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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 explicit causal relation if rxns connected via same input/output instance #301

Closed dustine32 closed 1 year ago

dustine32 commented 1 year ago

For #276.

This adds a check to inferProvidesInput to only replace the existing causally_upstream_of relation with provides_input_for if the matched input and output instance IRIs are not equal, aka not the same individual: https://github.com/geneontology/pathways2GO/blob/35f360cc43ffdbbaa01a0d10eacb78c57e1daf66/exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java#L1386 In either case, the existing causally_upstream_of relation will still be removed: https://github.com/geneontology/pathways2GO/blob/35f360cc43ffdbbaa01a0d10eacb78c57e1daf66/exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java#L1397