Review direct annotations to 'cell population proliferation'

[pgaudet]

It has been proposed to make 'cell proliferation' a do_not_annotate term. Please review your annotations to make them more precise (or remove them if they represent a read out and the molecular mechanism by which the cell is involved in proliferation is not known).

[ukemi]

I disagree with this proposal. It is quite useful when context is given in annotation extensions. Do we want to instantiate a class for every cell type whose population can proliferate?

[pgaudet]

So, how about making a rule that the extension is mandatory?

[pgaudet]

@ValWood OK for you ?

[ValWood]

yep. I suggested here that extended terms would also be OK https://github.com/geneontology/go-ontology/issues/16659

[hattrill]

Probably take me a couple of weeks to get round to reviewing these.

[pgaudet]

Annotations to cell proliferation without extensions are here: https://docs.google.com/spreadsheets/d/1VG9gsN2al1WyH2cy4VMkt5kiC_CShbr44CgIBAsbVpM/edit#gid=0

Manual annotations by group:

Group	Number of annotations	contact
AgBase	17	@
Alzheimers_University_of_Toronto	2 - checked but can't edit	@RLovering change to @pgarmiri
BHF-UCL	9 - done	@RLovering
CACAO	1	s>@sandyl27</s @dsiegele
dictyBase	3	@pfey03 (done ? please check/fill the spreadsheet)
FlyBase	54	@hattrill
GeneDB	15	@ggeorghiou
HGNC	3 - done	@RLovering
MGI	81	@hdrabkin
PINC	142	@pgaudet
RGD	35	@slaulederkind
TAIR	48	@tberardini
UniProt	162	@pgarmiri
WB	3	@vanaukenk
ZFIN	20	@sabrinatoro

[ValWood]

Wasn't the plan to have these be "soft checks" so that people could would work through them at their leisure

[pgaudet]

yes there is no emergency for these.

[hdrabkin]

As David points out we can use extensions with these terms, so this should not be made do not annotate. A rule could be made to require an extension if the term is used.

[pfey03]

I'm done, commented on the wrong issue yesterday.

The Dicty EXP were legacy and have been updated to term we use currently. These Dicty 'growth' IMP went years ago to 'cell proliferation' and then to 'asexual reproduction', which those were updated to.

I also deleted the legacy dictyBase ISS annotations

[vanaukenk]

The WB annotations are done. I removed one and changed the other two to variations on mitotic cell cycle.

[tberardini]

@ebakker2 : Still working on getting you on the list for 'Assignees'. This is the ticket we were talking about earlier today.

[sabrinatoro]

ZFIN annotations are done. I added some annotation extensions, and removed some.

[hdrabkin]

MGI done

[pgarmiri]

The UniProt-EBI annotations have been checked and the actions reported in the spreadsheet.

There are 66 SWIS annotation left. I added a purple colored tag in end of each relevant row. (@sylvainpoux ) Thanks, Penelope

[hattrill]

FB done

[pgaudet]

@Achchuthan Can you please review the GeneDB genes ? The task is to either add an annotation extension or remove the annotation.

[Achchuthan]

Thanks @pgaudet. I have removed all Trypanosoma brucei and Leishmania major annotations from GeneDB. I have also emailed Uli to review Plasmodium annotations.

[uliboehme]

Thanks @Achchuthan. I have now removed the Plasmodium annotations from GeneDB. @pgaudet It would be really great if you could let me know in the future if there are any obsolete Plasmodium GO terms. Thanks!

[pgaudet]

Dear @uliboehme

This is the error report for Plasmodium falciparum :

http://current.geneontology.org/reports/genedb_pfalciparum-report.html

These get updated about once a month, so you can check periodically if new errors have been detected.

Thanks, Pascale

[uliboehme]

Dear @pgaudet,

Thanks for your reply. I was not aware of this link.

Could you also please add me as contact for GeneDB (in addition to @Achchuthan).

Thanks very much. Uli

[dsiegele]

I decided to leave the annotation in CACAO until I discuss it further. I removed the annotation in CACAO. The paper (Figure 1A may have evidence for regulation of cell population proliferation, but the experiment tested overexpression of MOUSE:BOP1 in cell lines so I am not sure about it.

[pgaudet]

@dsiegele In this case I think the authors are testing the viability of the cells with and without the proper factors to process the ribosomal RNA. I dont think these genes are directly involved in cell proliferation.

Pascale