clean up of transcriptional regulation terms

[Antonialock]

So, Val and I think some terms need to be obsoleted in the ontology.

We started talking about it when I requested a long precomposed BP to describe fep1. Fep1 is a DNA binding transcriptional repressor that suppresses transcription of iron starvation genes when there is plenty of iron around. I requested: "negative regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron"

Melanie told me that the term is too specific and I could either annotate to "unconnected" process terms, or string them together using annotation extensions. I definitely want to nest the terms because they "belong" together.

Val then pointed out to me that I was trying to incorporate the function of the enzyme in my process term - and I could make the term a lot less nasty by taking the "MF part" out. We connect MFs to BPs using extensions, and I shouldn't treat the transcription factors any differently.

This is an example annotation for one of our kinases:

The kinase is also annotated to these biological processes as separate annotations, but here they have been connected to the MF.

So, instead of annotating fep1 to "negative regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron"

I should annotate it to the MF transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding has_input gene:sib1 part_of negative regulation of ferrichrome biosynthetic process in response to iron

and to the BP negative regulation of ferrichrome biosynthetic process in response to iron

I'm not focussing on transcripton factors at the moment, so it is very confusing that there are terms in the ontology that we "shouldn't" annotate to (if we can't request new sibling terms then I suppose we shouldn't really annotate to the existing terms anyway right?)

So, I'm asking if you could obsolete all the transcription regulatory terms that we "shouldn't" annotate to (and for which you won't create new sibling terms) - many are descendants of GO:0006357

@ValWood @mcourtot

[ValWood]

There now seem to be annotations to some of these terms, even though the spreadsheets are completed...

[pgaudet]

These have no more EXP annotations:

• [x] GO:0097239 positive regulation of transcription from RNA polymerase II promoter in response to methylglyoxal
• [x] GO:0036252 positive regulation of transcription from RNA polymerase II promoter in response to menadione
• [x] GO:1904765 positive regulation of transcription from RNA polymerase II promoter in response to maltose
• [x] GO:0061405 positive regulation of transcription from RNA polymerase II promoter in response to hydrostatic pressure
• [x] GO:0061399 positive regulation of transcription from RNA polymerase II promoter in response to cobalt ion
• [x] GO:0061410 positive regulation of transcription from RNA polymerase II promoter in response to ethanol

[pgaudet]

Obsoleted - no annotations:

• GO:1900464 negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA polymerase II promoter
• GO:1900463 negative regulation of cellular response to alkaline pH by negative regulation of transcription from RNA polymerase II promoter
• GO:0061394 regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance
• GO:0061395 positive regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance 1 SGD
• GO:0061421 positive regulation of transcription by oleic acid
• GO:0061422 positive regulation of transcription from RNA polymerase II promoter in response to alkaline pH
• GO:0061412 positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation
• GO:0061400 positive regulation of transcription from RNA polymerase II promoter in response to calcium ion
• GO:0061409 positive regulation of transcription from RNA polymerase II promoter in response to freezing
• GO:0036278 positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation
• GO:0061403 positive regulation of transcription from RNA polymerase II promoter in response to nitrosative stress
• GO:1990095 positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species
• GO:1990096 positive regulation of transcription from RNA polymerase II promoter in response to superoxide
• GO:1902901 positive regulation of transcription from RNA polymerase II promoter involved in stress response to cadmium ion
• GO:2000721 positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation
• GO:0061420 regulation of transcription from RNA polymerase II promoter in response to biotin starvation

[lreiser]

TAIR is done

[pgaudet]

• [x] GO:2000820 | 'negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation'
• [x] GO:1901522 | 'positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus'
• [x] GO:1902097 | 'positive regulation of transcription from RNA polymerase II promoter involved in defense response to Gram-negative bacterium'
• [x] GO:1904081 | 'positive regulation of transcription from RNA polymerase II promoter involved in neuron differentiation'
• [x] GO:2000763 | 'positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process'
• [x] GO:0006990 | 'positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response'

Reviewed here https://github.com/geneontology/go-annotation/issues/4694

[pgaudet]

Closing. Left overs are in #26002 #26003 and #26004

[pgaudet]

• [x] GO:0061425 positive regulation of ethanol catabolic process by positive regulation of transcription from RNA polymerase II promoter