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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Do not use ChEBI roles as physical entities - fall back on chemical entity #139

Closed dustine32 closed 2 years ago

dustine32 commented 2 years ago

Originated from an OWL consistency error in the GO-CAM for gomodel:PWY3O-981 translated from SGD pathways BioPAX.

We determined the issue was a ChEBI term (CHEBI:15339 - acceptor) for a chemical role being used as a physical entity: image

A check should be implemented to fall back on using CHEBI:24431 chemical entity if the attempted term is a role (CHEBI:50906) or descendant term: image

Tagging @thomaspd @ukemi @cmungall @deustp01

dustine32 commented 2 years ago

Suggestion from @balhoff https://github.com/geneontology/pathways2GO/pull/158#discussion_r853304938 to retain the chemical role by adding a "has role" edge. So, in this example we would now have:

Molecular Event -has_input-> chemical entity -has_role-> acceptor

@thomaspd What do you think? We would also need to add "has_role" (RO:0000087) to the ShEx spec.

dustine32 commented 2 years ago

Speaking with @thomaspd on 2022-05-02, we do not need to load the ChEBI roles (e.g. "acceptor") from BioPAX to GO-CAM since we aren't tracking stoichiometry.

cmungall commented 2 years ago

Indeed - and we can just get from Rhea if needed

On Thu, May 5, 2022 at 10:28 AM dustine32 @.***> wrote:

Speaking with @thomaspd https://github.com/thomaspd on 2022-05-02, we do not need to load the ChEBI roles (e.g. "acceptor") from BioPAX to GO-CAM since we aren't tracking stoichiometry.

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