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

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ukemi opened this issue Aug 14, 2024 · 2 comments
Open

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

ukemi opened this issue Aug 14, 2024 · 2 comments
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@ukemi
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ukemi commented Aug 14, 2024

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
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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.

@ukemi
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ukemi commented Dec 4, 2024

I'm still seeing this, for example model R-HSA-19675, inferred MF from reaction R-HSA-6803255.

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