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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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obsolete terms (non existent process) under histone acetylation #12490

Closed ValWood closed 8 years ago

ValWood commented 8 years ago

These terms (not used for any EXP annotation) Look the wrong way around to me? Histone acetylation regulates transcription, not transcription regulates histone acetylation. Did

Process GO:0100030 regulation of histone acetylation by transcription from RNA polymerase II promoter

Process GO:1900411 regulation of histone acetylation by regulation of transcription from RNA polymerase II promoter

I checked the history and I can't see a ref. Apologies if it was me... I don't recall it.....

RLovering commented 8 years ago

yes see also #11583

RLovering commented 8 years ago

this change was requested in the ticket listed above Best Ruth

tberardini commented 8 years ago

Hi all, I read through the linked issue and though related, I don't see a request to alter/edit either GO:0100030 or GO:1900411 in it.

However, the discussion both there and in this issue suggests that the following terms need obsoletion because the histone modification regulates transcription not the other way around. I looked in the ontology for the related terms and rounded up the following set. None of the terms have any annotations associated to them.

Unless there are any objections, I will send out an obsoletion notice for these terms.

Thanks,

Tanya

srengel commented 8 years ago

i read these terms as regulating the transcription of proteins involved in DOING the histone modification/methylation/acetylation, etc.

is that what they are supposed to mean?

ukemi commented 8 years ago

Scanning the original reference (PMID:15218150) that is in the xref for GO:1900411, it looks like the process actually exists.

tberardini commented 8 years ago

There are two sets of terms:

regulation of histone modification by regulation of transcription... and regulation of histone modification by transcription...

Is there a case for retention of one set (the regulation by regulation one) and not the other? Or should we keep both?

ValWood commented 8 years ago

Re PMID:15218150

ATF1 is a transcription factor, but I think this could be a moonlighting function where atf1 can nucleate heterochromatin assembly in the mating type region (it also has another role binding to recombination hotspots). This paper is not describing transcriptional regulation of histone modification....

tberardini commented 8 years ago

Resending comment from a month ago. I was getting ready to send obsoletion notice when we hit a snag. Please comment on the preferred course of action.

There are two sets of terms:

regulation of histone modification by regulation of transcription... and regulation of histone modification by transcription...

Is there a case for retention of one set (the regulation by regulation one) and not the other? Or should we keep both?

ValWood commented 8 years ago

For pombe, all examples of histone modification are regulated post-transcriptionally regulated. I still think they should go. The original ref used by us pointed out by David seems to be another role of Atf1, unrelated to its role in transcription (and, it could be an indirect effect at that...)

tberardini commented 8 years ago

@ValWood : " I still think they should go."

Which terms are 'they'? All of the ones I listed in the checklist above?

ValWood commented 8 years ago

anything or descendants regulation of histone acetylation by transcription

(I don't think any of these terms have experimental annotations?)

tberardini commented 8 years ago

Unless there are objections, I will send out an obsoletion notice for all SIX terms in the checklist above on Tuesday, 7/26.

tberardini commented 8 years ago

Obsoletion email sent out today:

Dear all,

The proposal has been made to obsolete the following terms:

GO:1900410, regulation of histone modification by regulation of transcription from RNA polymerase II promoter GO:1900411, regulation of histone acetylation by regulation of transcription from RNA polymerase II promoter GO:1900412, regulation of histone methylation by regulation of transcription from RNA polymerase II promoter GO:0100030, regulation of histone acetylation by transcription from RNA polymerase II promoter GO:0100029, regulation of histone modification by transcription from RNA polymerase II promoter GO:0100031, regulation of histone methylation by transcription from RNA polymerase II promoter

The reason for obsoletion is that the terms represent processes that do not exist, the histone modification regulates transcription not the other way around. The longer discussion on this issue can be reviewed and added to here:

https://github.com/geneontology/go-ontology/issues/12490

None of the terms have any annotations.

* Unless objections are received by August 9, 2016, we will assume that you agree to this change. *

On behalf of the GO ontology editors,

Tanya

tberardini commented 8 years ago

Whoops. Forgot about obsoleting these terms. Done now.