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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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human "cofactor metabolism" annotation over-inflated #1868

Closed ValWood closed 1 year ago

ValWood commented 6 years ago

A lot of these appear to come from annotations of lots of "nucleoporins" to "regulation of glycolytic process"

e.g.

http://www.uniprot.org/uniprot/O75694 A8CG34 O15504 Q8NFH3 Q8NFH4 Q8NFH5 etc

I'm not sure if this one is covered by the pending fixes?

v

@deustp01

ValWood commented 6 years ago

At the same time, these all appear to have mitotic nuclear envelope disassembly: : Reactome protein sumoylation Source: Reactome regulation of cellular response to heat Source: Reactome regulation of gene silencing by miRNA Source: Reactome

deustp01 commented 6 years ago

Val's first comment - this looks like a valid annotation to me. An important part of regulating glucose metabolism in mammals is moving a glucokinase from the cytosol where it is active to the nucleus where it is not, and this movement is mediated by the nuclear pore complex, each component of which plays its normal role, whateer than is (so we are missing some distinctions between contributes-to and directly-involved).

Val's second comment - to the extent I can track those down, it looks like they are all results of the now-fixed failure to distinguish cargo from transported so those annotations should go away.

ValWood commented 6 years ago

But are the nuclear pore proteins really "regulating glycolysis" ? The thing which regulates the moving, is the regulator of glycolysis, if anything, not the nuclear pore components?

deustp01 commented 6 years ago

Two practical choices here. 1) Spend half a day digging through all the details of our "Regulation of Glucokinase by Glucokinase Regulatory Protein" (https://reactome.org/PathwayBrowser/#/R-HSA-70326&SEL=R-HSA-170822&) to find the exact sub-detail within it that fits the narrow GO view of "regulation", time that neither I or any of my colleagues have right now given our own production, maintenance, and grant-writing benchmarks that need to be satisfied, or 2) Just delete the "regulation" GO term from the pathway. That hides some good biological annotation but preserves the integrity of the slim. Preferences?

ValWood commented 6 years ago

@pgaudet ? @ukemi ? Are the nuclear pore proteins are really regulating "glycolytic process" If not, is deletion the best option (there are quite a lot).

ValWood commented 1 year ago

closing since "cofactor metabolism/metabolic process" is obsolete