NTR: Reg of serine phosphorylation of STAT3

[gocentral]

Hi,

In process at the moment, we have:

GO:0042501 : serine phosphorylation of STAT protein --<GO:0033139 : regulation of peptidyl-serine phosphorylation of STAT protein --%GO:0033136 : serine phosphorylation of STAT3 protein

could I have a new term as a child of each of GO:0033139 and GO:0033136 please:

GO:NEW regulation of peptidyl-serine phosphorylation of STAT3 protein. Any process that modulates the frequency, rate or extent of the phosphorylation of a serine residue of the STAT 3(Signal Transducer and Activator of Transcription 3) protein.

Thanks, Becky

needed for curation of xTAK1 (O73613) in PMID:15004007. NLK directly phosphorylates the C-terminal serine residue in STAT3, and xTAK1 acts upstream of NLK. I could use GO:0033136, but think a new term would be more accurate.

Reported by: rebeccafoulger

Original Ticket: "geneontology/ontology-requests/5832":https://sourceforge.net/p/geneontology/ontology-requests/5832

[gocentral]

I dont understand why functions cannot represent specific gene products, while processes can? That seems inconsistent.

Pascale

Original comment by: pgaudet

[gocentral]

Classes of gene products, which are sometimes referred to by the names of specific well-characterized examples, can be included as substrates of processes. Neither the process nor the function ontology should include terms that describe a gene product.

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: mah11

[gocentral]

Do we really want to continue making such GO terms that refer to specific gene products? I'm thinking that it might be much more appropriate to annotate to GO:0033139 and then put STAT3 in column 16 (http://wiki.geneontology.org/index.php/Annotation\_Cross\_Products).

Original comment by: tberardini

[gocentral]

Switching over to using column 16 for these sorts of things would be fine with me; I was just explaining what our thinking and practice have been to date.

Do we want to grandfather in existing gp-specific terms, or merge them all with parents?

m

Original comment by: mah11

[gocentral]

I think we should merge them all with parents but am not sure of the right time to do that yet. Perhaps when all the relevant dbs (those that have existing annotations at the very least) have the ability to capture col 16 information somewhere in their database.

Original comment by: tberardini

[gocentral]

sounds good to me

We need a clever way to find the terms we'd want to merge ... any ideas?

Original comment by: mah11

[gocentral]

Hi Becky,

Are you ok with the suggestion to just annotate to GO:0033139 and then put STAT3 in column 16? If so, then we can close this request and open another one with the more broad subject of 'identifying gp specific process terms for merging' or something like that.

(Or do you just want to use this one, Midori?)

Tanya

Original comment by: tberardini

[gocentral]

I don't have a super-strong preference about SF items ... I guess a new item would be a bit easier to find.

m

Original comment by: mah11

[gocentral]

Hi Tanya and Midori,

I'm happy to annotate to GO:0033139, and I've put a note in our tool to add STAT3 to column 16 when it becomes available!

Thanks for looking at this. Looks like there's a lot of term merging that's going to be done!

cheers Becky

Original comment by: rebeccafoulger

[gocentral]

Thanks, Becky.

For finding the ones to merge, here's one strategy:

find all terms whose name ends in the word "protein" and are not obsolete

with this, I get 58 matches, many of which are specifically for particular STAT proteins.

Original comment by: tberardini

[gocentral]

oh, very clever!

Original comment by: mah11

[gocentral]

This request has been brought up again by Varsha in a new SF item. Please add any updates/comments in the new SF item:

https://sourceforge.net/tracker/?func=detail&aid=3174857&group\_id=36855&atid=440764

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-duplicate

Original comment by: rebeccafoulger