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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 mapping of R-HSA-2395872 from GO:0008828 to GO:0016818 or request a new term #130

Closed ukemi closed 3 years ago

ukemi commented 3 years ago

R-HSA-2395872 is: NUDT1 hydrolyses 2-OH-ATP to 2-OH-AMP GO:0008828 is: Catalysis of the reaction: deoxy-ATP + H2O = dAMP + diphosphate.

I think we need to either move this up to the very generic parent: GO:0016818--Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.

Or request a new term: term 2-hydroxy-ATP hydrolase activity def: Catalysis of the reaction: 2-hydroxy-ATP + H2O = 2-hydroxy-AMP + diphosphate. rhea: new reaction ref: PMID:11139615 is_a parent: GO:0016818

I think the latter, do you agree?

ukemi commented 3 years ago

I think we have a similar issue with R-HSA-2395818 but there is a Rhea for this: RHEA:31583 2-hydroxy-dATP + H2O = 2-hydroxy-dAMP + diphosphate + H+

deustp01 commented 3 years ago

Yes, that looks right - made the NTR request on github/.../go-ontology with pathways2GO label, so closing this one.