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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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question - mixing sets and complexes #61

Closed goodb closed 5 years ago

goodb commented 5 years ago

@deustp01 I'm looking at the complex Cyclin E/A:CDK2:p-S130-CDKN1A,p-T187-CDKN1B:CUL1:SKP1:SKP2:CKS1B which contains a mixture of 'has_component' and 'has_member' relationships to its parts.

Screen Shot 2019-04-03 at 10 21 17 AM

As I understand so far, the 'has_member' relations indicate a set, not a complex. When these occur at the top level, they are converted to Unions of the members. Right now the converter ignores this distinction and collapses all sub-complexes and sub-sets into one long parts list as if they were all equal members of the complex.

It seems like it would be more accurate to capture the set entities properly and attach them as units to the larger complex object. e.g. complex has_part union[a,b] , complex has_part c, etc..

Thoughts on that?

goodb commented 5 years ago

Closing. I think we have a solution working. Refinements to it can be their own issues as they arise.