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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Allow shared intermediate small molecules for Reactome #313

Closed dustine32 closed 5 months ago

dustine32 commented 8 months ago

For #308.

Removes the conditional criteria blocking the sharing of has_output/has_input small molecule instances for Reactome models.

This intermediate sharing pattern was initially added for YeastPathways models and just I realized there was previously no filter to restrict this to only SmallMolecule BioPAX classes. I think this was ok for YeastPathways since their pathway intermediate input/outputs were always small molecule classes. However, this change broke a test testInferProteinLocalizationProcess for Reactome R-HSA-4641262 because a protein CTNNB1 was an intermediate input/output in part to represent a protein transport activity and the new intermediate sharing pattern was breaking the inference logic. To fix, I just limited this intermediate sharing to SmallMolecule.

ukemi commented 8 months ago

This works! At risk of being uninformed, what if the input-output step was put after the inference of all functions? The CTNNB1 is the output of the 'Beta-catenin is released from the destruction complex' and the input of the black box 'Beta-catenin translocates to the nucleus'.

deustp01 commented 8 months ago

Other cases where gene products or complexes can be output / input connectors would include signaling cascades and initiation of DNA replication.

dustine32 commented 8 months ago

@ukemi Yes, I think that's a very sensible suggestion though with how the code is currently set up, it'll take some more refactoring work to plug that in. We may be forced to do that at some point.

dustine32 commented 5 months ago

Merging now as this commit has been used for the last two Reactome release loads (87 and 88).