Review annotations to GO:0065009 regulation of molecular function & children

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0065009 regulation of molecular function & children see https://github.com/geneontology/go-ontology/issues/22455

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1jO6KdfHndALNYWn24S_M6LHUYrCIBgOqBg34a5tsARk/edit#gid=805231635

Note that the annotation review includes ISS, ISO, IC, in addition to EXP annotations.

Impacted groups:

Group	Number manual annotations	assignee
AgBase	216	@pgaudet
AspGD	11	@pgaudet
Alzheimers_University_of_Toronto	19-done	@RLovering
ARUK-UCL	337	@RLovering
BHF-UCL	1074	@RLovering
HGNC	1-done	@RLovering
HGNC-UCL	59	@RLovering
ParkinsonsUK-UCL	114	@RLovering
SynGO-UCL	2-done	@RLovering
CACAO	74	@dsiegele
CAFA	84	@Antonialock
CGD	19	@marekskrzypek @jlewsmith
ComplexPortal	358	@sandraorchard
DFLAT	5	@pgaudet
DIBU	5
dictyBase	123	@pfey03
DisProt	2	@federicaquaglia
EcoCyc	60	@amandamackie
EcoliWiki	2	@dsiegele
FlyBase	392	@hattrill @gantonazzo
GDB	3	@pgaudet
GeneDB	9
GO_Central	5	@pgaudet
JCVI	2	@pgaudet
MGI	735	@LiNiMGI
MTBBASE	23	@pgaudet
PAMGO_MGG	1	@pgaudet
PINC	64	@pgaudet
PseudoCAP	37	@glwinsor
Reactome	21	@deustp01
RGD	456	@gthayman
SGD	231	@srengel
SynGO	71
TAIR	87	@tberardini
UniProt	1964	@Antonialock @pgaudet
WB	91	@vanaukenk
ZFIN	161	@sramachand

---

TO CHECK: Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) [LIST IDs + ADD ASSIGNEES] 

Thanks.

[ValWood]

Hi @pgaudet some of the annotations in the list are MF terms, like rum1 8 annotations to GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity I think these maybe come through as instantiated BP annotations to the BP "regulation of protein kinase" terms via GOC inferences from F-P links. So maybe if these connections are removed there will not be so many annotations for people to fix?

[pfey03]

I've already taken care of most of these. I have 126 total and not 123 regulation but 86 regulation the others are activation of MF

[pfey03]

@pgaudet what does it mean without IMP and IGI? I'm take care of all as most are IMP. I've done already almost 2/3 of all including IMP and IGI annotations. I will be done maybe next week with all including IMP and IGI

[amandamackie]

EcoCyc done

[pgaudet]

@ValWood @lreiser (and everyone) - I updated the spreadsheet (and the counts), to remove 'any MF annotation, and any regulation of binding, which we can do separately. Note that this list includes ISS, ISO, IC, and all EXP annotations.

[ValWood]

OK PomBase are done, all of my remaining are "regulation of binding" and I didn't quite know how to handle those yet. My name was against PseudoCap, so I removed it. I don't know if the relevant person is tagged for these?

[pgaudet]

For some reason (probably a download from QuickGO), all the annotations were from QuickGO. I replaced the annotations entities by MOD Ids for several groups. If I omitted a group that needs that, please let me know.

Pascale

[lreiser]

tair is done

[deustp01]

Reactome is done

[hattrill]

Hi @gantonazzo looks like you've done all the FB ones, is that correct?

[gantonazzo]

Hi @gantonazzo looks like you've done all the FB ones, is that correct?

Yes, I forgot to write here that FB is done! Thanks!

[uliboehme]

GeneDB is done. There is one gene from Leishmania major on the list (LMJF_28_0090). This cannot be changed. This genome is not curated anymore at VEuPathDB.

[ValWood]

Thanks Ully OK does anyone maintain Leishmania major ?

[ValWood]

I guess in this particular case it won't matter as the terms will be obsoleted. But it would be useful to know for other examples, or to allow us to edit them through UniPRto protein2GO (or maybe we can already)?

[uliboehme]

@ValWood Thanks for rechecking. At the moment, nobody maintains L. major.

[RLovering]

I have removed a HGNC annotation, as the relevant other BP and MF terms were already captured. Note that I should only be responsible for HGNC-UCL annotations not HGNC annotations that are created by Elspeth etc.

[pfey03]

@pgaudet there is a time lag to appear at QuickGO but there was just now a GOA release