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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Header on the "clone evidence" popup has a gomodel: that doesn't match the model title #244

Closed suzialeksander closed 9 months ago

suzialeksander commented 1 year ago

Leaving this for reference in case it becomes a bug: Screenshot 2023-04-12 at 23 18 41

The header on the "clone evidence" popup has a gomodel: that doesn't match the model title. A bit confusing to the curator, but not wholly unexpected:

According to @dustine32:

Those (gomodel:PSERTRANSAM-RXN and gomodel:YOR184W-MONOMER_PSERTRANSAM-RXN_controller) are the IRIs for the reactions in the model. It may get confusing and/or conflicts if the same reaction is used in multiple models.

I am used to seeing IRIs use the pattern gomodel:{model_id}/{individual_id} to prevent ID collisions so it might become a bug??

dustine32 commented 1 year ago

Yes, new ID standard for YeastPathways - Ex: gomodel:SERSYN-PWY/PSERTRANSAM-RXN

suzialeksander commented 9 months ago

@dustine32, this seems to be more a "fun fact for those that know the lore" rather than seriously affecting the YP project, for now. Is it ok to close? any tags/keywords that should be added to make this findable if it comes up again, or any reason to think this might be an issue for import anymore?

dustine32 commented 9 months ago

@suzialeksander Yep, I think it's ok to close for now. I don't know how useful a label of "ID convention" would be but we can at least associate it with https://github.com/geneontology/pathways2GO/issues/189.