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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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canonical glycolysis (GO:0061621) is part of "phosphorylation" #22596

Closed ValWood closed 1 year ago

ValWood commented 2 years ago

canonical glycolysis (GO:0061621) has ancestry to "phosphorylation" which seems strange?

phosphorylation events are a part of glycolysis?

deustp01 commented 2 years ago

True, but only because canonical glycolysis is_a GO:0006757 "ATP generation from ADP" and any process tagged with GO:0006757 is_a (via several intermediate steps) GO:0016310 "phosphorylation" process, so this looks like a problem with descendents of phosphoryation, much broader than glycolysis. At the same time, making ATP from ADP does indeed involve phosphorylation so the assertion is factually correct.

This probably takes us back to the unfinished discussion of a couple of years ago about "currency chemicals" (Larry Hunter's term) also know as housekeeping molecules, and how to handle them in a way that recognizes their essential roles in processes without creating odd groupings like this one under phosphorylation.

ValWood commented 2 years ago

I guess this problem will also go away once we no longer represent modifications in the process ontology.

pgaudet commented 2 years ago

GO:0006757 "ATP generation from ADP" has a single child, GO:0006096 glycolytic process. Maybe it can be obsoleted and the grand-parent ' GO:0006091 generation of precursor metabolites and energy' is sufficient to describe the cellular role of glycolysis?

pgaudet commented 2 years ago

Anyway GO:0006757 "ATP generation from ADP" is confusing, it is_a GO:0006091 generation of precursor metabolites and energy but its 2 direct annotations are to kinases, Human Adenylate kinase 9 (Q5TCS8) and E. coli ppk (P0A7B1), which, as far as I can tell, are not involved in generating precursor metabolites and energy.

deustp01 commented 2 years ago

GO:0006091 generation of precursor metabolites and energy' is sufficient to describe the cellular role of glycolysis?

@ukemi @hdrabkin That sounds like a really good parent for canonical glycolysis - are there other downstream consequences of the reorganization we should worry about, that I'm missing because I don't know the details of the process ontology?

ukemi commented 2 years ago

It makes sense to me that 'generation of precursor metabolites and energy' should be a parent of glycolysis.

pgaudet commented 1 year ago

Duplicate of #21176