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obophenotype / fungal-anatomy-ontology

A structured controlled vocabulary for the anatomy of fungi
https://obofoundry.org/ontology/fao
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Add taxon constraints to FAO #13

Open cmungall opened 7 years ago

cmungall commented 7 years ago

See also https://github.com/geneontology/go-ontology/issues/11313#issuecomment-151553984

cc @thomaspd

dianeoinglis commented 7 years ago

Is "only_in_fungi" the type of constraint you want to add? How granular do you think these should be? Some structures are not present in Ascomycetes, such as fused clamps which are structures made by Basidiomycetes, etc.

@cmungall cc @thomaspc

cmungall commented 7 years ago

For now I think high level distictions are best, at the Ascomycetes vs Basidiomycetes level seems good.

The main thing to be done is to do the initial plumbing so that you can add these. If you're working i oboedit this will take some futzing I'm afraid. Maybe we could explore keeping them in a separate file for now

ValWood commented 7 years ago

Yes it would be good to have "never in Ascomycetes" where possible so we can hide them from our community curators. Cheers

Val

dianeoinglis commented 7 years ago

@cmungall Currently, the FAO.obo does not have taxon constraints. Do you want the constraints in the FAO or in the xref'd GO term or both?

cmungall commented 7 years ago

Ideally in the FAO, but this will take some work setting up as it involves imports. It's much easiest if all work is done in Protege thereafter. If that isn't a problem, I can make a pull request with the changes. (the source file can stay as .obo)

dianeoinglis commented 7 years ago

@cmungall Could the goal of limiting the terms relevant to S. cerevisiae, etc be done as marked subsets as they are in the APO? For example, 'virulence' is marked as a Candida, Aspergillus and Cryptococcus subset so the cerevisiae curators never see the term, they only see terms in the S. cerevisiae subset. This seems cleaner and the majority of terms will not be in the Sc subset. I can't do the edits myself right now but I can work the specs out in the tracker. Right now there are about a dozen NTRs or modifications to make in addition to taxon limiters

dianeoinglis commented 7 years ago

@cmungall I don't know why but the master file in GitHub is missing the [Typedef] is_a whereas it is present in the same file in OBO Foundry

cmungall commented 7 years ago

is_a shouldn't be declared, it's built in

On 10 Mar 2017, at 8:27, Diane O Inglis wrote:

@cmungall I don't know why but the master file in GitHub is missing the [Typedef] is_a whereas it is present in the same file in OBO Foundry

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