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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Remove extraneous edges in imported models #276

Open suzialeksander opened 1 year ago

suzialeksander commented 1 year ago

There are some redundant edges added to models upon import:

image (3) Example from YeastPathways_YEAST-SALV-PYRMID-DNTP

I think the other major relation that did this was "casually upstream of".

Can we remove these before https://github.com/geneontology/pathways2GO/issues/275?

Also tagging @thomaspd

ukemi commented 11 months ago

Note that this is the opposite of what we do for the Reactome models. For those, we infer and retain the causal relationship between the functions.

dustine32 commented 11 months ago

@ukemi Right! In fact, the last commit 35f360c was made to fix a Reactome test that broke due to this. The fix ties the causal relation removal to the use of common intermediate input/output molecules as in the image from the top comment: image If relation chain 1 exists, then relation 2 will be removed.

For Reactome, (as you said above) I haven't yet switched the input/output molecule handling over to the scheme shown for relation chain 1, but weren't we talking about doing that? If yes, is the desired Reactome behavior that we have both relation chain 1 and relation 2 between input/output-connected reactions?

ukemi commented 11 months ago

I'd actually like both. To me removal of the causal relation (even if it can be inferred) goes against the GO-CAM data model which is supposed to link functions with causal relations..

ukemi commented 7 months ago

I think that the group decided that we would follow the method described above. We need to do this with the Reactome import as well.

deustp01 commented 7 months ago

follow the method described above

Sorry - which method above? Keep both of links 1 and 2 or only keep 1?