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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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carbon catabolite repression of transcription from RNA polymerase II promoter by glucose #21442

Open ValWood opened 3 years ago

ValWood commented 3 years ago

carbon catabolite repression of transcription from RNA polymerase II promoter by glucose (GO:0000433)

Which term do you propose this term merge into? Provide GO ID and term label GO:0000122 negative regulation of transcription by RNA polymerase II

Reason for merge This really describes the phenotype "carbon catabolite repression' and is non standard wording for GO terms

Any other information Obsoletion might be better because the correct way to annotate would be

GO:0000122 negative regulation of transcription by RNA polymerase II during GO:0071333 cellular response to glucose stimulus

ValWood commented 3 years ago

in fact it is so confusing, there are even semantically identical terms like

carbon catabolite repression of transcription from RNA polymerase II promoter by glucose (GO:0000433) AND GO:0061987 negative regulation of transcription from RNA polymerase II promoter by glucose

ValWood commented 3 years ago

To illustrate, we annotated the same thing in 3 ways!

Screenshot 2021-05-19 at 16 16 50
pgaudet commented 4 months ago

See https://github.com/geneontology/go-annotation/issues/5204

There is a good review here: https://pubmed.ncbi.nlm.nih.gov/31119370/

It seems this may be a signaling pathway that responds to nutrient sources, leading to transcription. In any case, I think this fit better under 'carbon utilization' than under transcription.

@srengel @marcfeuermann Any insights about these terms?

srengel commented 4 months ago

  1. this is specifically about transcription, so 'utilization' is not the best way to describe this.

  2. it's not a pathway that LEADS to transcription, it's a pathway that REPRESSES transcription of genes necessary for utilization of non-preferred carbon sources (the repression part) when preferred carbon sources are present (the glucose part).

but it's not just glucose, it can be other preferred carbon sources.

therefore, @ValWood 's suggestion to annotate as following is correct:

GO:0000122 negative regulation of transcription by RNA polymerase II during GO:xxxxxxx cellular response to [whichever] stimulus