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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Add 'Guide to Pharmacology' as drug prefix #178

Closed dustine32 closed 1 year ago

dustine32 commented 2 years ago

This is the fix for that "failed drug test" in #135. As such I've removed the hard-coded release version (2021-02-01) of the reacto.owl used by the tests. I actually switched the conversion code to start pulling these drug xref mappings directly from the Reactome BioPAX rather than checking the external reacto.owl. Since REACTO is generated from the Reactome BioPAX anyway it seemed like an unnecessary lag step (generate reacto.owl, wait for GO release).

Basically, this creates a drug prefix list for "IUPHAR" and adds "Guide to Pharmacology". This is needed because drug mappings are now coming through the Reactome BioPAX like:

  <bp:UnificationXref rdf:ID="UnificationXref97504">
    <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Guide to Pharmacology</bp:db>
    <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7168</bp:id>
  </bp:UnificationXref>
dustine32 commented 1 year ago

Merging this now as it's been successfully tested in models pushed to noctua-dev and prod.

deustp01 commented 1 year ago

@dustine32 Naive question: is this intended to make the filtering-out of reactions involving drugs in the build of GO-CAMs from Reactome more reliable, or something else? (If something else, no explanation needed.)

dustine32 commented 1 year ago

@deustp01 Oh this is nothing new, just merging the code that we used for the new models in #136 into the main code branch. I'm mainly doing this to cleanly add the code fix for the drug sets issue #182.