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geneontology / go-shapes

Schema for Gene Ontology Causal Activity Models defined using RDF Shapes
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Replace obsolete native cell with cell #304

Closed balhoff closed 6 months ago

balhoff commented 7 months ago

CL has obsoleted 'native cell'.

balhoff commented 7 months ago

@balhoff We have other places in the ShEx where we refer to NativeCell, e.g. CellDivision and CellFateCommitment shapes. We will need to update those, as well.

Not sure why I missed those! I was searching in the Github UI and for some reason didn't see them.

balhoff commented 7 months ago

Thanks for catching that @vanaukenk, I think I got it now.

balhoff commented 6 months ago

@vanaukenk the CI is failing because we have an instance of calcium oxalate in this test model: https://github.com/geneontology/go-shapes/blob/master/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl. Apparently this CHEBI term is not in any of our imports. Not sure why it passed before—maybe at some point we were importing the entire CHEBI?

I could just replace the CHEBI term with another. Does that sound reasonable?

balhoff commented 6 months ago

I could just replace the CHEBI term with another. Does that sound reasonable?

This is what I did, and tests are passing.

vanaukenk commented 6 months ago

Thanks @balhoff I've been on calls most of the afternoon, so sorry I missed this earlier.