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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Change R-HSA-74247 to map to hypoxanthine oxidase activity (GO:0070675) #127

Closed ukemi closed 3 years ago

ukemi commented 3 years ago

Currently this reaction: Hypoxanthine + H2O + O2 => Xanthine + H2O2

is mapped to xanthine oxidase activity (GO:0004855: Catalysis of the reaction: xanthine + H2O + O2 = urate + hydrogen peroxide.). I think it would be better mapped to GO:0070675: Catalysis of the reaction: hypoxanthine + H2O + O2 = xanthine + H2O2.

deustp01 commented 3 years ago

Yes. I'll fix the Reactome annotation. Specifically, 1) create parallel reactions proceeding via oxidase and dehydrogenase, both catalyzed by the same enzyme, and 2) look for annotatable evidence of a mechanism to switch between these two acticvity forms, starting from PMID: 7798166.

ukemi commented 3 years ago

I was actually going to open up a separate ticket for the parallel pathways. This ticket was just about switching a single activity. I assume by yes, you think this is an ok way to track tasks? Extending this, I wonder if it shouldn’t be a two way street. For example the discussion we just had via email could have been tasks in a ticket assigned to me, adding reactants and locations.

Yes. I'll fix the Reactome annotation. Specifically, 1) create parallel reactions proceeding via oxidase and dehydrogenase, both catalyzed by the same enzyme, and 2) look for annotatable evidence of a mechanism to switch between these two acticvity forms.

deustp01 commented 3 years ago

Right - good way to track. (In my mind fixing the existing reaction and creating the new one are two aspects of the same problem, but, yes, there's the immediate fix and a related new annotation to make)

deustp01 commented 3 years ago

Currently this reaction: Hypoxanthine + H2O + O2 => Xanthine + H2O2

is mapped to xanthine oxidase activity (GO:0004855: Catalysis of the reaction: xanthine + H2O + O2 = urate + hydrogen peroxide.). I think it would be better mapped to GO:0070675: Catalysis of the reaction: hypoxanthine + H2O + O2 = xanthine + H2O2.

Fixed - see revised reaction on development site (will become visible on public site with June 2021 Reactome release)