#11757 ER proteasome terms

[RFoulger]

Following on from: https://sourceforge.net/p/geneontology/ontology-requests/11715/:

What is the source for the ER proteasome terms?: ER proteasome complex ; GO:0031596 and 6 child terms.

The ER proteasome terms don't list a publication and there are no annotations to the terms. I've been annotating ERAD where misfolded/unfolded proteins are transported out of the ER and subsequently degraded by the cytosolic proteasome, but I haven't yet come across an ER proteasome in the literature.

If it doesn't exists, the terms should be obsoleted. If it does indeed exist, a reference should please be added to the term definitions.

Posting on SF incase anyone has better knowledge.

Thanks!

[Tanya Berardini]

Definition ref says GOC:mah. Consulting Midori in case her amazing memory holds more information.

Term history:
http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031596#term=history

Added in 2005.

[Tanya Berardini]

Midori -please check. Reassign back to me for any edits. Thanks.

[Midori Harris]

From the terms with neighboring IDs, I'm guessing that GO:0031596 traces back to a request we got to add terms for proteasomes in various subcellular locations. I don't remember from whom or by what route (email, SF, etc.). At the time, I added the requested terms, but probably trusted the requester(s) -- I didn't and don't have much relevant specialist knowledge, and I don't now remember how much supporting evidence accompanied the request. I infer that there weren't any literature references included, because if there had been I'd have put them in as def dbxrefs.

[Midori Harris]

I don't remember enough just this minute to make a case for keeping GO:0031596.

[Tanya Berardini]

Talking about obsoleting the following terms because of lack of proof of existence in the literature:

GO:0031602 ER proteasome core complex
GO:0031599 ER proteasome regulatory particle
GO:0031596 ER proteasome complex
GO:0031605 ER proteasome core complex, alpha-subunit complex
GO:0031608 ER proteasome core complex, beta-subunit complex
GO:0031611 ER proteasome regulatory particle, base subcomplex
GO:0031614 ER proteasome regulatory particle, lid subcomplex

I will send obsoletion email next week.

[Tanya Berardini]

Note that the term, 'GO:0000835 ER ubiquitin ligase complex' will lose the parentage to 'ER proteasome complex' but will retain its other parents.

[Tanya Berardini]

Sent today:
Dear all,

The proposal has been made to obsolete:

ER proteasome complex ; GO:0031596 and its 6 part_of child terms:

GO:0031602 ER proteasome core complex
GO:0031599 ER proteasome regulatory particle
GO:0031596 ER proteasome complex
GO:0031605 ER proteasome core complex, alpha-subunit complex
GO:0031608 ER proteasome core complex, beta-subunit complex
GO:0031611 ER proteasome regulatory particle, base subcomplex
GO:0031614 ER proteasome regulatory particle, lid subcomplex
Reasons for obsoletion and a proposed replacement term are discussed in the following Sourceforge issue:

https://sourceforge.net/p/geneontology/ontology-requests/11757/

Please review the above issue for full details and to make comments.

There are no direct annotations to this term or its 6 part_of children terms.

http://amigo.geneontology.org/amigo/term/GO:0031596

Unless objections are received by June 29th, we will assume that you agree to this change. Please direct all comments to the SF issue mentioned above.

Thanks,

Tanya Berardini
on behalf of the Ontology Editors group

[Tanya Berardini]

Terms have been made obsolete.