOC:pz] xref: MetaCyc:RXN-11566 xref: RHEA:34111 is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor

EC:1.5.1.43 covers both reactions => merge the above into a single term with the appropriate exact/broad/narrowMatch xrefs

id: GO:0008898 name: S-adenosylmethionine-homocysteine S-methyltransferase activity def: "Catalysis of the reaction: S-adenosyl-L-methionine + L-homocysteine = S-adenosyl-L-homocysteine + L-methionine." [EC:2.1.1.10, GOC:BHF, GOC:dph] xref: EC:2.1.1.10 {source="skos:broadMatch"} xref: MetaCyc:HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN xref: RHEA:21820 is_a: GO:0008172 ! S-methyltransferase activity is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25824" xsd:anyURI

id: GO:0061627 name: S-methylmethionine-homocysteine S-methyltransferase activity def: "Catalysis of the reaction: S-methyl-L-methionine + L-homocysteine = 2 L-methionine + H+." [EC:2.1.1.10, GOC:BHF, GOC:dph] xref: EC:2.1.1.10 {source="skos:broadMatch"} xref: MetaCyc:MMUM-RXN xref: RHEA:26337 is_a: GO:0008172 ! S-methyltransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25824" xsd:anyURI created_by: dph creation_date: 2014-05-14T14:32:02Z

=> these are OK? Seems like there might have been a good reason for having separate terms here (from given ticket), so better not to merge these even though they refer to specific substrates of EC:2.1.1.10 (GO:0008898 has 6 EXP annotations and has GO:0061627 1 EXP annotation)

id: GO:0102004 name: 2-octaprenyl-6-hydroxyphenol methylase activity def: "Catalysis of the reaction: 3-(all-trans-octaprenyl)benzene-1,2-diol + S-adenosyl-L-methionine = H+ + 2-methoxy-6-(all-trans-octaprenyl)phenol + S-adenosyl-L-homocysteine." [EC:2.1.1.222] xref: MetaCyc:2-OCTAPRENYL-6-OHPHENOL-METHY-RXN xref: RHEA:27770 is_a: GO:1990888 ! 2-polyprenyl-6-hydroxyphenol O-methyltransferase activity

id: GO:0102208 name: 2-polyprenyl-6-hydroxyphenol methylase activity def: "Catalysis of the reaction: S-adenosyl-L-methionine + a 3-(all-trans-polyrenyl)benzene-1,2-diol = S-adenosyl-L-homocysteine + H+ + a 2-methoxy-6-(all-trans-polyprenyl)phenol." [EC:2.1.1.222, GOC:pz] xref: MetaCyc:RXN-12160 xref: RHEA:31411 is_a: GO:0008168 ! methyltransferase activity

=> merge GO:0102004 (specific substrate) into GO:0102208 and assign appropriate xrefs, or just obsolete GO:0102004 since it has 0 annotations.

id: GO:0004644 name: phosphoribosylglycinamide formyltransferase activity def: "Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide." [EC:2.1.2.2] xref: EC:2.1.2.2 xref: MetaCyc:GART-RXN xref: RHEA:15053 is_a: GO:0016742 ! hydroxymethyl-, formyl- and related transferase activity

id: GO:0043815 name: phosphoribosylglycinamide formyltransferase 2 activity def: "Catalysis of the reaction: formate + ATP + 5'-phospho-ribosylglycinamide = 5'-phosphoribosyl-N-formylglycinamide + ADP + diphosphate." [EC:2.1.2.2, PMID:8117714] xref: MetaCyc:GARTRANSFORMYL2-RXN xref: RHEA:24829 is_a: GO:0016742 ! hydroxymethyl-, formyl- and related transferase activity

RHEA:24829 says this is EC:6.3.1.21, which doesn't appear to be in the GO => replace def xref with RHEA => add EC:6.3.1.21 as exactMatch term xref.

sjm41 commented 1 month ago

id: GO:0016744 name: transketolase or transaldolase activity def: "Catalysis of the transfer of an aldehyde or ketonic group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] xref: EC:2.2.1.- is_a: GO:0016740 ! transferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20486" xsd:anyURI

id: GO:0102647 name: D-ribose 5-phosphate:D-sedoheptulose 7-phosphate transaldolase activity def: "Catalysis of the reaction: sedoheptulose 7-phosphate + D-ribose 5-phosphate = D-glycero-D-altro-octulose 8-phosphate + D-erythrose 4-phosphate." [EC:2.2.1.-, GOC:pz] xref: MetaCyc:RXN-15789 is_a: GO:0016744 ! transketolase or transaldolase activity

id: GO:0102648 name: D-ribose 5-phosphate:D-fructose 6-phosphate transaldolase activity def: "Catalysis of the reaction: D-fructose 6-phosphate + D-ribose 5-phosphate = D-glycero-D-altro-octulose 8-phosphate + D-glyceraldehyde 3-phosphate." [EC:2.2.1.-, GOC:pz] xref: MetaCyc:RXN-15790 is_a: GO:0016744 ! transketolase or transaldolase activity

MetaCyc just maps these to "EC:2.2.1.-", as per the current GO def xref. => replace def xref with MetaCyc IDs, or could just obsolete since neither have any annotations.

id: GO:0004772 name: sterol O-acyltransferase activity def: "Catalysis of the reaction: acyl-CoA + a sterol = CoA + a sterol ester." [EC:2.3.1.26, GOC:mah] is_a: GO:0008374 ! O-acyltransferase activity

id: GO:0034736 name: cholesterol O-acyltransferase activity def: "Catalysis of the reaction: acyl-CoA + cholesterol = a cholesterol ester + CoA." [EC:2.3.1.26, RHEA:17729] xref: EC:2.3.1.26 xref: KEGG_REACTION:R01461 xref: MetaCyc:STEROL-O-ACYLTRANSFERASE-RXN xref: RHEA:17729 is_a: GO:0004772 ! sterol O-acyltransferase activity

EC:2.3.1.26 is "a long-chain fatty acyl-CoA + a sterol = a sterol ester + CoA" => make EC:2.3.1.26 an exactMatch on GO:0004772 and add RHEA:59816 and MetaCyc:RXN-20233 as other exactMatch xrefs => remove EC:2.3.1.26 as term and def xref on the more specific GO:0034736

id: GO:0016755 name: aminoacyltransferase activity def: "Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor)." [GOC:jl] synonym: "transferase activity, transferring amino-acyl groups" EXACT [] xref: EC:2.3.2.- is_a: GO:0016746 ! acyltransferase activity

id: GO:0102272 name: homophytochelatin synthase activity (polymer-forming) def: "Catalysis of the reaction: glutathionate + a poly gamma-glutamylcysteine-beta-alanine = glycine + a poly gamma-glutamylcysteine-beta-alanine." [EC:2.3.2.-, GOC:pz] xref: MetaCyc:RXN-12528 is_a: GO:0016755 ! aminoacyltransferase activity

[Term] id: GO:0102273 name: homophytochelatin synthase (dimmer forming) activity def: "Catalysis of the reaction: glutathionate + L-gamma-glutamyl-L-cysteinyl-beta-alaninate = gamma-Glu-Cys-gamma-Glu-Cys-beta-Ala + glycine." [EC:2.3.2.-, GOC:pz] xref: MetaCyc:RXN-12529 is_a: GO:0016755 ! aminoacyltransferase activity

MetaCyc just maps these to "EC:2.3.2.-", as per the current GO def xref. => replace def xref with MetaCyc IDs, or could just obsolete since neither have any annotations.

id: GO:0047268 name: galactinol-raffinose galactosyltransferase activity def: "Catalysis of the reaction: raffinose + 1-alpha-D-galactosyl-myo-inositol = stachyose + myo-inositol." [EC:2.4.1.67, MetaCyc:2.4.1.67-RXN] xref: EC:2.4.1.67 xref: MetaCyc:2.4.1.67-RXN xref: RHEA:20776 is_a: GO:0008378 ! galactosyltransferase activity

id: GO:0102827 name: galactosylononitol-raffinose galactosyltransferase activity def: "Catalysis of the reaction: raffinose + D-galactosylononitol = stachyose + 1D-4-O-methyl-myo-inositol." [EC:2.4.1.67, GOC:pz] xref: MetaCyc:RXN-8282 is_a: GO:0016758 ! hexosyltransferase activity

MetaCyc:RXN-8282 is mapped 2.4.1.-, not EC:2.4.1.67 => There are no annotations to GO:0102827, so suggest just obsolete

id: GO:0004760 name: serine-pyruvate transaminase activity namespace: molecular_function xref: EC:2.6.1.51 xref: KEGG_REACTION:R00585 xref: MetaCyc:SERINE--PYRUVATE-AMINOTRANSFERASE-RXN xref: RHEA:22852 is_a: GO:0008483 ! transaminase activity

id: GO:0005969 name: serine-pyruvate aminotransferase complex namespace: cellular_component def: "An enzyme complex that catalyzes the formation of hydroxypyruvate and alanine from serine and pyruvate." [EC:2.6.1.51] intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0004760 ! serine-pyruvate transaminase activity relationship: part_of GO:0005737 ! cytoplasm

=> Remove EC from CC term (GO:0005969) def xref => I don't see any evidence for this complex - there is one EXP annotation to mouse Eea1 from PMID:16399794, but I don't see mention of a "serine-pyruvate aminotransferase complex" in that paper => obsolete?

id: GO:0102352 name: phosphatidate kinase activity def: "Catalysis of the reaction: ATP + a 1,2-diacyl-sn-glycerol 3-phosphate = ADP + a 1,2-diacyl-sn-glycerol 3-diphosphate." [EC:2.7.4.-, GOC:pz] xref: MetaCyc:RXN-13336 is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor

id: GO:0102763 name: phytyl-P kinase activity def: "Catalysis of the reaction: phytyl phosphate(2-) + a nucleoside triphosphate = (E)-3,7,11,15-tetramethylhexadec-2-en-1-yl diphosphate + a nucleoside diphosphate." [EC:2.7.4.-, GOC:pz] xref: MetaCyc:RXN-7763 xref: RHEA:38099 is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor

MetaCyc just maps these to "EC:2.7.4.-", as per the current GO def xref. => Use RHEA as def xref (1 annotation)

id: GO:0004781 name: sulfate adenylyltransferase (ATP) activity def: "Catalysis of the reaction: ATP + sulfate = diphosphate + adenylylsulfate." [EC:2.7.7.4] xref: EC:2.7.7.4 xref: MetaCyc:SULFATE-ADENYLYLTRANS-RXN xref: RHEA:18133 is_a: GO:0004779 ! sulfate adenylyltransferase activity

id: GO:0102297 name: selenate adenylyltransferase activity def: "Catalysis of the reaction: selenic acid + ATP + 2 H+ = adenylyl selenate + diphosphoric acid." [EC:2.7.7.4, GOC:pz] xref: MetaCyc:RXN-12720 is_a: GO:0016779 ! nucleotidyltransferase activity

MetaCyc:RXN-12720 says it's an 'unofficial reaction of EC:2.7.7.4', even though selenate is different from sulfate (and the EC page doesn't mention selenate) => there are no annotations to GO:0102297 so suggest obsolete.

id: GO:0050659 name: N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity def: "Catalysis of the reactions: n 3'-phosphoadenylyl sulfate + chondroitin 4'-sulfate = n adenosine 3',5'-bisphosphate + chondroitin 4',6'-bissulfate + n H+, and n 3'-phosphoadenylyl sulfate + dermatan 4'-sulfate = n adenosine 3',5'-bisphosphate + dermatan 4',6'-bissulfate + n H+." [EC:2.8.2.33] xref: EC:2.8.2.33 xref: KEGG_REACTION:R10868 {source="skos:narrowMatch"} xref: KEGG_REACTION:R10869 {source="skos:narrowMatch"} xref: MetaCyc:RXN-7953 {source="skos:narrowMatch"} xref: MetaCyc:RXN-7954 {source="skos:narrowMatch"} xref: RHEA:54300 {source="skos:narrowMatch"} xref: RHEA:54304 {source="skos:narrowMatch"} is_a: GO:0008146 ! sulfotransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28136" xsd:anyURI

id: GO:0036443 name: dermatan 6-sulfotransferase activity def: "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + dermatan = adenosine 3',5'-bisphosphate + dermatan 6'-sulfate." [EC:2.8.2.33, GOC:bf, KEGG_REACTION:R07288] xref: KEGG_REACTION:R07288 is_a: GO:0008146 ! sulfotransferase activity created_by: bf creation_date: 2013-10-17T10:41:48Z

KEGG_REACTION:R07288 says this is EC:2.8.2.17, but that is specific for chondroitin R07288 isn't in RHEA => There are no annotations to GO:0036443, so suggest obsoletion

id: GO:0016788 name: hydrolase activity, acting on ester bonds def: "Catalysis of the hydrolysis of any ester bond." [GOC:jl] xref: EC:3.1.-.- is_a: GO:0016787 ! hydrolase activity

id: GO:0102666 name: indole-3-acetyl-beta-4-D-glucose hydrolase activity def: "Catalysis of the reaction: indole-3-acetyl-beta-4-D-glucose + H2O = H+ + indole-3-acetate + beta-D-glucose." [EC:3.1.-.-, GOC:pz] xref: MetaCyc:RXN-3164 is_a: GO:0016788 ! hydrolase activity, acting on ester bonds

id: GO:0102667 name: indole-3-acetyl-beta-1-D-glucose hydrolase activity def: "Catalysis of the reaction: 1-O-(indol-3-ylacetyl)-beta-D-glucose + H2O = H+ + indole-3-acetate + beta-D-glucose." [EC:3.1.-.-, GOC:pz] xref: MetaCyc:RXN-3165 is_a: GO:0016788 ! hydrolase activity, acting on ester bonds

MetaCyc just maps these to "EC:3.1.-.-", as per the current GO def xref. => Use MetaCyc as def xrefs, or obsolete since neither has any GO annotations

id: GO:0019156 name: isoamylase activity def: "Catalysis of the hydrolysis of alpha-(1,6)-D-glucosidic branch linkages in glycogen, amylopectin and their beta-limits dextrins." [EC:3.2.1.68] xref: EC:3.2.1.68 {source="skos:exactMatch"} xref: MetaCyc:3.2.1.68-RXN {source="skos:exactMatch"} xref: MetaCyc:RXN-12280 {source="skos:narrowMatch"} xref: MetaCyc:RXN-14380 {source="skos:narrowMatch"} is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI

id: GO:0102681 name: isoamylase (maltodextrin-releasing) activity def: "Catalysis of the reaction: n H2O + a glycogen = n a maltodextrin." [EC:3.2.1.68, GOC:pz] xref: MetaCyc:RXN-4301 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

=> obsolete GO:0102681 since specific substrate of GO:0019156 and 0 annotations.

sjm41 commented 1 month ago

id: GO:0003905 name: alkylbase DNA N-glycosylase activity

def: "Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site." [EC:3.2.2.21, GOC:elh, PMID:10872450, PMID:9224623] xref: EC:3.2.2.21 {source="skos:exactMatch"} xref: MetaCyc:3.2.2.21-RXN {source="skos:exactMatch"} is_a: GO:0019104 ! DNA N-glycosylase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28183" xsd:anyURI

id: GO:0052822 name: DNA-3-methylguanine glycosylase activity def: "Catalysis of the reaction: DNA containing 3-methylguanine + H2O = DNA with abasic site + 3-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methylguanine and the deoxyribose sugar to remove the 3-methylguanine, leaving an abasic site." [EC:3.2.2.21, GOC:elh, PMID:10872450, PMID:9224623] xref: EC:3.2.2.21 {source="skos:broadMatch"} is_a: GO:0043733 ! DNA-3-methylbase glycosylase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28183" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28514" xsd:anyURI created_by: ai creation_date: 2011-10-28T02:28:19Z

EC name is the specific "DNA-3-methyladenine glycosylase II" but EC def is the more general "Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine" => I don't think the specific GO:0052822 is needed (it has 0 EXP annotations) so could obsolete.

id: GO:0016811 name: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides def: "Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide." [EC:3.5.1.-] xref: EC:3.5.1.- is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

id: GO:0102281 name: formylaminopyrimidine deformylase activity def: "Catalysis of the reaction: formylaminopyrimidine + H2O = 4-amino-5-ammoniomethyl-2-methylpyrimidine + formate." [EC:3.5.1.-, GOC:pz] xref: MetaCyc:RXN-12612 is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides

id: GO:0102622 name: linuron hydrolase activity def: "Catalysis of the reaction: linuron + H2O = N,O-dimethylhydroxylamine + carbon dioxide + 3,4-dichloroaniline." [EC:3.5.1.-, GOC:pz] xref: MetaCyc:RXN-15526 is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides

MetaCyc:RXN-12612 is only mapped to EC:3.5.1.- at MetaCyc, while MetaCyc:RXN-15526 is mapped to the internal EC numbers 3.5.1.M20/3.5.1.M19/3.5.1.M21. => obsolete (0 annotations on either term)

=> already fixed

=> GO:0102328 already fixed (obsoleted)

id: GO:0102765 name: UDP-D-apiose synthase activity def: "Catalysis of the reaction: H+ + UDP-alpha-D-glucuronate = UDP-alpha-D-apiose + carbon dioxide." [EC:4.1.1.-, GOC:pz] xref: MetaCyc:RXN-7770 is_a: GO:0016831 ! carboxy-lyase activity

MetaCyc:RXN-7770 only mapped to EC:4.1.1.- in MetaCyc. Has 3 EXP annotations => change def xref to use MetaCyc

id: GO:0102895 name: colneleate synthase activity def: "Catalysis of the reaction: 9(S)-HPODE = colneleate + H2O." [EC:4.2.1.121, GOC:pz] xref: EC:4.2.1.121 xref: MetaCyc:RXN-8496 xref: RHEA:28174 is_a: GO:0016836 ! hydro-lyase activity

id: GO:0102896 name: colnelenate synthase activity def: "Catalysis of the reaction: (10E,12Z,15Z)-9-hydroperoxyoctadeca-10,12,15-trienoate = colnelenate + H2O." [EC:4.2.1.121, GOC:pz] xref: MetaCyc:RXN-8498 xref: RHEA:28178 is_a: GO:0016836 ! hydro-lyase activity

=> EC:4.2.1.121 covers both these reactions, so merge these two (though GO:0102896/RHEA:28178 has 0 annotations so could obsolete)

id: GO:0016857 name: racemase and epimerase activity, acting on carbohydrates and derivatives def: "Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule." [GOC:mah] xref: EC:5.1.3.- is_a: GO:0016854 ! racemase and epimerase activity

id: GO:0102540 name: D-mannose 6-phosphate 1-epimerase activity def: "Catalysis of the reaction: alpha-D-mannose 6-phosphate = beta-D-mannose 6-phosphate." [EC:5.1.3.-, GOC:pz] xref: MetaCyc:RXN-14815 is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives

id: GO:0102541 name: D-galactose 6-phosphate 1-epimerase activity def: "Catalysis of the reaction: alpha-D-galactose 6-phosphate = beta-D-galactose 6-phosphate." [EC:5.1.3.-, GOC:pz] xref: MetaCyc:RXN-14816 is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives

MetaCyc:RXN-14815 and MetaCyc:RXN-14816 are only mapped to EC:5.1.3.- in MetaCyc => oboslete (0 GO annotations to either term)

id: GO:0016860 name: intramolecular oxidoreductase activity def: "Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, and no oxidized product appears." [EC:5.3.-.-, GOC:curators] xref: EC:5.3.-.- is_a: GO:0016853 ! isomerase activity

id: GO:0102929 name: lachrymatory factor synthase activity def: "Catalysis of the reaction: 1-propenylsulfenate = propanethiol S-oxide." [EC:5.3.-.-, GOC:pz] xref: MetaCyc:RXN-8911 is_a: GO:0016860 ! intramolecular oxidoreductase activity

MetaCyc:RXN-8911 is mapped to EC:5.3.99.12, which is mapped to 3 RHEAs (RHEA:69336, RHEA:69340, RHEA:69344) GO:0102929 has 0 annotations, RHEAs have 1 associated protein (Onion LFS protein) => obsolete GO:0102929?

id: GO:0016881 name: acid-amino acid ligase activity def: "Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [GOC:jl, GOC:mah] xref: EC:6.3.2.- is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds

id: GO:0102650 name: cyclo-acetoacetyl-L-tryptophan synthetase activity def: "Catalysis of the reaction: acetoacetyl-ACP + L-tryptophan + ATP = cyclo-acetoacetyl-L-tryptophan + AMP + diphosphoric acid + 2 H+ + a holo-[acyl-carrier protein]." [EC:6.3.2.-, GOC:pz] xref: MetaCyc:RXN-15811 is_a: GO:0016881 ! acid-amino acid ligase activity

id: GO:0103044 name: ribosomal protein S6 glutamate-glutamate ligase activity def: "Catalysis of the reaction: L-glutamate + ATP + a [protein] C-terminal L-glutamate = ADP + hydrogenphosphate + H+ + a [protein] with C-terminal alpha-L-glutamate-alpha-L-glutamate." [EC:6.3.2.-, GOC:pz] xref: MetaCyc:RXN0-6726 is_a: GO:0018169 ! ribosomal S6-glutamic acid ligase activity

MetaCyc:RXN-15811 and MetaCyc:RXN0-6726 are only mapped to EC:6.3.2.- at MetaCyc; not in RHEA. => obsolete (0 annotations to either GO term)

id: GO:0047545 name: 2-hydroxyglutarate dehydrogenase activity def: "Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor." [EC:1.1.99.2, MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN] xref: EC:1.1.99.2 xref: MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN xref: RHEA:21252 is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors

id: GO:0051990 name: (R)-2-hydroxyglutarate dehydrogenase activity def: "Catalysis of the reaction: (R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor." [EC:1.1.99.39, MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN] xref: EC:1.1.99.39 xref: RHEA:38295 is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors

=> remove MetaCyc from GO:0051990 def xref; add RXN-14932 as term xref

id: GO:0033533 name: verbascose metabolic process def: "The chemical reactions and pathways involving verbascose, the pentasaccharide beta-D-fructofuranosyl alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-glucopyranoside." [GOC:mah, MetaCyc:CPD-8065] intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:28586 ! verbascose

id: GO:0033534 name: verbascose biosynthetic process def: "The chemical reactions and pathways resulting in the formation of verbascose, the pentasaccharide beta-D-fructofuranosyl alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-glucopyranoside." [GOC:mah, MetaCyc:CPD-8065] is_a: GO:0010325 ! raffinose family oligosaccharide biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28586 ! verbascose

=> remove MetaCyc compound ID from these def xrefs

sjm41 commented 1 month ago

id: GO:0033535 name: ajugose metabolic process def: "The chemical reactions and pathways involving ajugose, the hexasaccharide beta-D-fructofuranosyl alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-glucopyranoside." [GOC:mah, MetaCyc:CPD-8066] intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:28554 ! ajugose

id: GO:0033536 name: ajugose biosynthetic process def: "The chemical reactions and pathways resulting in the formation of ajugose, the hexasaccharide beta-D-fructofuranosyl alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-galactopyranosyl-(1->6)-alpha-D-glucopyranoside." [GOC:mah, MetaCyc:CPD-8066] is_a: GO:0010325 ! raffinose family oligosaccharide biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28554 ! ajugose

=> remove MetaCyc compound ID as def xefs

id: GO:0052671 name: geranylgeraniol kinase activity def: "Catalysis of the reaction: geranylgeraniol + nucleoside triphosphate = all-trans-geranyl-geranyl monophosphate + nucleoside diphosphate." [GOC:kd, MetaCyc:RXN-11629] synonym: "geranylgeraniol phosphotransferase activity" EXACT [] is_a: GO:0052673 ! prenol kinase activity created_by: ai creation_date: 2011-04-11T03:18:44Z

id: GO:0052672 name: CTP:geranylgeraniol kinase activity def: "Catalysis of the reaction: geranylgeraniol + CTP = all-trans-geranyl-geranyl monophosphate + CDP." [MetaCyc:RXN-11629] synonym: "CTP:geranylgeraniol phosphotransferase activity" EXACT [] xref: EC:2.7.1.216 {source="skos:broadMatch"} xref: MetaCyc:RXN-11629 is_a: GO:0052671 ! geranylgeraniol kinase activity created_by: ai creation_date: 2011-04-11T03:26:04Z

MetaCyc:RXN-11629 is specifically for GO:0052672 => remove as def xref on GO:0052671 and make exactMatch on GO:0052672 => add RHEA:63456 as xref to GO:0052672

id: GO:0052754 name: GTP:coenzyme F420 guanyltransferase activity def: "Catalysis of the reaction: GTP + factor gamma-F420-2 + H+ = coenzyme F390-G + diphosphate." [GOC:mengo_curators, MetaCyc:RXN-9385] xref: MetaCyc:RXN-18273 {source="skos:exactMatch"} is_a: GO:0070568 ! guanylyltransferase 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/28503" xsd:anyURI created_by: ai creation_date: 2011-09-22T03:25:30Z

id: GO:0043910 name: ATP:coenzyme F420 adenylyltransferase activity def: "Catalysis of the reaction: ATP + factor gamma-F420-2 + H+ = coenzyme F390-A + diphosphate." [GOC:jl, MetaCyc:RXN-9385, PMID:7957247, PMID:8550473] xref: MetaCyc:RXN-9385 is_a: GO:0070566 ! adenylyltransferase activity

=> replace def xref on GO:0052754 with MetaCyc:RXN-18273

id: GO:0008920 name: lipopolysaccharide heptosyltransferase activity def: "Catalysis of the reaction: a lipopolysaccharide + ADP-L-glycero-beta-D-manno-heptose = a heptosylated lipopolysaccharide + ADP + H+." [MetaCyc:RXN0-5061, MetaCyc:RXN0-5122, MetaCyc:RXN0-5127] synonym: "LPS heptosyltransferase activity" EXACT [] is_a: GO:0016757 ! glycosyltransferase activity

=> remove MetaCyc xrefs from the def of this grouping term.

id: GO:0008713 name: ADP-heptose-lipopolysaccharide heptosyltransferase activity def: "Catalysis of the reaction: heptosyl-KDO2-lipid A + ADP-L-glycero-beta-D-manno-heptose = heptosyl2-KDO2-lipid A + ADP + H+." [MetaCyc:RXN0-5061] xref: MetaCyc:RXN0-5061 xref: RHEA:28538 is_a: GO:0008920 ! lipopolysaccharide heptosyltransferase activity

=> change xrefs and def to use the more general form = RHEA:74071/MetaCyc:RXN-22477 => Add EC:2.4.99.24

id: GO:0071967 name: lipopolysaccharide core heptosyltransferase activity def: "Catalysis of the reaction: glucosyl-heptosyl2-KDO2-lipid A-phosphate + ADP-L-glycero-beta-D-manno-heptose = glucosyl-heptosyl3-KDO2-lipid A-phosphate + ADP + H+." [MetaCyc:RXN0-5122] xref: MetaCyc:RXN0-5122 xref: RHEA:29923 is_a: GO:0008920 ! lipopolysaccharide heptosyltransferase activity created_by: mah creation_date: 2010-10-14T05:13:31Z

id: GO:0071968 name: lipid A-core heptosyltransferase activity def: "Catalysis of the reaction: galactosyl-glucosyl3-heptosyl3-KDO2-lipid A-bisphosphate + ADP-L-glycero-beta-D-manno-heptose = lipid A-core + ADP + H+." [MetaCyc:RXN0-5127] xref: MetaCyc:RXN0-5127 xref: RHEA:30019 is_a: GO:0008920 ! lipopolysaccharide heptosyltransferase activity created_by: mah creation_date: 2010-10-14T05:15:22Z

id: GO:0016174 name: NAD(P)H oxidase H2O2-forming activity def: "Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + hydrogen peroxide." [EC:1.6.3.1, PMID:10401672, PMID:10601291, PMID:11822874, RHEA:11260] xref: EC:1.6.3.1 is_a: GO:0050664 ! oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor

id: GO:0106294 name: NADPH oxidase H202-forming activity def: "Catalysis of the reaction: NADPH + H+ + O2 = NADP + hydrogen peroxide (H2O2)." [RHEA:11260] xref: RHEA:11260 is_a: GO:0016174 ! NAD(P)H oxidase H2O2-forming activity created_by: hjd creation_date: 2020-08-19T17:38:36Z

=> remove RHEA as def xref on GO:0016174

id: GO:0009038 name: undecaprenol kinase activity def: "Catalysis of the reaction: ATP + undecaprenol = ADP + undecaprenyl phosphate." [EC:2.7.1.66, RHEA:23752] xref: EC:2.7.1.66 is_a: GO:0016301 ! kinase activity is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor

id: GO:0036432 name: all-trans undecaprenol kinase activity def: "Catalysis of the reaction: ATP + undecaprenol + all-trans-undecaprenyl phosphate + ADP + H+." [RHEA:23752] xref: RHEA:23752 is_a: GO:0009038 ! undecaprenol kinase activity created_by: bf creation_date: 2013-09-16T14:21:04Z

=> remove RHEA as def xref on GO:0009038 => also remove EC:2.7.1.66 as def and term xref on GO:0009038 and move to GO:0036433

id: GO:0016616 name: oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor def: "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP." [EC:1.1.1.-] xref: EC:1.1.1.- is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors

id: GO:0102182 name: 4alpha-carboxy-stigmasta-7,24(241)-dien-3beta-ol dehydrogenase/C4-decarboxylase activity def: "Catalysis of the reaction: 4alpha-carboxy-stigmasta-7,24(241)-dien-3beta-ol + NAD = avenastenone + NADH + carbon dioxide." [EC:1.1.1.-, GOC:pz] xref: MetaCyc:RXN-11938 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

id: GO:0102727 name: 3beta-hydroxysteroid dehydrogenase activity def: "Catalysis of the reaction: campest-4-en-3beta-ol + NAD = campest-4-en-3-one + NADH + H+." [EC:1.1.1.-, GOC:pz] xref: MetaCyc:RXN-710 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

MetaCyc:RXN-11938 is mapped to 1.1.1.418, but is the unofficial reaction - RXN-20374 is the offical one. => merge GO:0102182 into GO:0102191 (=EC:1.1.1.418), or just obsolete since there are 0 annotations => make MetaCyc:RXN-20374 exactMatch on GO:0102191

MetaCyc:RXN-710 is mapped to 1.1.1.357, but is the unofficial reaction - RXN-13688 is the offical one, which is itself mapped to 1.1.1.50/1.1.1.213/1.1.1.357 => just obsolete GO:0102727 given it has 0 annotations?

GO:0102006 has been fixed

id: GO:0016620 name: oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor def: "Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP." [GOC:jl] xref: EC:1.2.1.- is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors

id: GO:0102792 name: sinapaldehyde:NAD(P)+ oxidoreductase activity def: "Catalysis of the reaction: sinapoyl aldehyde + NADP + H2O = 2 H+ + trans-sinapate + NADPH." [EC:1.2.1.-, GOC:pz] xref: MetaCyc:RXN-8014 is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

id: GO:0102819 name: bixin aldehyde dehydrogenase activity def: "Catalysis of the reaction: bixin aldehyde + O2 + NAD = norbixin + NADH + H+." [EC:1.2.1.-, GOC:pz] xref: MetaCyc:RXN-8237 is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

MetaCyc:RXN-8014 and MetaCyc:RXN-8237 are just mapped to EC:1.2.1.- in MetaCyc and aren't in RHEA. => obsolete (neither has any GO annotations)

sjm41 commented 1 month ago

=> GO:0033805 has been obsoleted, but should remove EC from def

id: GO:0052729 name: dimethylglycine N-methyltransferase activity def: "Catalysis of the reaction: S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine." [EC:2.1.1.157] xref: EC:2.1.1.157 {source="skos:broadMatch"} xref: EC:2.1.1.161 {source="skos:exactMatch"} xref: EC:2.1.1.162 {source="skos:broadMatch"} xref: KEGG_REACTION:R07244 xref: MetaCyc:RXN-9680 {source="skos:exactMatch"} xref: RHEA:10072 {source="skos:exactMatch"} is_a: GO:0008170 ! N-methyltransferase activity is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28514" xsd:anyURI created_by: ai creation_date: 2011-08-16T03:45:16Z

id: GO:0052730 name: sarcosine N-methyltransferase activity def: "Catalysis of the reaction: S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine." [EC:2.1.1.157] xref: EC:2.1.1.156 {source="skos:broadMatch"} xref: EC:2.1.1.157 {source="skos:broadMatch"} xref: EC:2.1.1.162 {source="skos:broadMatch"} xref: KEGG_REACTION:R07243 xref: MetaCyc:RXN-9679 {source="skos:exactMatch"} xref: RHEA:15453 {source="skos:exactMatch"} is_a: GO:0008170 ! N-methyltransferase activity is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28514" xsd:anyURI created_by: ai creation_date: 2011-08-16T03:45:39Z

=> swap EC for RHEA in def xrefs

GO:0102731 has been fixed

id: GO:0016773 name: phosphotransferase activity, alcohol group as acceptor def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor)." [EC:2.7.1.-] xref: EC:2.7.1.- is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups

id: GO:0102238 name: ATP:geraniol kinase activity def: "Catalysis of the reaction: geraniol + ATP = geranyl monophosphate + ADP + H+." [EC:2.7.1.-, GOC:pz] xref: MetaCyc:RXN-12307 is_a: GO:0052670 ! geraniol kinase activity

MetaCyc:RXN-12307 is mapped to RHEA:61660 => add that RHEA and use as def xref; add EC:2.7.1.216 as broadMatch) (also need to delete existing RHEA:61660 xref on GO:0102243 and replace with correct RHEA:61664)

id: GO:0102770 name: inositol phosphorylceramide synthase activity def: "Catalysis of the reaction: an L-1-phosphatidyl-inositol + a dihydroceramide = an inositol phosphodihydroceramide + a 1,2-diacyl-sn-glycerol." [EC:2.7.1.-, GOC:pz] xref: MetaCyc:RXN-7795 is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor

MetaCyc:RXN-7795 is just mapped to EC:2.7.1.-, not in RHEA, 1 annotation (by UniProt) => use MetaCyc xref as def xref

id: GO:0102520 name: L-threonine O-3-phosphate phosphatase activity def: "Catalysis of the reaction: O-phospho-L-threonine + H2O = L-threonine + hydrogenphosphate." [EC:3.1.3.-, GOC:pz] xref: MetaCyc:RXN-14505 is_a: GO:0016791 ! phosphatase activity

MetaCyc:RXN-14505 only mapped to EC:3.1.3.-, not in RHEA, no annotations => obsolete

id: GO:0102537 name: ecdysone-phosphate phosphatase activity def: "Catalysis of the reaction: ecdysone 22-phosphate + H2O = ecdysone + hydrogenphosphate." [EC:3.1.3.-, GOC:pz] xref: MetaCyc:RXN-14766 is_a: GO:0016791 ! phosphatase activity

MetaCyc:RXN-14766 is xref on RHEA:63576/GO:0102531: id: GO:0102531 name: ecdysteroid-phosphate phosphatase activity def: "Catalysis of the reaction: H2O + an ecdysteroid 22-phosphate = hydrogenphosphate + an ecdysteroid." [GOC:pz, PMID:12721294] xref: MetaCyc:RXN-14734 xref: RHEA:63576 is_a: GO:0016791 ! phosphatase activity

RHEA:63576 is "ecdysone 22-phosphate + H2O = ecdysone + phosphate" MetaCyc:RXN-14766 is "ecdysone 22-phosphate + H2O → ecdysone + phosphate MetaCyc:RXN-14734 is "an ecdysteroid 22-phosphate + H2O → an ecdysteroid + phosphate" (not in RHEA)

=> merge GO:0102531 and GO:0102537, just keeping MetaCyc:RXN-14766 as exactMatch xref

id: GO:0103026 name: fructose-1-phosphatase activity def: "Catalysis of the reaction: beta-D-fructofuranose 1-phosphate + H2O = beta-D-fructofuranose + hydrogenphosphate." [EC:3.1.3.-, GOC:pz] xref: MetaCyc:RXN0-5186 xref: RHEA:35603 is_a: GO:0016791 ! phosphatase activity

=> use RHEA as def xref

id: GO:1901022 name: 4-hydroxyphenylacetate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505] intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:48999 ! 4-hydroxyphenylacetate created_by: yaf creation_date: 2012-06-18T02:31:37Z

id: GO:1901023 name: 4-hydroxyphenylacetate catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505, PMID:8550403] intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:48999 ! 4-hydroxyphenylacetate created_by: yaf creation_date: 2012-06-18T02:31:58Z

id: GO:1901024 name: 4-hydroxyphenylacetate biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505] intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:48999 ! 4-hydroxyphenylacetate created_by: yaf creation_date: 2012-06-18T02:32:06Z

=> remove MetaCyc:RXN-8505 from these BP terms

id: GO:0102298 name: selenocystathione synthase activity def: "Catalysis of the reaction: L-selenocysteine + O-phosphonato-L-homoserine = hydrogenphosphate + L-selenocystathionine." [EC:2.5.1.-, GOC:pz] xref: MetaCyc:RXN-12728 is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups

MetaCyc:RXN-12728 only mapped to EC:2.5.1.- in MetaCyc, not in RHEA, no GO annotations => obsolete

id: GO:0102747 name: chlorophyllide-a:geranyl-geranyl diphosphate geranyl-geranyl transferase activity def: "Catalysis of the reaction: H+ + chlorophyllide a(1-) + 2-trans,6-trans,10-trans-geranylgeranyl diphosphate(3-) = geranylgeranyl-chlorophyll a + diphosphoric acid." [EC:2.5.1.-, GOC:pz] xref: MetaCyc:RXN-7663 is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups

id: GO:0102753 name: chlorophyllide b:geranyl-geranyl diphosphate geranyl-geranyltransferase activity def: "Catalysis of the reaction: H+ + chlorophyllide b(1-) + 2-trans,6-trans,10-trans-geranylgeranyl diphosphate = geranylgeranyl-chlorophyll b + diphosphoric acid." [EC:2.5.1.-, GOC:pz] xref: MetaCyc:RXN-7673 is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups

id: GO:0102754 name: chlorophyllide-b:phytyl-diphosphate phytyltransferase activity def: "Catalysis of the reaction: H+ + chlorophyllide b + (E)-3,7,11,15-tetramethylhexadec-2-en-1-yl diphosphate = chlorophyll b + diphosphoric acid." [EC:2.5.1.-, GOC:pz] xref: MetaCyc:RXN-7674 is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups

MetaCyc:RXN-7663, MetaCyc:RXN-7673 and MetaCyc:RXN-7674 are mapped to EC:2.5.1.62, suggesting they are included as part of GO:0046408 chlorophyll synthetase activity (EC:2.5.1.62) Though none of them have any GO annotations => either merge these three with GO:0046408 or obsolete

id: GO:0047070 name: 3-carboxyethylcatechol 2,3-dioxygenase activity alt_id: GO:0008669 def: "Catalysis of the reaction: O2 + 3-(2,3-dihydroxyphenyl)propanoate = 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate." [EC:1.13.11.16, MetaCyc:1.13.11.16-RXN] synonym: "2,3-dihydroxy-beta-phenylpropionate oxygenase activity" RELATED [EC:1.13.11.16] synonym: "2,3-dihydroxy-beta-phenylpropionic dioxygenase activity" RELATED [EC:1.13.11.16] synonym: "3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.16] synonym: "3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase activity" RELATED [EC:1.13.11.16] xref: EC:1.13.11.16 xref: MetaCyc:1.13.11.16-RXN xref: RHEA:23840 is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen

id: GO:1901790 name: 3-(2,3-dihydroxyphenyl)propanoate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving 3-(2,3-dihydroxyphenyl)propanoate." [GOC:TermGenie, GOC:yaf, MetaCyc:1.13.11.16-RXN, MetaCyc:HCAMHPDEG-PWY] intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:46951 ! 3-(2,3-dihydroxyphenyl)propanoate created_by: yaf creation_date: 2013-01-16T11:40:57Z

id: GO:1901791 name: 3-(2,3-dihydroxyphenyl)propanoate catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of 3-(2,3-dihydroxyphenyl)propanoate." [GOC:TermGenie, GOC:yaf, MetaCyc:1.13.11.16-RXN, MetaCyc:HCAMHPDEG-PWY, UniPathway:UPA00836] intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:46951 ! 3-(2,3-dihydroxyphenyl)propanoate property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI created_by: yaf creation_date: 2013-01-16T11:41:02Z

id: GO:1901792 name: 3-(2,3-dihydroxyphenyl)propanoate biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of 3-(2,3-dihydroxyphenyl)propanoate." [GOC:TermGenie, GOC:yaf, MetaCyc:1.13.11.16-RXN] intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:46951 ! 3-(2,3-dihydroxyphenyl)propanoate property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI created_by: yaf creation_date: 2013-01-16T11:41:06Z

=> remove the MetaCyc from the def xrefs on the BP terms

id: GO:0103079 name: 2-(3'-methylthio)propylmalate synthase activity def: "Catalysis of the reaction: 5-methylthio-2-oxopentanoate + acetyl-CoA + H2O = H+ + 2-(3-methylthiopropyl)malate + coenzyme A." [EC:2.3.3.-, GOC:pz] xref: MetaCyc:RXNQT-4163 xref: RHEA:25605 is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer

id: GO:0103082 name: 2-(4'-methylthio)butylmalate synthase activity def: "Catalysis of the reaction: 2-oxo-6-methylthiohexanoate + acetyl-CoA + H2O = H+ + 2-(4'-methylthio)butylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz] xref: MetaCyc:RXNQT-4166 is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer

id: GO:0103085 name: 2-(5'-methylthio)pentylmalate synthase activity def: "Catalysis of the reaction: 2-oxo-7-methylthioheptanoate + acetyl-CoA + H2O = H+ + 2-(5'-methylthio)pentylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz] xref: MetaCyc:RXNQT-4169 is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer

id: GO:0103088 name: 2-(6'-methylthio)hexylmalate synthase activity def: "Catalysis of the reaction: 2-oxo-8-methylthiooctanoate + acetyl-CoA + H2O = H+ + 2-(6'-methylthio)hexylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz] xref: MetaCyc:RXNQT-4172 is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer

id: GO:0103091 name: 2-(7'-methylthio)heptylmalate synthase activity def: "Catalysis of the reaction: 2-oxo-9-methylthiononanoate + acetyl-CoA + H2O = H+ + 2-(7'-methylthio)heptylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz] xref: MetaCyc:RXNQT-4175 is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer

All 5 terms above involved specific substrates of GO:0010177 (EC:2.3.3.17) => merge all into GO:0010177

Also: => add RHEA:50624 as exactMatch on GO:0010177 => redefine GO:0010177 based on current EC/RHEA def => add MetaCyc:RXN-18197 as exactMatch on GO:0010177

id: GO:0003899 name: DNA-directed 5'-3' RNA polymerase activity def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [EC:2.7.7.6, GOC:pf] xref: EC:2.7.7.6 xref: MetaCyc:DNA-DIRECTED-RNA-POLYMERASE-RXN is_a: GO:0034062 ! 5'-3' RNA polymerase activity relationship: part_of GO:0032774 ! RNA biosynthetic process

id: GO:0034062 name: 5'-3' RNA polymerase activity def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template, via extension of the 3'-end." [EC:2.7.7.6, GOC:mah, GOC:pf] xref: RHEA:21248 {source="skos:exactMatch"} is_a: GO:0097747 ! RNA polymerase activity

id: GO:0003901 name: obsolete DNA-directed RNA polymerase II activity def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)." [EC:2.7.7.6] comment: This term was made obsolete because it represents the specific complex represented by the cellular component term 'DNA-directed RNA polymerase II, core complex ; GO:0005665'. synonym: "DNA-directed RNA polymerase II activity" EXACT [] is_obsolete: true replaced_by: GO:0003899

id: GO:0003900 name: obsolete DNA-directed RNA polymerase I activity def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)." [EC:2.7.7.6] comment: This term was made obsolete because it represents the specific complex represented by the cellular component term 'DNA-directed RNA polymerase I complex ; GO:0005736'. synonym: "DNA-directed RNA polymerase I activity" EXACT [] is_obsolete: true replaced_by: GO:0003899

id: GO:0003902 name: obsolete DNA-directed RNA polymerase III activity def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)." [EC:2.7.7.6] comment: This term was made obsolete because it represents the specific complex represented by the cellular component term 'DNA-directed RNA polymerase III complex ; GO:0005666'. synonym: "DNA-directed RNA polymerase III activity" EXACT [] is_obsolete: true replaced_by: GO:0003899

=> remove EC from def of GO:0034062 (use RHEA instead) (EC is for "DNA-directed RNA polymerase") => remove EC from def on 3 obsolete terms

id: GO:0103086 name: methylthiopentylmalate isomerase activity def: "Catalysis of the reaction: 2-(5'-methylthio)pentylmalate = 3-(5'-methylthio)pentylmalate." [EC:5.4.4.-, GOC:pz] xref: MetaCyc:RXNQT-4170 is_a: GO:0050486 ! intramolecular hydroxytransferase activity

id: GO:0103080 name: methylthiopropylmalate isomerase activity def: "Catalysis of the reaction: 2-(3-methylthiopropyl)malate(2-) = 3-(3'-methylthio)propylmalate." [EC:5.4.4.-, GOC:pz] xref: MetaCyc:RXNQT-4164 xref: RHEA:50644 is_a: GO:0050486 ! intramolecular hydroxytransferase activity

id: GO:0103083 name: methylthiobutylmalate isomerase activity def: "Catalysis of the reaction: 2-(4'-methylthio)butylmalate = 3-(4'-methylthio)butylmalate." [EC:5.4.4.-, GOC:pz] xref: MetaCyc:RXNQT-4167 is_a: GO:0050486 ! intramolecular hydroxytransferase activity

id: GO:0103089 name: methylthiohexylmalate isomerase activity def: "Catalysis of the reaction: 2-(6'-methylthio)hexylmalate = 3-(6'-methylthio)hexylmalate." [EC:5.4.4.-, GOC:pz] xref: MetaCyc:RXNQT-4173 is_a: GO:0050486 ! intramolecular hydroxytransferase activity

id: GO:0103092 name: methylthioalkylmalate isomerase activity def: "Catalysis of the reaction: 2-(7'-methylthio)heptylmalate = 3-(7'-methylthio)heptylmalate." [EC:5.4.4.-, GOC:pz] xref: MetaCyc:RXNQT-4176 is_a: GO:0050486 ! intramolecular hydroxytransferase activity

these are all substrate-specific versions of EC:4.2.1.170, which isn't in GO -> make new term and merge the five terms above into it: 2-(omega-methylthio)alkylmalate dehydratase a 2-(omega-methylsulfanyl)alkylmalate = a 2-(omega-methylsulfanyl)alkylmaleate + H2O (RHEA:50632) a 3-(omega-methylsulfanyl)alkylmalate = a 2-(omega-methylsulfanyl)alkylmaleate + H2O (RHEA:50636)

Others have been fixed - only the following needs fixing:

id: GO:0102582 name: cyanidin 3-O-p-coumaroylglucoside 2-O''-xylosyltransferase activity def: "Catalysis of the reaction: cyanidin 3-O-(6-O-(E)-4-coumaroyl-beta-D-glucoside) + UDP-alpha-D-xylose = cyanidin 3-O-[2''-O-xylosyl) 6''-O-(p-coumaroyl) glucoside + UDP + H+." [EC:2.4.2.-, GOC:pz] xref: MetaCyc:RXN-15328 is_a: GO:0016763 ! pentosyltransferase activity

MetaCyc:RXN-15328 Only mapped to EC:2.4.2.- in MetaCyc, not in RHEA, no annotations => obsolete

sjm41 commented 1 month ago

GO:0036137 and GO:0036136 are fixed

id: GO:0103105 name: 2-oxo-6-methylthiohexanoate aminotransferase activity def: "Catalysis of the reaction: 2-oxo-6-methylthiohexanoate + a standard alpha amino acid = dihomomethionine + a 2-oxo carboxylate." [EC:2.6.1.-, GOC:pz] xref: MetaCyc:RXNQT-4345 is_a: GO:0008483 ! transaminase activity

id: GO:0102658 name: 2-oxo-5-methylthiopentanoate aminotransferase activity def: "Catalysis of the reaction: 5-methylthio-2-oxopentanoate + a standard alpha amino acid = L-homomethionine + a 2-oxo carboxylate." [EC:2.6.1.-, GOC:pz] xref: MetaCyc:RXN-2205 is_a: GO:0008483 ! transaminase activity

id: GO:0102570 name: tyrosine:phenylpyruvate aminotransferase activity def: "Catalysis of the reaction: keto-phenylpyruvate + L-tyrosine = L-phenylalanine + 3-(4-hydroxyphenyl)pyruvate." [EC:2.6.1.-, GOC:pz] xref: MetaCyc:RXN-15200 is_a: GO:0008483 ! transaminase activity

id: GO:0102081 name: homotaurine:2-oxoglutarate aminotransferase activity def: "Catalysis of the reaction: homotaurine + 2-oxoglutarate(2-) = 3-sulfopropanal + L-glutamate(1-)." [EC:2.6.1.-, GOC:pz] xref: MetaCyc:RXN-10822 is_a: GO:0008483 ! transaminase activity

None of these are in RHEA or have any GO annotations => obsolete these 4 GO terms

GO:0035885 and GO:0008843 are fixed

id: GO:0102224 name: GDP-2,4-diacetamido-2,4,6-trideoxy-alpha-D-glucopyranose hydrolase/2-epimerase activity def: "Catalysis of the reaction: GDP-2,4-diacetamido-2,4,6-trideoxy-alpha-D-glucopyranose + H2O = 2,4-diacetamido-2,4,6-trideoxy-alpha-D-mannopyranose + GDP + H+." [EC:3.2.1.-, GOC:pz] xref: MetaCyc:RXN-12236 xref: RHEA:46316 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

=> change def xref to use RHEA => add EC:3.2.1.184 as broadMatch

id: GO:0102509 name: cyanidin 3,5-diglucoside glucosidase activity def: "Catalysis of the reaction: cyanin betaine + H2O = cyanidin 3-O-beta-D-glucoside betaine + beta-D-glucose." [EC:3.2.1.-, GOC:pz] xref: MetaCyc:RXN-14436 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

Not in RHEA, no GO annotations, no precise EC mapping => obsolete

id: GO:0102508 name: cyanidin 3,7-diglucoside glucosidase activity def: "Catalysis of the reaction: cyanidin 3,7-di-O-beta-D-glucoside betaine + H2O = cyanidin 3-O-beta-D-glucoside betaine + beta-D-glucose." [EC:3.2.1.-, GOC:pz] xref: MetaCyc:RXN-14435 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

Not in RHEA, no GO annotations, no precise EC mapping => obsolete

id: GO:0102413 name: 6-O-methyl-deacetylisoipecoside beta-glucosidase activity def: "Catalysis of the reaction: 6-O-methyl-N-deacetylisoipecoside + H2O = 6-O-methyl-N-deacetylisoipecoside aglycon + beta-D-glucose." [EC:3.2.1.-, GOC:pz] xref: MetaCyc:RXN-13791 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

=> add RHEA:78891 xref, and use for def xref

id: GO:0016803 name: ether hydrolase activity def: "Catalysis of the hydrolysis of an ether bond, -O-." [EC:3.3.2.-, GOC:ai] xref: EC:3.3.2.- is_a: GO:0016801 ! hydrolase activity, acting on ether bonds

id: GO:0102546 name: mannosylglycerate hydrolase activity def: "Catalysis of the reaction: H2O + 2-(alpha-D-mannosyl)-D-glycerate = alpha-D-mannose + D-glycerate." [EC:3.3.2.-, GOC:pz] xref: MetaCyc:RXN-14900 xref: RHEA:58456 is_a: GO:0016803 ! ether hydrolase activity

=> use RHEA as def xref => add EC:3.2.1.170 xref

id: GO:0102071 name: 9,10-epoxy-18-hydroxystearate hydrolase activity def: "Catalysis of the reaction: 9,10-epoxy-18-hydroxystearate + H2O = 9,10,18-trihydroxystearate." [EC:3.3.2.-, GOC:pz] xref: MetaCyc:RXN-1065 is_a: GO:0016803 ! ether hydrolase activity

Not in RHEA, no GO annotations, no precise EC mapping => obsolete

id: GO:0103005 name: 9,10-epoxystearate hydrolase activity def: "Catalysis of the reaction: 9,10-epoxystearate + H2O = (9R,10S)-dihydroxystearate." [EC:3.3.2.-, GOC:pz] xref: MetaCyc:RXN-9806 is_a: GO:0016803 ! ether hydrolase activity

Not in RHEA, no GO annotations, no precise EC mapping => obsolete

id: GO:0102547 name: glucosylglycerate hydrolase activity def: "Catalysis of the reaction: H2O + 2-O-(alpha-D-glucopyranosyl)-D-glycerate = alpha-D-glucose + D-glycerate." [EC:3.3.2.-, GOC:pz] xref: MetaCyc:RXN-14901 xref: RHEA:32059 is_a: GO:0016803 ! ether hydrolase activity

=> Use RHEA in def xref, add EC:3.2.1.208

id: GO:0102564 name: aurachin C epoxide hydrolase/isomerase activity def: "Catalysis of the reaction: aurachin C epoxide + H+ + NAD(P)H = aurachin B + H2O + NAD(P)." [EC:3.3.2.-, GOC:pz] xref: MetaCyc:RXN-15030 xref: RHEA:48728 is_a: GO:0016803 ! ether hydrolase activity

The GO/MetaCyc def doesn't quite match the RHEA def (3,4-dihydroxy-2-methyl-1-oxo-4-[(2E,6E)-farnesyl]-3,4-dihydroquinoline 1-oxide + NAD(+) = 4-hydroxy-2-methyl-3-oxo-[(2E,6E)-farnesyl]-3,4-dihydroquinoline 1-oxide + H(+) + NADH) here There are no GO/RHEA annotations, so suggest obsoletion

GO:0080131 has been fixed

id: GO:0102142 name: [dermatan sulfate]-L-iduronyl 2-Osulfotransferase activity def: "Catalysis of the reaction: 3'-phosphonato-5'-adenylyl sulfate + [dermatan]-alpha-L-iduronate = adenosine 3',5'-bismonophosphate + [dermatan-sulfate]-2-O-sulfo-alpha-L-iduronate." [EC:2.8.2.-, GOC:pz] xref: MetaCyc:RXN-11561 is_a: GO:0008146 ! sulfotransferase activity

Not in RHEA, no GO annotations, no precise EC mapping => obsolete

id: GO:0019111 name: phenanthrol sulfotransferase activity def: "Catalysis of the reaction: phenanthrol + X-SO3(-) = HX + phenanthrylsulfate." [EC:2.8.2.-] is_a: GO:0008146 ! sulfotransferase activity

=> obsolete (no xrefs, no annotations)

id: GO:0050698 name: proteoglycan sulfotransferase activity def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + proteoglycan = adenosine 3',5'-bisphosphate + proteoglycan sulfate. A proteoglycan is a glycoprotein whose carbohydrate units are glycosaminoglycans." [EC:2.8.2.-, GOC:ai] is_a: GO:0008146 ! sulfotransferase activity

=> remove EC from def

id: GO:0001537 name: N-acetylgalactosamine 4-O-sulfotransferase activity def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + N-acetyl-D-galactosamine = adenosine 3',5'-bisphosphate + N-acetyl-D-galactosamine 4-sulfate." [EC:2.8.2.-, GOC:ai] is_a: GO:0008146 ! sulfotransferase activity

=> no xrefs, but has 12 EXP annotations. Doesn't seem to be a matching reaction in RHEA/MetaCyc => remove EC as def xref

id: GO:0103104 name: 6-methylthiohexyldesulfoglucosinolate sulfotransferase activity def: "Catalysis of the reaction: 6-methylthiohexyldesulfoglucosinolate + 3'-phosphonato-5'-adenylyl sulfate = adenosine 3',5'-bismonophosphate + H+ + 6-methylthiohexylglucosinolate." [EC:2.8.2.-, GOC:pz] xref: MetaCyc:RXNQT-4331 is_a: GO:0008146 ! sulfotransferase activity

MetaCyc:RXNQT-4331 is specific instance of 2.8.2.38 (MetaCycRXN-18179/RHEA:52724) which isn't in GO (Same applies to GO:0080068, GO:0080066, GO:0080070, GO:0080067, GO:0080069) => NTR for EC:2.8.2.38 and then merge these 6 GO terms into it.

id: GO:0102141 name: [chondroitin sulfate]-D-glucuronyl 2-O-sulfotransferase activity def: "Catalysis of the reaction: 3'-phosphonato-5'-adenylyl sulfate + [chondroitin-sulfate]-beta-D-glucuronate = adenosine 3',5'-bismonophosphate + [chondroitin-sulfate]-2-O-sulfo-beta-D-glucuronate." [EC:2.8.2.-, GOC:pz] xref: MetaCyc:RXN-11560 is_a: GO:0008146 ! sulfotransferase activity

Not in RHEA, no GO annotations, no precise EC mapping => obsolete

GO:0102760 is already fixed GO:0016705 is the grouping term for EC:1.14.-.- so correctly has that as def xref

id: GO:0102123 name: gibberellin A4 16alpha,17 epoxidase activity def: "Catalysis of the reaction: gibberellin A4 + O2 + H+ + NAD(P)H = 16alpha,17-epoxy gibberellin A4 + H2O + NAD(P)." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-11385 is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

id: GO:0102124 name: gibberellin A12 16alpha,17 epoxidase activity def: "Catalysis of the reaction: gibberellin A12 + O2 + H+ + NAD(P)H = 16alpha, 17-epoxy gibberellin A12 + H2O + NAD(P)." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-11387 is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

id: GO:0102730 name: cathasterone hydroxylase activity def: "Catalysis of the reaction: cathasterone + O2 + a reduced electron acceptor = teasterone + H2O + an oxidized electron acceptor." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-716 is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

id: GO:0102371 name: betulin dehydrogenase activity def: "Catalysis of the reaction: betulin + NADPH(4-) + H+ + O2 = betulinic aldehyde + NADP(3-) + 2 H2O." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-13498 is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

id: GO:0102125 name: gibberellin A9 16alpha,17 epoxidase activity def: "Catalysis of the reaction: gibberellin A9 + O2 + H+ + NAD(P)H = 16alpha, 17-epoxy gibberellin A9 + H2O + NAD(P)." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-11388 is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

id: GO:0102764 name: 6-deoxotyphasterol C-23 hydroxylase activity def: "Catalysis of the reaction: 6-deoxotyphasterol + O2 + a reduced electron acceptor = 6-deoxocastasterone + H2O + an oxidized electron acceptor." [EC:1.14.-.-, GOC:pz] xref: MetaCyc:RXN-777 is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

=> none of these 6 GO terms have any annotations, propose obsoletion

GO:0102085, GO:0102087, GO:0102086 and GO:0102088 already fixed GO:0016879 is the grouping term, so correctly has EC:6.3.-.- def xref These others just have a MetaCyc term xref and non annotations, so can be obsoleted:| GO:0102052, GO:0102950, GO:0102951, GO:0102050, GO:0102665, GO:0102664, GO:0102051

GO:0016838 is the EC:4.2.3.- grouping term, so correctly has EC:4.2.3.- def xref

GO:0010333 is a grouping term: id: GO:0010333 name: terpene synthase activity def: "Catalysis of the formation of cyclic terpenes through the cyclization of linear terpenes (e.g. isopentenyl-PP, geranyl-PP, farnesyl-PP and geranylgeranyl-PP) containing varying numbers of isoprene units." [EC:4.2.3.-, GOC:tair_curators] is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates => remove EC from def

GO:0010334 is a grouping term: id: GO:0010334 name: sesquiterpene synthase activity def: "Catalysis of the reaction: trans,trans-farnesyl diphosphate = a sesquiterpene + diphosphate. Sesquiterpenes are terpenes containing three isoprene units, i.e. 15 carbons." [EC:4.2.3.-, GOC:tair_curators] is_a: GO:0010333 ! terpene synthase activity => remove EC from def

GO:0102889 has 4 annotations id: GO:0102889 name: beta-elemene synthase activity def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate = beta-elemene + diphosphoric acid." [EC:4.2.3.-, GOC:pz] xref: MetaCyc:RXN-8432 is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates => use MetaCyc ID as def xref

GO:0102700 has 2 annotations id: GO:0102700 name: alpha-thujene synthase activity def: "Catalysis of the reaction: geranyl diphosphate(3-) = alpha-thujene + diphosphoric acid." [EC:4.2.3.-, GOC:pz] xref: MetaCyc:RXN-5105 is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates => use MetaCyc ID as def xref

These others just have a MetaCyc term xref and no annotations, so can be obsoleted: GO:0102907, GO:0102063, GO:0102385, GO:0102888, GO:0102065, GO:0102880, GO:0102066, GO:0102356, GO:0102886

GO:0102111 - 23 annotations id: GO:0102111 name: gibberellin A20,2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A20 + 2-oxoglutarate + O2 = gibberellin A29 + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN-113 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc says this is version of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity) -> merge

GO:0102924 - 23 annotations id: GO:0102924 name: gibberellin A44,2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: 2 H+ + gibberellin A44 + 2-oxoglutarate + O2 = gibberellin A98 + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN-886 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc says this is version of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity) -> merge

GO:0102652 - 23 annotations id: GO:0102652 name: gibberellin A9,2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A9 + 2-oxoglutarate + O2 = gibberellin A51 + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN-171 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc says this is version of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity) -> merge

GO:0103055 - 2 annotations id: GO:0103055 name: gibberelli A15, 2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A15 + 2-oxoglutarate + O2 = gibberellin A24 + succinate + carbon dioxide + H2O." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN1F-163 xref: RHEA:60780 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc just maps this to EC:1.14.11.- but it looks like another instance of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity) -> merge

GO:0103054 - 2 annotations id: GO:0103054 name: gibberellin A12, 2-oxoglutarate:oxygen oxidoreductase activity (gibberellin A15-forming) def: "Catalysis of the reaction: gibberellin A12 + O2 + 2-oxoglutarate = gibberellin A15 + carbon dioxide + succinate." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN1F-162 xref: RHEA:60776 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc just maps this to EC:1.14.11.- but it looks like another instance of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity) -> merge

GO:0103056 - 2 annotations id: GO:0103056 name: gibberellin A53, 2-oxoglutarate:oxygen oxidoreductase activity def: "Catalysis of the reaction: gibberellin A53 + O2 + 2-oxoglutarate = gibberellin A44 diacid + carbon dioxide + succinate." [EC:1.14.11.-, GOC:pz] xref: MetaCyc:RXN1F-167 xref: RHEA:60800 is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity => MetaCyc just maps this to EC:1.14.11.- but it looks like another instance of EC:1.14.11.13 (GO:0045543 gibberellin 2-beta-dioxygenase activity) -> merge

These others just have a MetaCyc term xref and no annotations, so can be obsoleted: GO:0102663, GO:0102569, GO:0102712, GO:0102495, GO:0102715, GO:0103008, GO:0102716, GO:0102496, GO:0102768, GO:0102972, GO:0102713, GO:0102714, GO:0103010, GO:0102653, GO:0102711, GO:0102494, GO:0103057, GO:0102755

GO:0102215 - 3 annotations id: GO:0102215 name: thiocyanate methyltransferase activity def: "Catalysis of the reaction: thiocyanate + S-adenosyl-L-methionine = methyl thiocyanate + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz] xref: MetaCyc:RXN-12189 xref: RHEA:28014 is_a: GO:0008168 ! methyltransferase activity => use RHEA as def xref, add EC:2.1.1.n4 as xref

GO:0016435 - 100,000+ annotations id: GO:0016435 name: rRNA (guanine) methyltransferase activity def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylguanine." [EC:2.1.1.-] is_a: GO:0008649 ! rRNA methyltransferase activity => change def xref to GOC:curators

GO:0102913 - 1 annotation id: GO:0102913 name: 3-aminomethylindole N-methyltransferase activity def: "Catalysis of the reaction: indol-3-ylmethylamine + S-adenosyl-L-methionine = H+ + N-methyl-3-aminomethylindole + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz] xref: MetaCyc:RXN-8686 xref: RHEA:52268 is_a: GO:0008168 ! methyltransferase activity => use RHEA as def xref

GO:0102990 - 1 annotation id: GO:0102990 name: 5-n-alk(en)ylresorcinol O-methyltransferase activity def: "Catalysis of the reaction: 5-(pentadeca-8,11,14-trien-1-yl)resorcinol + S-adenosyl-L-methionine = H+ + 5-(pentadeca-8,11,14-trien-1-yl)resorcinol monomethyl ether + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz] xref: MetaCyc:RXN-9619 xref: RHEA:26325 is_a: GO:0008168 ! methyltransferase activity => use RHEA as def xref, add EC:2.1.1.n7 as xref

GO:0102168 - 2 annotations id: GO:0102168 name: 5-methyl-phenazine-1-carboxylate N-methyltransferase activity def: "Catalysis of the reaction: phenazine-1-carboxylate + S-adenosyl-L-methionine = 5-methylphenazine-1-carboxylate + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz] xref: MetaCyc:RXN-11897 xref: RHEA:49112 is_a: GO:0008168 ! methyltransferase activity => use RHEA as def xref, add EC:2.1.1.327 as xref

GO:0102964 - 1 annotation id: GO:0102964 name: S-adenosyl-L-methionine:(S)-corytuberine-N-methyltransferase activity def: "Catalysis of the reaction: (S)-corytuberine + S-adenosyl-L-methionine = H+ + magnoflorine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz] xref: MetaCyc:RXN-9315 xref: RHEA:51524 is_a: GO:0008168 ! methyltransferase activity => use RHEA as def xref, add EC:2.1.1.337 as broadMatch as xref

These others just have a MetaCyc term xref (a couple also have a RHEA) and no GO annotations, so can be obsoleted: GO:0102528, GO:0102941, GO:0102914, GO:0102603, GO:0102708, GO:0102147, GO:0102820, GO:0102122, GO:0102119, GO:0102438, GO:0102608, GO:0102399, GO:0102631, GO:0102630, GO:0102398, GO:0102709, GO:0102400, GO:0102942, GO:0102363, GO:0102939, GO:0102821, GO:0102436, GO:0102940, GO:0102629

GO:0016747 is correct grouping term for EC:2.3.1.-, so correctly has EC:2.3.1.- xref

GO:0102104 - already fixed

GO:0102922 - 1 annotation id: GO:0102922 name: phenylpropanoyltransferase activity def: "Catalysis of the reaction: baccatin III + (3R)-3-amino-3-phenylpropanoyl-CoA = N-debenzoyl-(3'-RS)-2'-deoxytaxol + coenzyme A." [EC:2.3.1.-, GOC:pz] xref: MetaCyc:RXN-8857 xref: RHEA:42488 is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups => use RHEA as def xref

GO:0102923 - 10,000+ annotations id: GO:0102923 name: 3'-N-debenzoyl-2'-deoxytaxol N-benzoyltransferase activity def: "Catalysis of the reaction: 3'-N-debenzoyltaxol + benzoyl-CoA = H+ + paclitaxel + coenzyme A." [EC:2.3.1.-, GOC:pz] xref: MetaCyc:RXN-8859 xref: RHEA:33687 is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups => This only has 1 direct annotation, so use the RHEA as def xref => other annotations seem to be because of an incorrect child of GO:0033812 3-oxoadipyl-CoA thiolase activity (EC:2.3.1.174) (which should instead have GO:0003988 acetyl-CoA C-acyltransferase activity as its parent following RHEA hierarchy) -> see #28845

These others just have a MetaCyc term xref and no GO annotations, so can be obsoleted: GO:0102301, GO:0102583, GO:0102775, GO:0102247, GO:0102589, GO:0102817, GO:0102287, GO:0102737, GO:0102989, GO:0102093, GO:0102814, GO:0102594, GO:0102330, GO:0102595, GO:0102649, GO:0102586, GO:0102774, GO:0102248, GO:0102591, GO:0102806, GO:0102592, GO:0102660, GO:0102812, GO:0102581, GO:0102787, GO:0102333, GO:0102286, GO:0102788, GO:0102295, GO:0102275, GO:0102331, GO:0102332, GO:0102800

GO:0016709 is EC:1.14.13.- grouping term so correctly has EC:1.14.13.- def xref

GO:0102780, GO:0102677, GO:0102367, GO:0102366, GO:0102759 - already fixed

GO:0102627 - 1 annotation id: GO:0102627 name: parthenolide 3beta-hydroxylase activity def: "Catalysis of the reaction: parthenolide + NADPH + O2 + H+ = 3beta-hydroxyparthenolide + NADP + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-15532 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 => add RHEA:61328 as xref and update def

GO:0102517 - 1 annotation id: GO:0102517 name: oleate 12-hydroxylase activity def: "Catalysis of the reaction: oleoyl-CoA + NADH + O2 + H+ = ricinoleyl-CoA + NAD + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-14487 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 => MetaCyc says this is version of EC:1.14.18.4 = GO:0050183 => merge with that term

GO:0102469 - 2 annotations id: GO:0102469 name: naringenin 2-hydroxylase activity def: "Catalysis of the reaction: (S)-naringenin + NADPH + O2 = 2-hydroxynaringenin + NADP + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-14069 xref: RHEA:57588 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 => use RHEA as def xref

GO:0102614 - 3 annotations id: GO:0102614 name: germacrene A acid 8beta-hydroxylase activity def: "Catalysis of the reaction: germacra-1(10),4,11(13)-trien-12-oate + NADPH + O2 + H+ = 8beta-hydroxy-germacra-1(10),4,11(13)-trien-12-oate + NADP + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-15460 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 => MetaCyc says this is EC:1.14.14.168 = RHEA:57964 => add xrefs and use RHEA as def xref; change parent to match EC classification

GO:0102171 - 2 annotations id: GO:0102171 name: DMNT synthase activity def: "Catalysis of the reaction: H+ + (3S,6E)-nerolidol + NADPH + O2 = (E)-4,8-dimethyl-1,3,7-nonatriene + buten-2-one + NADP + 2 H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-11911 xref: RHEA:55424 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 => use RHEA as def xref, add EC:1.14.14.59 xref; change parent to match EC classification

GO:0102628 - 1 annotation id: GO:0102628 name: costunolide 3beta-hydroxylase activity def: "Catalysis of the reaction: costunolide + NADPH + O2 + H+ = 3beta-hydroxycostunolide + NADP + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-15533 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 => use MetaCyc as def xref

GO:0103096 - 1 annotation id: GO:0103096 name: CYP79F1 dihomomethionine monooxygenase activity def: "Catalysis of the reaction: dihomomethionine + 2 O2 + 2 NADPH + 2 H+ = 5-methylthiopentanaldoxime + 3 H2O + carbon dioxide + 2 NADP." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXNQT-4309 xref: RHEA:32719 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 => make new term to match EC:1.14.14.42 and merge into that (also GO:0103098)

GO:0103097 - 1 annotation id: GO:0103097 name: CYP79F1 trihomomethionine monooxygenase activity def: "Catalysis of the reaction: trihomomethionine + 2 O2 + 2 NADPH + 2 H+ = 3 H2O + carbon dioxide + 2 NADP + 6-methylthiohexanaldoxime." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXNQT-4310 xref: RHEA:32723 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 => make new term to match EC:1.14.14.42 and merge into that (also GO:0103098)

GO:0102472 - 1 annotation id: GO:0102472 name: eriodictyol 2-hydroxylase activity def: "Catalysis of the reaction: eriodictyol + NADPH + O2 + 2 H+ = 2-hydroxyeriodictyol + NADP + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-14077 xref: RHEA:57596 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 => specific substrate of EC:1.14.14.162 => merge into flavanone 2-hydroxylase GO:0033771

GO:0102626 - 1 annotation id: GO:0102626 name: parthenolide synthase activity def: "Catalysis of the reaction: costunolide + NADPH + O2 + H+ = parthenolide + NADP(3-) + H2O." [EC:1.14.13.-, GOC:pz] xref: MetaCyc:RXN-15531 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 => add RHEA:61320 and use as def xref

These others just have a MetaCyc term xref (and sometimes a RHEA xref) but have 0 GO annotations, so can be obsoleted: GO:0102898, GO:0102599, GO:0102897, GO:0102181, GO:0102370, GO:0102901, GO:0102368, GO:0102178, GO:0102902, GO:0102633, GO:0102606, GO:0102781, GO:0102427, GO:0103009, GO:0102639, GO:0102743, GO:0102899, GO:0102620, GO:0102372, GO:0102605, GO:0102152, GO:0102173, GO:0102680, GO:0102563, GO:0102376, GO:0102640, GO:0102602, GO:0102179, GO:0102292, GO:0102607, GO:0102600, GO:0102615, GO:0103098, GO:0102900, GO:0102133, GO:0102621, GO:0102476, GO:0102782, GO:0102466, GO:0102699, GO:0102992, GO:0102174

sjm41 commented 1 month ago

+[Term] +id: GO:0120526 +name: homomethionine N-monooxygenase activity +namespace: molecular_function +def: "Catalysis of the reaction: an L-polyhomomethionine + 2 O2 + 2 reduced [NADPH--hemoprotein reductase] = an (E)-omega-(methylsulfanyl)-alkanal oxime + CO2 + 2 H(+) + 3 H2O + 2 oxidized [NADPH--hemoprotein reductase]." [RHEA:51972] +xref: EC:1.14.14.42 {source="skos:exactMatch"} +xref: KEGG_REACTION:R11646 {source="skos:exactMatch"} +xref: MetaCyc:RXN-18175 {source="skos:exactMatch"} +xref: RHEA:51972 {source="skos:exactMatch"} +is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI +created_by: sjm +creation_date: 2024-09-05T07:47:05Z +

+[Term] +id: GO:0120527 +name: aliphatic desulfoglucosinolate sulfotransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + an aliphatic (Z)-desulfo-glucosinolate = a (Z)-omega-(methylsulfanyl)-N-sulfo-alkylhydroximate S-glucoside + adenosine 3',5'-bisphosphate + H+." [RHEA:52724] +xref: EC:2.8.2.38 {source="skos:exactMatch"} +xref: MetaCyc:RXN-18179 {source="skos:exactMatch"} +xref: RHEA:52724 {source="skos:exactMatch"} +is_a: GO:0008146 ! sulfotransferase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI +created_by: sjm +creation_date: 2024-09-05T07:53:33Z

+[Term] +id: GO:0120528 +name: 2-(omega-methylthio)alkylmalate dehydratase activity +namespace: molecular_function +def: "Catalysis of the reactions: a 2-(omega-methylsulfanyl)alkylmalate = a 2-(omega-methylsulfanyl)alkylmaleate + H2O and a 3-(omega-methylsulfanyl)alkylmalate = a 2-(omega-methylsulfanyl)alkylmaleate + H2O." [EC:4.2.1.170] +xref: EC:4.2.1.170 {source="skos:exactMatch"} +xref: RHEA:50632 {source="skos:narrowMatch"} +xref: RHEA:50636 {source="skos:narrowMatch"} +is_a: GO:0016836 ! hydro-lyase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI +created_by: sjm +creation_date: 2024-09-05T08:00:08Z

+[Term] +id: GO:0120529 +name: secoisolariciresinol dehydrogenase activity +namespace: molecular_function +def: "Catalysis of the reaction: (-)-secoisolariciresinol + 2 NAD+ = (-)-matairesinol + 2 H(+) + 2 NADH." [RHEA:33887] +xref: EC:1.1.1.331 {source="skos:exactMatch"} +xref: KEGG_REACTION:R10129 {source="skos:exactMatch"} +xref: MetaCyc:RXN-13433 {source="skos:exactMatch"} +xref: RHEA:33887 {source="skos:exactMatch"} +is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI +created_by: sjm +creation_date: 2024-09-05T08:19:32Z +

sjm41 commented 1 month ago

Of the 61 reported cases where the same xref is used as the def xref on multiple GO terms, 1 had already been addressed and 19 can be fixed just by adding/correcting the xref - I have fixed all these.

The remaining 41 cases require merges or obsoletions. (Several also involve GO terms requiring xref edits - I have fixed these and noted them above.)

I'll make separate tickets for each proposed merge. I'll also make separate tickets for each obsoletion that requires explanation/discussion.

I'll also make a separate, single ticket proposing bulk obsoletion of ~200 term that can be obsoleted without further review - they have 0 annotations and have a single xref to a MetaCyc ID (a few also have a RHEA xref, but there are no RHEA annotations). = #28848