Regulation of proliferation IPR026872

[gocentral]

This annotation is a little 'indirect' for this family. (In fission yeast, practically everything is involved in proliferation in some way...personally I think this is a phenotype and should not be in GO)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10718

[gocentral]

I think the mapping gives some information about the role of farnesylation in proliferation, which is important in metazoa. Also it is not wrong for pombe as FTase also contributes to cell cycle progression in this organism [PMID:11580838]. I agree it is not very informative or useful for pombe, but if I remove the term the information willd also be lost for other eukaryotic proteins...Anyway, I'll remove the term if you think it is not correct for pombe.

Original comment by: asangrador

[gocentral]

OK, I think this really is a GO issue rather than a mapping problem. I believe proliferation is a phenotype. If it remains in GO it needs to be linked to most processes related to growth and division

Thanks

Original comment by: ValWood

[gocentral]

Ticket moved from /p/geneontology/annotation-issues/1151/

Original comment by: ValWood

[gocentral]

I agree with Val on that one. We'll end up annotating too many things to proliferation. One question though is: what would be good evidence for a role in cell proliferation ?

• Pascale

Original comment by: pgaudet

[gocentral]

For PomBase we do not use it in annotation, as we would end up annotating every gene which was involved in growth, or division, or was essential.

I don't like to have annotation inconsistency internally (we either use the term comprehensively or we don't have any annotation to it at all, so we remove any mappings)

My preferred long term solution is to identify all of the "phenotype" terms in GO and obsolete them, because for community curation it is difficult to explain to our users that this is a "GO term we do not use" . In the meantime, we will just continue to filter out the IEA annotation.

Original comment by: ValWood

[gocentral]

This is in the wrong tracker but I can't figure out how to move it in the new SF!

Original comment by: jl242

[gocentral]

Oh I see it's now an ontology issue - fine!

Original comment by: jl242

[gocentral]

Most of the manual annotations are mouse, cell proliferation - it's obviously important in multicellular org development, immune processes etc.

Original comment by: jl242

[gocentral]

• Description has changed:

Diff:

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+++ new
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 This annotation is a little 'indirect' for this family.
 (In fission yeast, practically  everything is involved in proliferation in some way...personally I think this is a phenotype and should not be in GO)

• assigned_to: Jane Lomax

Original comment by: jl242

[gocentral]

Yeah maybe it should be restricted to cell type proliferation in multicellular? It makes less sense for single celled organimss...

Original comment by: ValWood

[gocentral]

So we want to make a taxon restriction such that 'cell proliferation' can only be used for multicellular organisms?

Original comment by: jl242

[gocentral]

I don't know:

UniProtKB (581) + - RGD (236) + - WB (211) + - MGI (164) + - TAIR (48) + - FB (32) + - ENSEMBL (24) + - AspGD (20) + - ZFIN (13) + - CGD (11) + - dictyBase (5) + - Gene (2) + - NCBI (2) + - GeneDB_Pfalciparum (1) + - SGD (1)

AspGD, CGD and SGD have use this term, but not consistently. I will ask if they think these should be re-annotated. If everyone agrees I would be happy for a taxon restriction to be applied.

Maybe a "not for direct annotation" option would be appropriate to ensure that the specific proliferating cell type is captured? (although this might be an instance where the cell type has been captured with an extension?)

One thing though, I am sure TIGR used to use this term for bacterial annotation....where did all their annotations go?

Original comment by: ValWood

[gocentral]

I'm getting smaller numbers for AspGD than that, Val, and none for SGD/CGD - which filters do you have on? From the 'cell proliferation' term page, I've got document_category: annotation, 'evidence used in manual assertion' and direct annotation. I think.

Maybe the TIGR annotations went out of date?

The problem we have with a taxon constraint is that there isn't a taxonomic grouping that corresponds to 'multicellular organism'.

Original comment by: jl242

[gocentral]

Ah I think I switched to +ve reg of proliferation. Really, I should sum reg,+ve, and -ve but I don't know how to do that.

Re the taxon constraints, I think we could just add fungi for now, and then add others later. I still wonder if a not for direct annotation would work, but that would take longer.

Original comment by: ValWood

[gocentral]

There are only 2 IMP annotations in AspGD, the rest are IEAs with EBI: IPR026872 (same is true for CGD and SGD). Seems to me that this would be a better term to use in those two AspGD cases: GO:0072690 single-celled organism vegetative growth phase Synonyms: vegetative growth of a single-celled organism Definition: A phase of population growth during which single celled organisms reproduce by budding, fission, or other asexual methods.

Original comment by: mskrzypek

[gocentral]

I'm not sure about that. Jane, shouldn't GO:0072690 single-celled organism vegetative growth phase be a 'phase' term? ...that probably needs looking at too.

Marek, If these annotations are only about viability shouldn't they just be captured as phenotypes?

Original comment by: ValWood

[gocentral]

Right, it looks like this is just a slow-growth phenotype. We never capture that as GO, only as phenotypes.. Now removed.

Original comment by: mskrzypek

[gocentral]

• status: open --> closed-fixed
• Group: None --> PomBase

Original comment by: jl242

[gocentral]

I've added a never_in_taxon to Fungi and added a comment.

Moved GO:0072690 single-celled organism vegetative growth phase to be is_a biological phase.

Original comment by: jl242