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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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GPAD export erroneous line for molecular_event as subject #286

Open dustine32 opened 1 year ago

dustine32 commented 1 year ago

In pathway R-HSA-983189 (Kinesins - imported from: Reactome), the GPAD export produces only one annotation line and it's kind of weird:

!gpa-version: 1.1
obo go/extensions/reacto.owl#molecular_event    part_of GO:0007018  Reactome:R-HSA-983189   ECO:0000313         20230905    Reactome        contributor=GOC:reactome_curators|noctua-model-id=gomodel:R-HSA-983189|model-state=development

There are no annotatable entities (e.g. controllers) in this model. All activities are molecular_event. I think this GPAD export should just return blank/no annotations. Not sure if this behavior is being triggered by bad model data or the GPAD export function in minerva.

Tagging @balhoff

balhoff commented 1 year ago

@dustine32 we might need to add a filter for this term. I think it would go here: https://github.com/geneontology/minerva/blob/a6a9d0b84aac558fb077b3f2596bb5412710e74c/minerva-converter/src/main/resources/org/geneontology/minerva/legacy/sparql/gpad-basic.rq#L68

Does that sound right?