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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0071554 cell wall organization and biogenesis taxon restrictions #16108

Closed ValWood closed 6 years ago

ValWood commented 6 years ago

Should have never in vertebrates (minimally)? Human 6 annotations, D. rereio 8 annotations etc

Or only in fungi, plants bacteria?

Do dicty have a "cell wall" @pfey03 ? (7 annotations purpureum 21 discoideum) @vanaukenk C.elegans don't do they? (11 annotations)

pfey03 commented 6 years ago

In the Dicty fruiting body, the stalk cells and the spores have a cell wall. All our annotations are to 'spore wall assembly' or similar. Dicty 'spore coats' as they are traditionally called consist of secreted proteins, a polysaccharide and cellulose.

vanaukenk commented 6 years ago

@ValWood

In some cases here I think we're looking at annotations to antimicrobials, i.e. immune effectors.

We could make a ticket in the go-annotation tracker to do more thorough annotation review, but there does seem to be some legitimate annotation as part of an evolved host defense process of cell wall catabolism.

ValWood commented 6 years ago

I still think these types of annotation are strange (both host defense responses and pathogen host interactions)

There should be clear pathogen-host and host-defense response branches in the ontology like there used to be (IMHO). I really wish we could go return to this. Otherwise in the future annotations will become (are already) very confusing. - I wonder even if the existing annotations include the taxon ID of the pathogen or host for example.

In addition to being confusing, this representation makes annotation difficult and will make it increasingly difficult to implement taxon checks.

Not many people actively annotating pathogens right now but when we are this will become a bigger problem.

We should discuss this at a future meeting @pgaudet .

vanaukenk commented 6 years ago

Added to agenda for next QC/QA call.

ValWood commented 6 years ago

I'm still confused. Do we have examples of vertebrates degrading cell walls (other than by digestion). Would people expect to see digestive enzymes annotated to "cell wall catabolism"? of the ingested organism (this is similar).

I wouldn't refer to the breakdown of another organism carbohydrate component as "cell wall catabolism", but it isn't easy to see how to prevent it ...

ValWood commented 6 years ago

For now, put the taxon restriction on GO:0042546 cell wall biogenesis

pgaudet commented 6 years ago

Added never in vertebrates

pgaudet commented 6 years ago

@vanaukenk I'm working with @ValWood on tickets, I fixed this one.