Fix EC to one-to-one-xrefs-by-value-violation

pgaudet commented 1 month ago

See PR here: https://github.com/geneontology/go-ontology/pull/26235

I made a spreadsheet here: https://docs.google.com/spreadsheets/d/17QvDQoIXe-Rim9ReReVlZGntr-WkIGJ0cbPhaQDB_As/edit#gid=0

pgaudet commented 1 month ago

[x] EC:1.1.1.117 | GO:0106271 | GO:0045290: removed EC from GO:0106271 since EC not specific for NAD/NADP
[x] EC:1.1.1.146 | GO:0070524 | GO:0102196: removed EC from GO:0102196 (too broad); added parent GO:0070524 ! 11-beta-hydroxysteroid dehydrogenase (NADP+) activity to match RHEA 'more general' reaction
[x] EC:1.1.1.188 | GO:0047017 | GO:0036131: Removed EC from GO:0036131; EC seems non-directional but RHEA only maps to the 'synthase' direction
[x] EC:1.1.1.195 | GO:0045551 | GO:0052747: +xref: RHEA:10392 : added {source="skos:narrowMatch"} +xref: RHEA:45704 {source="skos:narrowMatch"} +xref: RHEA:45724 {source="skos:narrowMatch"}
GO:0050268 coniferyl-alcohol dehydrogenase activity: change def xref to RHEA:22444
Obsolete GO:0052747 sinapyl alcohol dehydrogenase activity (only IEA annotations) + replace by GO:0045551 cinnamyl-alcohol dehydrogenase activity
EC:1.14.11.13 | GO:0052634 | GO:0045543: remove EC from GO:0052634 as this is a mre specific reaction. Kept activities because some plant enzymes seem to be specific for C-19 gibberellin versus C-20 gibberellin (see PMID:12509528)

pgaudet commented 1 month ago

[x] EC:1.1.1.237 | GO:0102742 | GO:0047995: GO:0102742 R(+)-3,4-dihydroxyphenyllactate:NADP+ oxidoreductase activity >> replace by GO:0047995 hydroxyphenylpyruvate reductase activity; because GO:0102742 represents a specific substrate. No manual annotations
[x] EC:1.1.1.303 | GO:0052587 | GO:0019152 >> removed EC from grouping class GO:0019152; should only have been on child GO:0052587
[x] EC:1.1.1.304 | GO:0052588 | GO:0019152 >> removed EC from grouping class GO:0019152; should only have been on child GO:0052588
[x] GO:1990137 plant seed peroxidase activity: fixed term label and def to match EC:1.11.2.3

pgaudet commented 1 month ago

[x] GO:0000140 acylglycerone-phosphate reductase activity
changed label to acylglycerone-phosphate reductase (NADP+) activity
fixed xref scope: xref: RHEA:17341 {source="skos:exactMatch"}
added xref: RHEA:36175 {source="skos:narrowMatch"}
[x] GO:0018529 nitrilotriacetate monooxygenase activity -fixed def from "Catalysis of the reaction: nitrilotriacetate + NADH + H+ + O2 = NAD+ + H2O + glyoxylate + iminodiacetate." [UM-
new def: "Catalysis of the reaction: nitrilotriacetate + FMNH2 + O2 = aminodiacetate + FMN + glyoxylate + H2O." [RHEA:31359]
added xref type +xref: EC:1.14.14.10 {source="skos:exactMatch"}
added xref: KEGG_REACTION:R09798
added xref: MetaCyc:RXN-9508
added xref: RHEA:31359 {source="skos:exactMatch"}
removed is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
added 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
[x] GO:0102136 '3-epi-6-deoxocathasterone C-23 hydroxylase activity': change parent from 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 to 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
[x] GO:0052869 arachidonic acid omega-hydroxylase activity:
remove EC:1.14.15.3; add RHEA:3975 and MetaCyc:RXN-19677
change parent to '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'
[x] GO:0050183 phosphatidylcholine 12-monooxygenase activity
fix def to match RHEA: from def: "Catalysis of the reaction: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine + H+ + NADH + O2 = 1-acyl-2-[(S)-12-hydroxyoleoyl]-sn-glycero-3-phosphocholine + H2O + NAD+." [RHEA:46360] new def: "Catalysis of the reaction: 1-acyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphocholine + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = 1-acyl-2-[(R)-12-hydroxyoleoyl]-sn-glycero-3-phosphocholine + 2 Fe(III)-[cytochrome b5] + H2O." [RHEA:46360]
fix parent from 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 to GO:0016716 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen

pgaudet commented 1 month ago

[x] EC:7.4.2.1 | GO:0015599 | GO:0015426: Removed EC from GO:0015599 ATPase-coupled L-glutamine transmembrane transporter activity; added RHEA:29895
[x] GO:0102013 ATPase-coupled L-glutamate tranmembrane transporter activity: Removed EC; added RHEA:29035

pgaudet commented 1 month ago

Dear all,

The proposal has been made to obsolete the following terms, with replacements:

-GO:0102742 R(+)-3,4-dihydroxyphenyllactate:NADP+ oxidoreductase activity >> replace by GO:0047995 hydroxyphenylpyruvate reductase activity; because GO:0102742 represents a specific substrate. No manual annotations

GO:0046563 methanol oxidase activity: EC was retired. No annotations
GO:0052589 malate dehydrogenase (menaquinone) activity (RHEA:30095): replace by GO:0008924 malate dehydrogenase (quinone) activity
GO:0102070 18-hydroxyoleate peroxygenase activity & replace by GO:1990137 plant seed peroxidase activity because GO:0102070 represents a specific substrate. No manual annotations
GO:0102300 linoleate 9R-lipoxygenase activity & replace by GO:0102299 linolenate 9R-lipoxygenase activity because GO:0102300 represents a specific substrate. No annotations
GO:0052860 2'-deoxymugineic-acid 3-dioxygenase activity & replace by GO:0033761 'mugineic-acid 3-dioxygenase activity' (enzyme has 2 substrates). No annotations
GO:0102804 oripavine 6-O-demethylase activity & replace by GO:0102802 thebaine 6-O-demethylase activity (enzyme has 2 substrates). No annotations
GO:0102566 1-acyl dihydroxyacetone phosphate reductase activity & replace by GO:0000140 acylglycerone-phosphate reductase activity because GO:0102566 represents a specific substrate. No manual annotations
GO:0102803 thebane O-demethylase activity & replace by GO:0102805 codeine O-demethylase activity because GO:0102803 represents a specific substrate. No annotations
GO:0106317 methane monooxygenase NADH activity and GO:0106318 methane monooxygenase NADPH activity into GO:0015049 methane monooxygenase activity; enzyme is not specific for NAD or NADP. No annotations
GO:0102321 2,2'-hydroxybiphenyl monooxygenase activity & replace by GO:0047544 2-hydroxybiphenyl 3-monooxygenase activity because GO:0047544 represents a specific substrate. No annotations
GO:0102977 nitrilotriacetate monooxygenase activity (FMN-dependent) & replace by GO:0018529 nitrilotriacetate monooxygenase activity. No annotations
GO:0102374 ursolic aldehyde 28-monooxygenase activity & replace by GO:0102373 uvaol dehydrogenase activity & change label to match EC: beta-amyrin 28-monooxygenase activity. No annotations
GO:0102136 3-epi-6-deoxocathasterone C-23 hydroxylase activity & replace by GO:0102097 (22S)-22-hydroxy-5alpha-campestan-3-one C-23 hydroxylase activity because GO:0102136 represents a specific substrate. No manual annotations
GO:0102290 beta-amyrin monooxygenase activity and GO:0102291 11alpha-hydroxy-beta-amyrin dehydrogenase activity & replace by GO:0102289 beta-amyrin 11-oxidase activity. These are sub-reactions of GO:0102289. No annotations.
GO:0047092 27-hydroxycholesterol 7-alpha-monooxygenase activity into GO:0033783 25-hydroxycholesterol 7alpha-hydroxylase activity because GO:0047092 represents a specific substrate. No annotations.
GO:0052616 ent-kaur-16-en-19-ol oxidase activity and GO:0052617 ent-kaur-16-en-19-al oxidase activity & replace by GO:0052615 ent-kaurene oxidase activity because these are subreactions. No manual annotations.
GO:0047103 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity and GO:0047749 cholestanetriol 26-monooxygenase activity & replace by GO:0047748 cholestanetetraol 26-dehydrogenase activity (subreactions) - 1 EXP UniProt, will be automatically replaced.
GO:0102518 (11Z)-eicosenoate 14-hydroxylase activity & replace by GO:0050183 phosphatidylcholine 12-monooxygenase activity - specific substrate

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/28070

Thanks, Pascale

pgaudet commented 1 month ago

[x] Obsolete GO:0102858 1-18:2-2-18:3-phosphatidylcholine desaturase activity](http://purl.obolibrary.org/obo/) : removed from MetaCyc (only source for the term)

pgaudet commented 3 weeks ago

[x] GO:0050184 phosphatidylcholine desaturase activity
fixed label to align with EC: acyl-lipid omega-6 desaturase (cytochrome b5) activity
fixed reaction to align with RHEA: "Catalysis of the reaction: a (9Z)-octadecenoyl-containing glycerolipid + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = a (9Z,12Z)-octadecadienoyl-containing glycerolipid + 2 Fe(III)-[cytochrome b5] + 2 H2O." [RHEA:46332]
change rhea xref type to exact
added MetaCyc:RXN-9669 exactMatch (was missing)
- [x] delta7-sterol 5(6)-desaturase activity:
- changed RHEA to the more general parent (that actually corresponds to the GO reaction: from RHEA:46556 to RHEA:54320
- and MetaCyc from MetaCyc:1.14.21.6-RXN to MetaCyc:RXN-16378
- [x] Removed EC:1.18.1.4 from GO:0015046 rubredoxin-NADP+ reductase activity
- [x] Removed EC:1.3.1.24 from GO:0106277 'biliverdin reductase (NADP+) activity' and GO:0106276 'biliberdin reductase (NAD+) activity'
- [x] GO:0052889 9,9'-di-cis-zeta-carotene desaturation to 7,9,7',9'-tetra-cis-lycopene (BP): remove EC, MetaCyc Rxn xrefs , add MetaCyc:PWY-6475
- [x] Removed xef for GO:0004486; grouping class, no EC, no RHEA
- [x] Remove EC on 'GO:0019116 hydroxy-nicotine oxidase activity' >> grouping class for R and S-hydroxy-nicotine
[ ] GO:0102988: 9,12-cis-hexadecadienoic acid delta 15 desaturase activity: added EC:1.14.19.13. Not sure whether the RHEA should be RHEA:46232 or RHEA:37599? seems like the acceptor is ferrichrome (see RHEA query spreadsheet

pgaudet commented 3 weeks ago

Obsoletions 2024-06-18:

GO:0102853 1-18:1-2-18:1-sn-glycerol-3-phosphocholine desaturase activity & replace by GO:0050184 phosphatidylcholine desaturase activity because GO:0102853 represents a specific substrate. No annotations.
GO:0102851 1-18:2-2-16:0-phosphatidylglycerol desaturase activity & replace by GO:0102654 palmitoyl-[glycerolipid] 3-(E)-desaturase activity because GO:0102851 represents a specific substrate. No annotations.
GO:0102656 1-18:2-2-trans-16:1-phosphatidylglycerol desaturase activity: replace by GO:0102993 sn-2 acyl-lipid omega-3 desaturase (ferredoxin) activity because GO:0102656 represents a specific substrate. No annotations.
GO:0102845 1-18:3-2-16:0-monogalactosyldiacylglycerol desaturase activity & replace by GO:0102654 palmitoyl-[glycerolipid] 3-(E)-desaturase activity because GO:0102845 represents a specific substrate. No annotations.
GO:0102852 1-18:3-2-16:0-phosphatidylglycerol desaturase activity : replace by GO:0102654 palmitoyl-[glycerolipid] 3-(E)-desaturase activity because GO:0102852 represents a specific substrate. No annotations.
GO:0102846 1-18:3-2-16:1-monogalactosyldiacylglycerol desaturase activity: replace by GO:0102850 acyl-lipid (n+3)-(Z)-desaturase (ferredoxin) activity because GO:0102846 represents a specific substrate. No annotations.
GO:0102847 1-18:3-2-16:2-monogalactosyldiacylglycerol desaturase activity: replace by GO:0102993 sn-2 acyl-lipid omega-3 desaturase (ferredoxin) activity because GO:0102847 represents a specific substrate. No annotations.
GO:0102863 1-18:3-2-18:1-phosphatidylcholine desaturase activity : replace by GO:0050184 acyl-lipid omega-6 desaturase (cytochrome b5) activity because GO:0102863 represents a specific substrate. No annotations.
GO:0102864 1-18:3-2-18:2-phosphatidylcholine desaturase activity: replace by GO:0102859 acyl-lipid omega-3 desaturase (cytochrome b5) activity because GO:0102864 represents a specific substrate. No annotations.
GO:0102676 avenasterol-desaturase activity : replace by GO:0050046 delta7-sterol 5(6)-desaturase activity because GO:0102676 represents a specific substrate. No annotations.
GO:0102916 sesamin synthase activity: replaced by GO:0102915 piperitol synthase activity because GO:0102916 represents a specific substrate. No annotations.
GO:0102987 palmitoleic acid delta 12 desaturase activity: replace by GO:0102985 delta12-fatty-acid desaturase activity because GO:0102987 represents a specific substrate. 1 annotation (UniProt; removed, many other MFs)
GO:0018697 carbonyl sulfide nitrogenase activity: replace by GO:0016163 nitrogenase activity because GO:0018697 represents a specific substrate. No annotations.
GO:0102794 cinnamaldehyde:oxygen oxidoreductase activity: replace by GO:0018488 aryl-aldehyde oxidase activity because GO:0102794 represents a specific substrate. No annotations.
GO:0102796 protocatechualdehyde:oxygen oxidoreductase activity: replace by GO:0018488 aryl-aldehyde oxidase activity because GO:0102796 represents a specific substrate. No annotations.
GO:0102795 1-naphthaldehyde:oxygen oxidoreductase activity: replace by GO:0018488 aryl-aldehyde oxidase activity because GO:0102795 represents a specific substrate. No annotations.
GO:0102791 sulfuretin synthase activity: replace by GO:0033793 aureusidin synthase activity because GO:0102791 represents a specific substrate. No annotations.
GO:0102706 butein:oxygen oxidoreductase activity: replace by GO:0033793 aureusidin synthase activity because GO:0102706 represents a specific substrate. No annotations.
GO:0052886 9,9'-dicis-carotene:quinone oxidoreductase activity: replace by GO:0016719 9,9'-di-cis-zeta-carotene desaturase activity (sub-reaction) - 1 TAIR annotation; also annotated to GO:0016719
GO:0052887 7,9,9'-tricis-neurosporene:quinone oxidoreductase activity: replace by GO:0016719 9,9'-di-cis-zeta-carotene desaturase activity (sub-reaction) - no manual annotations
GO:0044318 L-aspartate:fumarate oxidoreductase activity: replace by GO:0008734 L-aspartate oxidase activity: enzyme can use O2 or fumarate as acceptor under different conditions. 1 EcoCyc annotation, already annotated to GO:0008734. Also add RHEA:30043 (narrowMatch)
GO:0052600 propane-1,3-diamine oxidase activity: replace with GO:0052597 diamine oxidase activity because GO:0052600 represents a specific substrate
GO:0052599 methylputrescine oxidase activity: replace with GO:0052597 diamine oxidase activity because GO:0052600 represents a specific substrate
GO:0052808 reduced coenzyme F420:NADP+ oxidoreductase activity: replace by GO:0102261 8-hydroxy-5-deazaflavin:NADPH oxidoreductase activity: same reaction
GO:0018548 obsolete pentaerythritol trinitrate reductase activity: substrate more specific than any known enzyme. No annotations
GO:0050141 nitroethane oxidase activity: replace by parent GO:0052664 nitroalkane oxidase activity because GO:0050141 represents a specific substrate. Added RHEA:20976 and RHEA:26490 on GO:0052664.

Obsoletions 2024-06-25

GO:0102094 S-adenosylmethionine:2-demethylmenaquinol methyltransferase activity: replace by GO:0043770 demethylmenaquinone methyltransferase activity because GO:0102094 represents a specific substrate. No annotations.
GO:0102955 S-adenosylmethionine:2-demethylmenaquinol-7 methyltransferase activity: replace by GO:0043770 demethylmenaquinone methyltransferase activity because GO:0102955 represents a specific substrate. No annotations.
GO:0102027 S-adenosylmethionine:2-demethylquinol-8 methyltransferase activity: replace by GO:0043770 demethylmenaquinone methyltransferase activity because GO:0102955 represents a specific substrate. No annotations.
GO:0102308 erythromycin D 3''-o-methyltransferase activity >> replace by GO:0102307 erythromycin C 3''-o-methyltransferase activity & rename erythromycin 3''-o-methyltransferase activity; make EC exact and RHEA narrow. No annotations.
GO:0070448 laricitrin 5'-O-methyltransferase activity: replace by GO:0033799 myricetin 3'-O-methyltransferase activity and chage label to match EC, flavonoid 3',5'-methyltransferase. No annotations.
GO:0102918 (R)-reticuline 7-O-methyltransferase activity: replace by GO:0102917 (S)-reticuline 7-O-methyltransferase activity & rename as EC label, (R,S)-reticuline 7-O-methyltransferase activity; enzyme is non-stereo-specific. No annotations.
GO:0102707 S-adenosyl-L-methionine:beta-alanine N-methyltransferase activity: replace by GO:0030748 amine N-methyltransferase activity - same activity. No annotations
GO:0102090 adrenaline O-methyltransferase activity : replace by GO:0016206 catechol O-methyltransferase activity because GO:0102090 represents a specific substrate. No annotations.
GO:0080101 phosphatidyl-N-dimethylethanolamine N-methyltransferase activity: replace by GO:0000773 phosphatidyl-N-methylethanolamine N-methyltransferase activity because GO:0080101 represents a specific substrate. All annotations same.
GO:0102279 lecithin:11-cis retinol acyltransferase activity : replace by GO:0047173 phosphatidylcholine-retinol O-acyltransferase activity: represents the same reaction. No annotations.
GO:0102420 sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity: replace by GO:0004366 glycerol-3-phosphate O-acyltransferase activity
GO:0102815 caffeoyl-CoA:delphinidin-3,5-diglucoside 5-O-glucoside-6-O-hydroxycinnamoyltransferase activity: replace by GO:0047183 anthocyanin 5-aromatic acyltransferase activity: represents the same reaction. No annotations.
GO:0102777 caffeoyl-CoA:pelargonidin-3,5-diglucoside 5-O-glucoside-6-O-hydroxycinnamoyltransferase activity: replace by GO:0047183 anthocyanin 5-aromatic acyltransferase activity: represents the same reaction. No annotations.
GO:0102920: acyl coenzyme A: isopenicillin N acyltransferase activity: replace with GO:0050640 isopenicillin-N N-acyltransferase activity because GO:0102920 represents a specific substrate. No annotations.
GO:0102588 cyanidin 3-O-glucoside 6''-O-malonyltransferase activity : replace with GO:0033809 anthocyanin 6''-O-malonyltransferase activity because GO:0102588 represents a specific substrate. No annotations.
GO:0102480 5-fluorocytosine deaminase activity: not a physiological susbtrate. No manual annotations.
GO:0102139 2-hydroxy-6-oxo-6-(2'-aminophenyl)-hexa-2,4dienoate hydrolase activity: replace by GO:0018768 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoate hydrolase activity; represents the same reaction. No annotations
GO:0043727 5-amino-4-imidazole carboxylate lyase activity: replace by GO:0004638 phosphoribosylaminoimidazole carboxylase activity; No annotations.
GO:0102361 esculetin 4-O-beta-glucosyltransferase activity : replace by GO:0047218 hydroxycinnamate 4-beta-glucosyltransferase activity because GO:0102361 represents a specific substrate. No manual annotations.
GO:0102359 daphnetin 4-O-beta-glucosyltransferase activity : replace by GO:0047218 hydroxycinnamate 4-beta-glucosyltransferase activity because GO:0102361 represents a specific substrate. No manual annotations.
GO:0102360 daphnetin 3-O-glucosyltransferase activity: replace by GO:0047893 flavonol 3-O-glucosyltransferase activity. No manual annotations.
GO:0102425 myricetin 3-O-glucosyltransferase activity: replace by GO:0047893 flavonol 3-O-glucosyltransferase activity. No manual annotations.
GO0102387 2-phenylethanol acetyltransferase activity: replace by acetyl-coenzyme A:acetyl alcohol acetyltransferase activity ; GO:0102720. No annotations
GO:0106325 acetylgalactosaminyl-O-glycosyl-seryl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity: replace by GO:0047225 acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity: more specific than the activity of any known enzyme. No annotations.
GO:0106326 acetylgalactosaminyl-O-glycosyl-threonyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity: replace by: GO:0047225 acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity: more specific than the activity of any known enzyme. No annotations.
GO:0102996 beta,beta digalactosyldiacylglycerol galactosyltransferase activity: replace by GO:0003844 1,4-alpha-glucan branching enzyme activity; GO:0102996 represents a specific substrate. No annotations
GO:0103101 UDP-glucose:7-methylthioheptylhydroximate S-glucosyltransferase activity
GO:0103102 UDP-glucose:8-methylthiooctylhydroximate S-glucosyltransferase activity
GO:0103100 UDP-glucose: 6-methylthiohexylhydroximate S-glucosyltransferase activity
GO:0103103 UDP-glucose: 9-methylthiononylhydroximate S-glucosyltransferase activity
GO:0102659 UDP-glucose: 4-methylthiobutylhydroximate S-glucosyltransferase activity
GO:0103099 UDP-glucose:5-methylthiopentylhydroximate S-glucosyltransferase activity

merge into GO:0047251 thiohydroximate beta-D-glucosyltransferase activity. Sprcific substrates. No annotations.
GO:0102500 beta-maltose 4-alpha-glucanotransferase activity: replace by GO:0004134 4-alpha-glucanotransferase activity; GO:0102500 represents a specific substrate. No annotations
GO:0102468 wogonin 7-O-glucuronosyltransferase activity & GO:0102467 scutellarein 7-O-glucuronosyltransferase activity >> merge into GO:0102159 baicalein 7-O-glucuronosyltransferase activity because they represent specific substrates. No annotations
GO:0102493 wogonin 7-O-glucosyltransferase activity : replace by GO:0033836 flavonol 7-O-beta-glucosyltransferase activity; represents a specific substrate. No annotations
GO:0102891 2'4'6'34-pentahydroxychalcone 4'-O-glucosyltransferase activity: replace by GO:0102890 naringenin chalcone 4'-O-glucosyltransferase activity: specific substrate. No annotations. Rename chalcone 4'-O-glucosyltransferase activity
GO:0102458 cyanidin 3-O-glucoside 5-O glucosyltransferase (vanilloyl-glucose dependent) activity
GO:0102456 cyanidin 3-O-glucoside 5-O-glucosyltransferase (sinapoyl-glucose dependent) activity
GO:0102512 delphinidin 3-O-glucoside 5-O-glucosyltransferase (acyl-glucose dependent) activity
GO:0102510 pelargonidin 3-O-glucoside 5-O-glucosyltransferase (acyl-glucose dependent) activity

Replace by GO:0102506 cyanidin 3-O-glucoside 5-O-glucosyltransferase (acyl-glucose dependent) activity. Represent different acyl-glucose donors
GO:0103047 'methyl beta-D-glucoside 6-phosphate glucohydrolase activity' replace by GO:0008706 6-phospho-beta-glucosidase activity: represents a specific substrate.

Thanks, Pascale

2024-06-28

GO:0036141 L-phenylalanine-oxaloacetate transaminase activity: replace by GO:0080130 L-phenylalanine-2-oxoglutarate transaminase activity: same activity. No annotations
GO:0070546 L-phenylalanine transaminase activity: unnecessary grouping term. Consider: GO:0080130 L-phenylalanine-2-oxoglutarate transaminase activity and GO:0047312 L-phenylalanine-pyruvate transaminase activity. No annotations.
GO:0070547 : L-tyrosine aminotransferase activity: unnecessary grouping term. Consider: GO:0004838 L-tyrosine transaminase activity and GO:0080098 L-tyrosine:pyruvate aminotransferase activity No annotations.
- GO:0043840 branched-chain amino acid:2-keto-4-methylthiobutyrate aminotransferase activity: represents a specific substrate of GO:0004084 branched-chain-amino-acid transaminase activity. No annotations
GO:0046571 aspartate-2-keto-4-methylthiobutyrate transaminase activity: represents a specific substrate of GO:0004084 branched-chain-amino-acid transaminase activity. No annotations
GO:0052819 heteroglycan 2-alpha-mannosyltransferase activity: replace by parent GO:0047264 heteroglycan alpha-mannosyltransferase activity. No annotations
GO:0052818 heteroglycan 3-alpha-mannosyltransferase activity: replace by parent GO:0047264 heteroglycan alpha-mannosyltransferase activity. No annotations
GO:0102638 [1-(2-amino-7-methyl-4-oxo-7,8-dihydro-3H-pteridin-6-yl)]ethyl-4-(beta-D-ribofuranosyl)aminobenzene 5'-phosphate synthase activity: replace by GO:0102041 7,8-dihydropterin-6-yl-methyl-4-(beta-D-ribofuranosyl)aminobenzene 5'-phosphate synthase ; represents a specific substrate. No annotations
GO:0102104 demethoxycurcumin synthase activity (0 annotations): merge into GO:0102103 demethoxycurcumin synthase activity; specific substrate
GO:0018733 3,4-dihydrocoumarin hydrolase activity: replace by GO:0047856 dihydrocoumarin hydrolase activity: represent the same activity. 1 EXP, will be automatically replaced
GO:0018732 sulfolactone hydrolase activity: replace by GO:0102998 4-sulfomuconolactone hydrolase activity ; represent the same activity
GO:0102402 2-phenylethyl 6-O-beta-D-xylopyranosyl-beta-D-glucopyranoside glucosidase (Yabukita) activity and GO:0102404 linalyl 6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside glucosidase (Yabukita) activity: replace by GO:0050535 beta-primeverosidase activity; represent specific substrates. No annotations
GO:0102253 neoagarobiose 1,3-alpha-3,6-anhydro-L-galactosidase activity, GO:0102256 neoagarohexaose 1,3-alpha-3,6-anhydro-L-galactosidase activity and GO:0102254 neoagarotetraose 1,3-alpha-3,6-anhydro-L-galactosidase activity: replace by GO:0033954 alpha-neoagaro-oligosaccharide hydrolase activity; represent specific substrates. No annotations
GO:0102151 3-oxo-myristate decarboxylase activity, GO:0102577 3-oxo-palmitate decarboxylase activity, GO:0102328 3-oxoacid decarboxylase activity >> replace by GO:0050410 3-oxolaurate decarboxylase activity; represent specific substrates. No annotations
GO:0051909 acetylenecarboxylate hydratase activity, producing 3-hydroxypropenoate: replace by GO:0050079 acetylenecarboxylate hydratase activity, producing 3-oxopropanoate & change label to acetylenecarboxylate hydratase activity. EC has comment "The reaction is effectively irreversible, favoring oxopropanoate (malonic semialdehyde) and its tautomers. Also acts on but-3-ynoate forming acetoacetate." No annotations
GO:0102056 11-hydroxyjasmonate sulfotransferase activity and GO:0102055 12-hydroxyjasmonate sulfotransferase activity; replace by GO:0080131 hydroxyjasmonate sulfotransferase activity. No manual annotations
GO:0102560 5-phospho-alpha-D-ribose 1,2-cyclic phosphate 1-phosphohydrolase activity: replace by GO:0102561 D-ribose 2,5-bisphosphate 2-phosphohydrolase activity: very similar substrates, same gene annotated to both terms (1 annotation)
GO:0102507 cyanidin 3-O-glucoside 7-O-glucosyltransferase (hydroxybenzoly-glucose dependent) activity
GO:0102511 pelargonidin 3-O-glucoside 7-O-glucosyltransferase (acyl-glucose dependent) activity
GO:0102513 delphinidin 3-O-glucoside 5-O-glucosyltransferase (vanilloyl-glucose dependent) activity
GO:0102514 cyanidin 3-O-glucoside 7-O-glucosyltransferase (feruloyl-glucose dependent) activity
GO:0102515 pelargonidin 3-O-glucoside 7-O-glucosyltransferase (feruloyl-glucose dependent) activity
GO:0102516 delphinidin 3-O-glucoside 7-O-glucosyltransferase (feruloyl-glucose dependent) activity
GO:0102584 cyanidin 3-O-[2''-O-(xylosyl)-6''-O-(p-coumaroyl) glucoside] 5-O-glucosyltransferase activity

replace by GO:0102457 cyanidin 3-O-glucoside 7-O-glucosyltransferase (vanilloyl-glucose dependent) activity, because these represent specific substrates. No annotations to any of these terms.
GO:0102751 UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity; replace with GO:0008466 glycogenin glucosyltransferase activity : subreaction. 3 UniProt EXP, will be mapped automatically
GO:0102740 theobromine:S-adenosyl-L-methionine 1-N-methyltransferase activity: merge into GO:0102741 caffeine synthase activity because GO:0102740 represents a specific substrate. No annotations (broaden definition of GO:0102741)
GO:0052667 phosphomethylethanolamine N-methyltransferase activity merge into GO:0000234 phosphoethanolamine N-methyltransferase activity. EC states: "The enzyme may catalyze the transfer of two further methyl groups to the product." RHEA describes this as 3 reactions: RHEA:20365 (first methylation), RHEA:25321 (second) and RHEA:25325 (third). 1 EXP, TAIR. Will be automatically replaced
GO:0102128 chalcone synthase activity : replace by GO:0016210 naringenin-chalcone synthase activity: specific substrate.

pgaudet commented 2 weeks ago

[x] GO:0016412 serine O-acyltransferase activity: remove EC:2.3.1.30; add RHEA:68272
[x] GO:0016419 S-malonyltransferase activity: remove EC:2.3.1.39; also on the child term.

geneontology / go-ontology

Fix EC to one-to-one-xrefs-by-value-violation #28070