Review mf_needs_review subset - possible obsoletions

[pgaudet]

Hello @hdrabkin

At a receont ontology call we elected you to review the terms in the 'mf_needs_review' slim (and then presumably retiring that slim).

The following have a comment that the obsoletion is planned:
FMN reductase activity' http://purl.obolibrary.org/obo/GO_0008752 DONE IN #16166
'carotene 7,8-desaturase activity' http://purl.obolibrary.org/obo/GO_0016719 DONE in #2050
'dihydroorotate oxidase activity' http://purl.obolibrary.org/obo/GO_0004158 obsoleted in #23789
'hydroxynitrilase activity' http://purl.obolibrary.org/obo/GO_0047606 add RHEA xrefs and missing children

GO:0052891 aliphatic (S)-hydroxynitrile lyase activity
+xref: RHEA:56588 {source="skos:narrowMatch"}
+xref: RHEA:56592 {source="skos:narrowMatch"}
+is_a: GO:0047606 ! hydroxynitrilase activity

GO:0052892 aromatic (S)-hydroxynitrile lyase activity
+is_a: GO:0047606 ! hydroxynitrilase activity

GO:0052919 'aliphatic (R)-hydroxynitrile lyase activity'
+is_a: GO:0047606 ! hydroxynitrilase activity

'polyamine oxidase activity' http://purl.obolibrary.org/obo/GO_0046592 branch improved in #24701
'tRNA adenylyltransferase activity' http://purl.obolibrary.org/obo/GO_0004810 DONE in #19854

Those have no comment:

'DNA-N1-methyladenine dioxygenase activity' http://purl.obolibrary.org/obo/GO_0043734
'alcohol dehydrogenase (acceptor) activity' http://purl.obolibrary.org/obo/GO_0018468 Merged (cannot find the ticket)
'amine dehydrogenase activity' http://purl.obolibrary.org/obo/GO_0030058 OK Has a RHEA
'aspartyl esterase activity' http://purl.obolibrary.org/obo/GO_0045330 ?????
'chondroitin ABC lyase activity' http://purl.obolibrary.org/obo/GO_0047486 Obsoleted in #24702
'clavaminate synthase activity' http://purl.obolibrary.org/obo/GO_0033758 OK Has a RHEA and an EC
'cobyrinic acid a,c-diamide synthase activity' http://purl.obolibrary.org/obo/GO_0042242 OK Has a RHEA and an EC
'dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity' http://purl.obolibrary.org/obo/GO_0004584 Obsoleted in #14578
'gibberellin 20-oxidase activity' http://purl.obolibrary.org/obo/GO_0045544 ?? No RHEA, some TAIR annotations
'glutamin-(asparagin-)ase activity' http://purl.obolibrary.org/obo/GO_0050417 Could obsolete in favor of asparaginase activity and glutaminase activity (no annotations)
'linoleate diol synthase activity' http://purl.obolibrary.org/obo/GO_0033751 obsoleted in
#22050
'oxidosqualene cyclase activity' http://purl.obolibrary.org/obo/GO_0031559 OK grouping class
'polyamine oxidase activity' http://purl.obolibrary.org/obo/GO_0046592 branch improved in #24701
'protein-N-terminal glutamine amidohydrolase activity' http://purl.obolibrary.org/obo/GO_0070773 OK Has a RHEA and an EC
thalianol synthase activity' http://purl.obolibrary.org/obo/GO_0051746 OK Has a RHEA and an EC

Thanks, Pascale
'tRNA cytidylyltransferase activity' http://purl.obolibrary.org/obo/GO_0016437 Fixed in #19854
'trans-octaprenyltranstransferase activity' http://purl.obolibrary.org/obo/GO_0050347 Done in #23417
'trans-pentaprenyltranstransferase activity' http://purl.obolibrary.org/obo/GO_0048045 Obsoleted in #23202

[hdrabkin]

I'm holding off on obsoleting the two tRNA terms. A merge might be more appropriate; let me think for a bit;
'tRNA adenylyltransferase activity' http://purl.obolibrary.org/obo/GO_0004810;
'tRNA cytidylyltransferase activity' http://purl.obolibrary.org/obo/GO_0016437

[hdrabkin]

Yes, I remember
EC 2.7.7.71 was transferred to EC 2.7.7.72 (GO_0016437) and EC 2.7.7.25 was also transferred to EC 2.7.7.72 (GO_0004810)
I think a merge would be more appropriate, and that way no annotations need fixing;
the same enzyme catalyzes both reactions (except in ONE organism, which needs two separate enzymes (one to add the Cs, and the other to add the As).

[hdrabkin]

FMN reductase activity' http://purl.obolibrary.org/obo/GO_0008752 has 29 annotations

EC 1.5.1.29
Deleted entry: FMN reductase [NAD(P)H]. Now covered by EC 1.5.1.38 [FMN reductase (NADPH)], EC 1.5.1.39 [FMN reductase [NAD(P)H])] and EC 1.5.1.41 (riboflavin reductase [NAD(P)H])

Fixed ECs

• GO:0008752 FMN reductase activity
  changed label: FMN reductase (NAD(P)H) activity

• removed xref: EC:1.5.1.39
  +synonym: "NAD(P)H-dependent FMN reductase activity" RELATED []
  +xref: EC:1.5.1.39 {source="skos:exactMatch"}
  +xref: RHEA:21620 {source="skos:broadMatch"}
  +xref: RHEA:21624 {source="skos:broadMatch"}

• GO:0042602 riboflavin reductase (NADPH) activity

• remove xref: EC:1.5.1.41

• GO:0052873 FMN reductase (NADPH) activity

• remove xref: EC:1.5.1.39

• GO:0052874 FMN reductase (NADH) activity

• add xref: EC:1.5.1.42

carotene 7,8-desaturase activity' http://purl.obolibrary.org/obo/GO_0016719 3 annotations (1 IEA, 1 IDA, and 1 IBA; gene product name is the name of the new EC
EC:1.14.99.30; transferred to EC 1.3.5.6; we have this EC activity as a synonym for GO_0016719

'dihydroorotate oxidase activity' http://purl.obolibrary.org/obo/GO_0004158 38 annotations (16 IEA)
EC 1.3.3.1 Transferred entry: 1.3.98.1
Different defs
(S)-dihydroorotate + O(2) = H(2)O(2) + orotate, vs
(S)-dihydroorotate + fumarate <=> orotate + succinate
Now, EC says molecular oxygen can replace fumarate in vitro...; thus would not get succinate if not using fuarate..

[hdrabkin]

'hydroxynitrilase activity' http://purl.obolibrary.org/obo/GO_0047606; no annotations
EC:4.1.2.37; now EC 4.1.2.47, (S)-hydroxynitrile lyase
a hydroxynitrile = cyanide + an aldehyde or ketone to now is:
An aliphatic (S)-hydroxynitrile <=> cyanide + an aliphatic aldehyde or ketone
An aromatic (S)-hydroxynitrile <=> cyanide + an aromatic aldehyde

• polyamine oxidase activity' http://purl.obolibrary.org/obo/GO_0046592 75 annotations, 19 IEA see Make GO:0046592 polyamine oxidase activity a parent of several GO classes #24701

EC:1.5.3.11, transferred to 5 different EC ids
There are currently in GO as broad/related synonym to various terms; some to multiple terms
See #12432 (comment)

• Transferred entry: 1.5.3.13 GO:0052899, GO:0052904, GO:0052903, GO:0052902, and GO:0052901
• Transferred entry: 1.5.3.14 GO:0052893, GO:0052896, and GO:0052900
• OBSOLETED Transferred entry: 1.5.3.15 GO:0052898, and GO:0052897
• Transferred entry: 1.5.3.16 GO:0052895, GO:0052894, and GO:0052901
• Transferred entry: 1.5.3.17 GO:005899, GO:0052904, GO:0052903, GO:0052902, GO:0052901,

Owners of annotations need to figure out which of these is a more appropriate term

[hdrabkin]

So for the ones with no comment it is hard to know why it is in this slim
http://www.ontobee.org/ontology/GO?iri=http://purl.obolibrary.org/obo/GO_0043734
The EC mapping to this is a grouping term (1.14.11) and need to be removed or remapped; I think it's closest to EC 1.14.11.51 although 0043734 mentions both N1-methyladenine and N3-methylcytosine wherease the EC id only mentions N1-methyladenine
Has 131 annotations!!! 17 IEA and the bulk of the rest are ISO/ISS/ etc. with 8 manual via experiment (IDA, IMP,

[hdrabkin]

clavaminate synthase activity' http://purl.obolibrary.org/obo/GO_0033758 EC:1.14.11.21
Nothing wrong with this but has no annotations; Resolved; leave this in place

cobyrinic acid a,c-diamide synthase activity http://www.ontobee.org/ontology/GO?iri=http://purl.obolibrary.org/obo/GO_0042242
Has 2 EC numbers, but only one matches EC:6.3.5.10 (Adenosylcobyric acid synthase (glutamine-hydrolyzing).) and EC:6.3.5.11 (Cobyrinate a,c-diamide synthase (glutamine-hydrolyzing). )
THe latter fits the def, the former actually maps to GO:0051921; I could fix this by removing EC:6.3.5.10 from GO_0042242 DONE; removed EC:6.3.5.10 from def

[hdrabkin]

@pgaudet , if I can fix some immediately, do you want me to just remove them as a member of the for review slim? Let me know (I will continue doing the analysis and put results in this ticket).

[pgaudet]

Hi @hdrabkin
I think that review slim should be deleted. If you want I can delete it now (well, soon). This ticket is just to make sure that the terms needing review are getting reviewed (and it seems OK to be that some are right and stay in the ontology).

OK with you?

[hdrabkin]

'alcohol dehydrogenase (acceptor) activity' http://purl.obolibrary.org/obo/GO_0018468
This term has an EC that has been transferred
EC 1.1.99.8 now is EC:1.1.2.8 (Alcohol dehydrogenase (cytochrome c).) and 1.1.2. 7 (Methanol dehydrogenase (cytochrome c).
1.1.28 maps to three GO terms , GO:0052936, GO:0052934, and GO:0052935
1.1.2.7 has no mapping in GO; the methanol dehydrogenases in GO does not use cytochrome but uses NAD and maps to 1.1.1.244
GO:001846 looks more like a grouping term; it has 16; I would just remove the EC mapping.
'alcohol dehydrogenase
(acceptor) activity" acceptor could be either NAD or cytochrome so all of the alcohol dehydrogenases could be children of this term

--

[hdrabkin]

@pgaudet: Sure; this ticket suffices to my being able to be tracking them. As I make final fixes I can mark them resolved.

[ukemi]

It would be optimal that if we are retaining these terms, a Rhea xref could be added to the generic reaction if it exists. Otherwise we should make a note that we need to request the reaction from Rhea.

[hdrabkin]

thalianol synthase activity' http://purl.obolibrary.org/obo/GO_0051746; add EC 5.4.99.31; RHEA:26163 DONE
'linoleate diol synthase activity' http://purl.obolibrary.org/obo/GO_0033751
has :EC:1.13.11.44; MetaCyc:1.13.11.44-RXN; change
EC transfered to 1.13.11.60; add RHEA:25395; remove MetaCyc mapping DONE

Clavaminate synthase. EC 1.14.11.21; catalysis of 3 reactions This is how EC has it as does GO.
However, RHEA has 3 separate RHEA ids for this.
Deoxyamidinoproclavaminate + 2-oxoglutarate + O(2) <=> amidinoproclavaminate + succinate + CO(2)
Proclavaminate + 2-oxoglutarate + O(2) <=> dihydroclavaminate + succinate + CO(2) + H(2)O
Dihydroclavaminate + 2-oxoglutarate + O(2) <=> clavaminate + succinate + CO(2) + H(2)O
RHEA:19785, RHEA:12773, and RHEA:20021;