The direction of transport in model R-HSA-6787639 is backwards

geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)

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The direction of transport in model R-HSA-6787639 is backwards #319

Open ukemi opened 1 month ago

ukemi commented 1 month ago

In the Reactome pathway R-HSA-6787639 (GDP-fucose biosynthesis) the last step is the transport of the GDP-fucose from the cytosol to the Golgi. Reactome has an input with the molecule in the cytosol and the output in the Golgi, but the imported model says the target start location is in the Golgi and the end location is in the cytosol. This is backwards.

deustp01 commented 1 month ago

It indeed looks like a correctly annotated Reactome reaction got incorrectly converted to GO-CAM. I've checked the annotation details in gk_central and it looks like everything is correct there: the input is truly localized to the cytosol and the output to the Golgi lumen.