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geneontology / go-shapes

Schema for Gene Ontology Causal Activity Models defined using RDF Shapes
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GP located_in CC error #254

Open tmushayahama opened 3 years ago

tmushayahama commented 3 years ago

Dustin and I were looking at a model and It says "GP located_in CC" is wrong and must be Anatomical Entity. However isn't CC an Anatomical entity?

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tag @dustine32 @vanaukenk @ukemi @pgaudet

balhoff commented 3 years ago

Some CCs are anatomical entities, but not all. Only the ones under 'cellular anatomical entity'.

ukemi commented 3 years ago

This is an interesting conundrum for root annotations. When the annotation is to the root and the evidence is ND the default relation should be is_active_in (RO:0002432).

https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md

I thought we had already changed that in our file. Please let me know if we haven't and let us know if this doesn't pass the ShEX.

vanaukenk commented 3 years ago

@balhoff Following up on the 2021-02-22 ontology editors' call, when you have time, can we take a look at the ShEx together to add root CC (exactly, not root CC or children) as an allowed value for CC annotations where applicable in the schema?

Thx.

balhoff commented 3 years ago

This is probably addressed by #259, but that PR only dealt with is_active_in. Does the form editor need to be updated to use the new relation?

vanaukenk commented 3 years ago

@balhoff Thx for your help with the ShEx yesterday. Yes, the form needs to be update for that relation.