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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 intervening Molecular Event between MFs and black box BPs #294

Open vanaukenk opened 8 months ago

vanaukenk commented 8 months ago

From the 2023-10-12 Reactome2GO NYU meeting:

When a black box reaction with a corresponding GO BP exists, remove the intervening Molecular Event between that BP and the upstream MF.

The upstream MF will be 'part of' the BP.

We will wait to see if there are any cases where this rule may not be correct, for example when a black box BP is inserted into the causal chain.

dustine32 commented 8 months ago

For example, in test model R-HSA-9842908 GOCAM Nuclear signaling by ERBB4 image

dustine32 commented 8 months ago

Following the string pattern "is xrefed to this process" to this line: https://github.com/geneontology/pathways2GO/blob/d199888241a08188f85f2376b1c5e1f45f42e3c2/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java#L1609 This block should be where we can plug in the change.