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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Merge GO:0036459 thiol-dependent ubiquitinyl hydrolase activity into GO:0004843 thiol-dependent ubiquitin-specific protease activity #19723

Closed pgaudet closed 4 years ago

pgaudet commented 4 years ago

GO:0036459 thiol-dependent ubiquitinyl hydrolase activity and GO:0004843 thiol-dependent ubiquitin-specific protease activity

seem to only differ by the substrate - ie removal of ubiquitin from a protein (GO:0004843) versus from any molecule ( GO:0036459) - but we cannot find evidence that molecules other than proteins are ubiquitinated (see also https://github.com/geneontology/go-ontology/issues/17398).

I propose to merge and change the label to 'thiol-dependent deubiquitinase activity'

@ValWood @deustp01 @ukemi OK ?

Thanks, Pascale

ValWood commented 4 years ago

I do not see any difference in the our annotation. Seems to be a completely overlapping set. All thiol-dependent to so is that required in the term name?

sjm41 commented 4 years ago

'Thiol-dependent' is needed here, as we're trying to disentangle/distinguish the thiol-dependent (cysteine-type) deubiquitinases (which are the majority) from the metal-dependent deubiquitinases (the JAMM family) - see #17398.

ValWood commented 4 years ago

Oh. We have at least some of the JAMMs as thiol-dependent https://www.pombase.org/gene/SPAC31G5.13 and this was community curated...I will ask about that.

sjm41 commented 4 years ago

As far as I know, all JAMMs are metallopeptidases - see the review mentioned on the linked ticket (PMID:19489724).

I think the problem is/was that we haven't previously had a good term for these metal-dependent deubiquitinases, leading to mis-annotations/assertions - this is the main point now being addressed in #17398. May well be more annotations to review depending on how exactly things get fixed...

ValWood commented 4 years ago

OK, I will fix PomBase when the terms are in place.

pgaudet commented 4 years ago

Hi @deustp01

Note that there are Reactome mappings to the term being merged (GO:0036459); those should be moved (automatically I think in the Reactome pipeline) to the new main ID GO:0004843.

Thanks, Pascale

pgaudet commented 4 years ago

@sjm41 Are the following parents OK ?

+is_a: GO:0008242 ! omega peptidase activity +is_a: GO:0101005 ! ubiquitinyl hydrolase activity

Thanks, Pascale

sjm41 commented 4 years ago

Yep, those parents look good to me.