search

geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
8 stars 0 forks source link

Orphan gene products are showing up in pathways #237

Closed ukemi closed 1 year ago

ukemi commented 1 year ago

As part of the checking the build 83 release, I went to my favorite pathway, gomodel:R-HSA-70171 . I noticed two 'orphaned' individuals NEUROD1 and PDX1 in the pathway. These are coming from an upstream event R-HSA-211346 that is in the current model as an upstream event, but that information seems to be getting lost in the current conversion. Although the function types are molecular events in the previous import, they make sense given the nature of black box reactions.

ukemi commented 1 year ago

The same thing is happening in R-HSA-204174. The GSH is showing up in the model as an orphan, but it activates a reaction that is filtered out by the drug rule. ping @deustp01

ukemi commented 1 year ago

It looks like this is happening generally for regulatory (controller) reactions that don't involve a chemical. See my comment here: #204

ukemi commented 1 year ago

This seems to have been 'cured' in the latest load.