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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Recursive drug tests required for sets and complexes for #182 #206

Closed dustine32 closed 1 year ago

dustine32 commented 1 year ago

For #182.

This just digs into set and complex member components to look for the drug flag. If found on any member component, the entire set or complex is tossed.

ukemi commented 1 year ago

@deustp01 Is this ok for now, or do we want to retain the members of sets and complexes that aren't drugs?

deustp01 commented 1 year ago

Is this ok for now

Good question!

We will always want to exclude a complex that includes a drug as one of its parts as long as we want to say no activities mediated or influenced by drugs.

In the case of a set with both drug and non-drug members, the correct fix is to break the set into one of only drugs and one of everything else, so we can say no to the former. If Dustin's tally of weird sets is complete, there are only five of these, so just tossing them until Reactome does the correct patch looks like the orderly way to proceed.