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Source ontology files for the Gene Ontology
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Rhea reactions (mapped to GO) set to OBSOLETE #22050

Closed hdrabkin closed 2 years ago

hdrabkin commented 3 years ago

received via email on 8/26/2021

Dear Harold, Pascale,

I’m using summertime to do some cleaning 😉

FYI, today I set the status to OBSOLETE for the following reactions

  1. RHEA:10504 GO:0033778 RHEA:10504 has been replaced by RHEA:46752 >>>>>> this has already been done. EC 1.14.13.95 has been transferred to EC 1.14.14.139 >>>>>> done 8/27/2021 Also added PMIDs to def ref.

  2. DONE RHEA:11760 GO:0050565 TWO annotations exists via IMP by UniProt; These need to be removed so term can be obsoleted. Not enough experimental evidence to support the reaction. 6.3.2.27-RXN deleted by Ron Caspi on 2/3/12 R04357 no more valid

  3. RHEA:12564 GO:0050184 DONE (#23472 RHEA:12564 has been replaced by RHEA:46332; This RHEA:46332 already in use by GO:0102855 EC 1.3.1.35 has been transferred to EC 1.14.19.22 This is already assigned to GO:0102855 and well as GO:0050184. Neither GO reaction seems to fit with RHEA:46332; further analysis /comment required. Skipping

  4. RHEA:13393 GO:0004516 DONE RHEA:13393 has been replaced by RHEA:36163 (EC 6.3.4.21 update) >>> EC was done; fixed RHEA 8/27/21 and added PMID to def ref R-HSA-197186.3 needs to be updated too >>> Reactome will be contacteted

  5. RHEA:13533 GO:0050229 No annotations to this term in Amigo; safe to obsolete. DONE: #23521 status set to OBSOLETE EC 1.1.1.246 This activity is now known to be catalysed by two enzymes, vestitone reductase (EC 1.1.1.348) and medicarpin synthase (EC 4.2.1.139). Never suggested rxn are in GO.

Cheers, Anne

Additionally sent on 8-27-2021 by Anne

  1. RHEA:15441 GO:0004158 DONE: #23472 This reaction was no correct. The correct reaction is RHEA:30059. RHEA:30059 is already in use by GO:1990663 which correctly mentions fumarate in the reaction to yield succinate. GO:0004158 does not. It yields H2O2 + Orotate. (capitalized because autocorrect changes it to 'rotate' RHEA:15441 IS the correct reaction for GO:0004158 RHEA:15441 has no refs, etc. SHould GO:0004158 be obsoleted?

  2. RHEA:15701 GO:0016719 Done in #23098 This reaction created for EC 1.14.99.30 (carotene 7,8-desaturase) EC 1.14.99.30 (carotene 7,8-desaturase) is now EC 1.3.5.6, 9,9′-dicis-zeta-carotene desaturase. RHEA:15701 has been replaced by RHEA:30955 Frame 1.14.99.30-RXN has been deleted by Ron Caspi on 6/15/11

  3. RHEA:16681 GO:0018660 DONE #23098 This reaction was created for EC 1.14.13.3 EC 1.14.13.3 is now EC 1.14.14.9 RHEA:16681 has been replaced by RHEA:30595; already in use by GO:0052881;

  4. DONE in #23481 RHEA:17189 GO:0050173 EC 2.7.7.54 (phenylalanine adenylyltransferase). Deleted entry. The activity is part of EC 6.3.2.40, cyclopeptine synthase. Frame PHENYLALANINE-ADENYLYLTRANSFERASE-RXN has been deleted by Anamika Kothari on 3/21/13 2:07

  5. RHEA:17981 GO:0047786 >>>>>> Nothing annotated to this term in Amigo Done in #23098 Not enough evidence to support this reaction Was created for EC 1.3.1.4, cortisone α-reductase

  6. DONE RHEA:18713 GO:0047302 RHEA:18713 has been replaced by RHEA:31663 >>>>>> Changed on 8/27/21 Update of EC 2.6.1.34 EC was already updated. ; PMID added to def refs

amorgat commented 3 years ago
  1. DONE IN #23417 RHEA:11324 GO:0050347 (trans-octaprenyltranstransferase activity) RHEA:11324 has been replaced by RHEA:27563 (EC 2.5.1.84)

The RHEA:27563 already in use by GO_0052923 (all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity) Also using the same EC.

amorgat commented 3 years ago
  1. RHEA:21872 GO:0016275 RHEA:21872 has been replaced by RHEA:48100 (EC 2.1.1.124 deleted)

    RHEA:48100 already in use for GO:0035241 protein-arginine omega-N monomethyltransferase activity

Should GO:0016275 be merged into GO:0035241?

I guess

[DONE] see (https://github.com/geneontology/go-ontology/issues/23472)

  1. RHEA:14897 GO:0033770

    1.14.13.86 was deleted and 'replaced' with 1.14.14.87. So are BOTH incorrect? Is RHEA:14897 now incorrect also? Is GO:0033770 incorrect? 3 annotations all via UniProt.

Sorry Harold I made a typo in my original comment. RHEA:14897 was created for EC 1.14.13.86, that has now been deleted with the comment at IUBMB: "This enzyme was classified on the basis of an incorrect reaction. The activity is covered by EC 1.14.14.87, 2-hydroxyisoflavanone synthase" (see https://www.enzyme-database.org/query.php?ec=1.14.13.86)

GO:0033770 is incorrect, I will send a mail to the UniProt curators Hi @amorgat ; to the new EC has two reactions and two rheas. Are these separate or sequential? If the latter then do we need a RHEA for the overall reaction. If the reaction in GO is defined is incorrect, I would opt to obsolete the term

@hdrabkin, EC 1.14.14.87 has a broad name "2-hydroxyisoflavanone synthase" but only describes 2 separate reactions (https://www.enzyme-database.org/query.php?ec=1.14.14.87) [31723] liquiritigenin + O2 + reduced [NADPH—hemoprotein reductase] = (2R,3S)-2,4',7-trihydroxyisoflavanone + H+ + H2O + oxidized [NADPH—hemoprotein reductase] [35487] (2S)-naringenin + O2 + reduced [NADPH—hemoprotein reductase] = 2-hydroxy-2,3-dihydrogenistein + H+ + H2O + oxidized [NADPH—hemoprotein reductase] I would suggest that you obsolete GO:0033770 and create 2 new terms to annotate both reactions. Emmanuel Boutet (UniProt curator, @SuperManu74) removed the annotations with GO:0033770. He currently replaced them by GO:0016709 (a parent term) and will change for the specific terms if you create them.

Pascale: merged and kept GO:0033770 as it is consistent with EC, and the two reactions are catalyzed by the same enzyme. see #23415

amorgat commented 3 years ago

GO:0004164 is mapped to RHEA:20145 Please update GO:0004164 and map it to RHEA:36415 according to the update of EC 2.1.1.98 >>>> DONE https://www.enzyme-database.org/query.php?ec=2.1.1.98 I set the status of RHEA:20145 to obsolete

DONE >>>>>>>Replaced RHEA mapping and added 3 PMIDs from RHEA to replace EC xref uses for def.

amorgat commented 3 years ago

To check GO:0050600 - EC 1.14.19.24 - RHEA:46396 Corrected GO def to remove mention of NADP and remove any synonym using NADP https://www.enzyme-database.org/query.php?ec=1.14.19.24 GO:0050601 - EC 1.14.19.5 - RHEA:25852 Corrected GO def to remove mention of NADP https://www.enzyme-database.org/query.php?ec=1.14.19.5 Should these be merged: The mapping is correct but the definition should be changed (the EC numbers have been updated)

It appears that the EC and RHEAs are less specific? eg, The GO terms specifically mention myristoyl-CoA as the substrate, whereas the EC and RHEAs 'an Acyl-CoA. I might set the xrefs as 'broad' to these two GO terms.

@hdrabkin : if we find some papers describing the myristoyl-CoA 11-(E) desaturase reaction, we can create the more specific reaction .... If I'm reading Amigo correctly, there appear to be no annotations associated with either of these terms.

amorgat commented 3 years ago

...... DONE hjd RHEA:20760 GO:0050056 RHEA:20760 has been replaced by RHEA:32635 according to EC 1.14.99.28 update https://www.enzyme-database.org/query.php?ec=1.14.99.28 EC 1.14.99.28 Transferred entry: linalool 8-monooxygenase. Now EC 1.14.14.84, linalool 8-monooxygenase https://www.enzyme-database.org/query.php?ec=1.14.14.84

amorgat commented 3 years ago

RHEA:22196 GO:0016213 RHEA:22196 (now obsolete) has been replaced by RHEA:47140 (EC 1.14.19.3, Supersedes EC number: 1.14.99.25) Done also added a couple of PMIDs from rhea record to def.

amorgat commented 3 years ago

DONE RHEA:22392 GO:0033751 DONE RHEA:22392, now obsolete (EC 1.13.11.44 has been deleted by the Enzyme Commission.) Obsoleted. GO:0033751 (linoleate 8R-lipoxygenase) Note that you have GO:0052878 (linoleate 8R-lipoxygenase activity) which is correctly mapped to RHEA:25395

@amorgat : For GO:0033751 the substrate appears to be different from the term name (8S not 8R) anyways. Catalysis of the reaction: linoleate + O2 = (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate. Looking at all of the linoleate x-lipoxygenease terms, I wonder if this is beyond scope and should be merged into a more general term linoleate lipoxygenase activity, and map the RHEAs as narrow xrefs. 6 terms total @pgaudet do you agree based on our past decision?

amorgat commented 3 years ago

RHEA:22412 GO:0047671 RHEA:22412, now obsolete (EC 2.7.7.55 has been deleted by the Enzyme Commission, Transferred entry: 6.3.2.40) The new EC maps to RHEA:35091 Done also added pmid to def based on RHEA

amorgat commented 3 years ago

RHEA:22556 GO:0008924 GO:0008924 should be mapped to RHEA:46012 - EC 1.1.5.4 Malate dehydrogenase (quinone) RHEA:46012 (S)-malate + a quinone = a quinol + oxaloacetate Done also added pmid from rhea to def.

amorgat commented 3 years ago

DONE

RHEA:22632 GO:0048045 RHEA:22632, now obsolete. It was created for EC 2.5.1.33, which has been deleted by the Enzyme Commission. EC 2.5.1.33 was transferred to EC 2.5.1.82 and EC 2.5.1.83 ** Neither of the substrates for the new ECs agrees with the GO def; Geranylgeranyl diphosphate + 2 isopentenyl diphosphate (.83) (2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate (.82) GO:all-trans-pentaprenyl diphosphate + isopentenyl diphosphate

Note pentaprenyl disphosphate has geranylfarnesyl disphosphate as a synonym in chebi). There IS GO:0044687 geranylfarnesyl diphosphate synthase activity, mapping to EC:2.5.1.81 and RHEA:25694 once RHEA removed there is no def ref. This term has no annotations in amigo I propose to obsolete.

amorgat commented 3 years ago

RHEA:23528 GO:0047370 RHEA:23528 has been replaced by RHEA:38287 Please update GO:0047370 accordingly PS: MetaCyc reaction 2.8.3.7-RXN was mapped to both RHEA:23528 and RHEA:38287 (now fixed in Rhea) DONE also added pmid from rhea to def ref.

amorgat commented 3 years ago

DONE also added pmid from rhea to def ref RHEA:21344 GO:0047152 RHEA:21344 (now obsolete) has been replaced by RHEA:45204 (update of EC 2.1.1.90) Please GO:0047152 accordingly

amorgat commented 3 years ago

RHEA:23740 GO:0047085 RHEA:23740, now obsolete. It was created for EC 1.14.13.68, which has been deleted by the Enzyme Commission and transferred to EC 1.14.14.37 RHEA:23740 has been replaced by RHEA:50732, one of the three step reaction of EC 1.14.14.37 EC 1.14.14.37 is mapped to RHEA:18401 (multi-step reaction: RHEA:50724, RHEA:50728 and RHEA:50732) DONE

amorgat commented 3 years ago

This one is moved to new ticket : #23669 RHEA:24124 GO:0004744 RHEA:24124, now obsolete. It was created for EC 5.2.1.3, which has been deleted by the Enzyme Commission Deleted entry: retinal isomerase. Now known to be catalysed by a pathway involving EC 1.1.1.300, NADP-retinol dehydrogenase; EC 2.3.1.135, phosphatidylcholine--retinol O-acyltransferase; EC 3.1.1.64, retinoid isomerohydrolase; and EC 1.1.1.315, 11-cis-retinol dehydrogenase. [EC 5.2.1.3 created 1961, modified 1976, deleted 2011] Best to obsolete this term Check annotations to see which EC they can be mapped to.

Anne: I noticed that GO:0004744 is used in UniProt https://www.uniprot.org/uniprot/?query=goa:(%22retinal%20isomerase%20activity%20[4744]%22) I will send a mail to UniProt curators to updated the corresponding entries

amorgat commented 3 years ago

DONE
RHEA:24532 GO:0047119 RHEA:24532 has been replaced by RHEA:43780 RHEA:24532 (obsolete) was created for EC:1.3.1.52 which has been deleted by the Enzyme Commission and transferred to EC 1.3.8.5 Please update GO:0047119 also added PMIDs from RHEA to def ref

amorgat commented 3 years ago

DONE Also added PMID from RHEA to def ref. RHEA:24584 GO:0047103 RHEA:24584 (now obsolete) was created for EC 1.2.1.40 which has been deleted by the Enzyme Commission and transferred to EC 1.14.13.15 then EC 1.14.13.15 was transferred to EC 1.14.15.15

RHEA:24584 has been replaced by RHEA:34627 (part of RHEA:34631) MetaCyc xref: RHEA:34627 is mapped to 1.2.1.40-RXN (part of RXN-13690)

harold commented 3 years ago

Hi, @harold here- this looks intense. I imagine that you intended to @ mention a different Harold. When they arrive, let them know I think they have a tremendous name.

Good luck with everything.

amorgat commented 3 years ago

Hi, @harold here- this looks intense. I imagine that you intended to @ mention a different Harold. When they arrive, let them know I think they have a tremendous name.

Good luck with everything.

You imagine correctly ;-) Sorry for the noise!

hdrabkin commented 3 years ago

Hi @amorgat my handle is @hdrabkin, not the 'at symbol harold'

amorgat commented 3 years ago

DONE PG 2022-07-11

I added PMID:17606922 & PMID:20035867 citations to RHEA:17629 I think you could map RHEA:17629 to GO:0015574 (or GO:0015771)

amorgat commented 3 years ago

DONE RHEA:20836 GO:0000010 DONE #23472 RHEA:20836 (obsolete) has been replaced by RHEA:27794 (EC 2.5.1.30) RHEA:27794 is mapped to GO:0036422 the two go terms appear to refer to the same reaction; perhaps a merge

amorgat commented 3 years ago

DONE RHEA:20868 GO:0004555 RHEA:20868 (obsolete) has been replaced by RHEA:32675 (EC 3.2.1.28) RHEA:32675 is mapped to GO:0015927

RHEA:32675 refers to alpha-alpha substrate, GO:0004555, whereas GO:0015927 is very general. I will remove RHEA:32675 from GO:0015927 and use for GO:0004555 The EC also refers specifically to Alpha,alpha-trehalose + H(2)O <=> beta-D-glucose + alpha-D-glucose GO:0015927 is a grouping term, perhaps better served by PMID:31925485 as a reference

amorgat commented 3 years ago

DONE

RHEA:11144 GO:0047918 RHEA:11144 (obsolete) has been replaced by RHEA:63800 and RHEA:63804 (EC 5.3.1.18)

@amorgat 5.3.1.18 appears deleted EC https://enzyme.expasy.org/EC/5.3.1.18 Neither RHEA seems to agree with GO def (text) for the term : Catalysis of the reaction: GDP-mannose = GDP-L-galactose.

RHEA:63800 | GDP-α-D-mannose = GDP-β-L-gulose RHEA::63804 is GDP-β-L-gulose = GDP-β-Lglactose.

gulose is not galactose synonym.

amorgat commented 3 years ago

RHEA:21056 GO:0018819 DONE #23098 RHEA:21056 (obsolete) has been replaced by ~RHEA:63800~ RHEA:34691 (update of EC 4.2.1.54)

~@amorgat GO:0018819 is lactoyl-CoA = acryloyl-CoA + H2O. EC is (R)-lactoyl-CoA <=> acryloyl-CoA + H(2)O~

~RHEA:63800 | GDP-α-D-mannose = GDP-β-L-gulose No match to term.~

~@hdrabkin, sorry for the typo : RHEA:63800 is effectively incorrect, RHEA:34691 is the correct one RHEA:34691 (R)-lactoyl-CoA = acryloyl-CoA + H2O~

amorgat commented 3 years ago

DONE: RHEA:25864 GO:0052898 H2O + N1-acetylspermidine + O2 = 4-acetamidobutanal + H2O2 + propane-1,3-diamine

We initially created this reaction according to Federico, R., Ercolini, L., Laurenzi, M. and Angelini, R. Oxidation of acetylpolyamines by maize polyamine oxidase. Phytochemistry 43 (1996)339-341.

A second look at the paper revealed that N1-acetylspermidine was not studied for this reaction. If you don't have experimental evidence on your side GO:0052898, I'll obsolete RHEA:25864 DONE

pgaudet commented 3 years ago

@hdrabkin To answer to the comment above https://github.com/geneontology/go-ontology/issues/22050#issuecomment-919859087 RHEA:22392 GO:0033751

DONE We should obsolete GO:0033751 linoleate 8R-lipoxygenase - no annotations, term is obsoleted by both EC and RHEA.

hdrabkin commented 2 years ago

GO:0033751 was obsoleted.