Linking targets of GO functions / modifications

[gocentral]

I'm working with Alan Ruttenberg to see what kinds of information we can associate with PRO. We're looking at protein modifications (phosphorylation, methylation, and so on). One route is to look at the GO functions corresponding to the modifications. An example is 'histone H3-monomethyl-K4' (GO:0034649). We understand that the proteins annotated to this term act as the catalyst, but couldn't find any links to the target of this activity (the target seems to be methylated SETD7).

I would like to request axioms that link functions corresponding to modifications like this to their targets.

Reported by: jpbona

Original Ticket: geneontology/ontology-requests/10530

[gocentral]

Val - I didn't write the question but I directed Jonathan here.

Jonathan, I thought you were after logical definitions connecting GO activities to their targets (specific modified forms in PRO) - but it sounds like you are interested in the gene product carrying out the activity (for the latter, this is encoded in annotations)

On Sat, Nov 16, 2013 at 1:02 AM, Valerie Wood val_wood@users.sf.net wrote:

Hi Chris,

I don't understand the q, but do you mean the 'target' or the 'effector' the target is histone H3, so its a special case as its encoded in the term. val

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\ [ontology-requests:#10530] Linking targets of GO functions / modifications**

Status: open Created: Fri Nov 15, 2013 08:44 PM UTC by Jonathan Bona Last Updated: Fri Nov 15, 2013 08:44 PM UTC Owner: Chris Mungall

I'm working with Alan Ruttenberg to see what kinds of information we can associate with PRO. We're looking at protein modifications (phosphorylation, methylation, and so on). One route is to look at the GO functions corresponding to the modifications. An example is 'histone H3-monomethyl-K4' (GO:0034649). We understand that the proteins annotated to this term act as the catalyst, but couldn't find any links to the target of this activity (the target seems to be methylated SETD7).

I would like to request axioms that link functions corresponding to modifications like this to their targets.

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Original comment by: cmungall

[gocentral]

This was discussed on the GO annotation call, minutes here:

http://gocwiki.geneontology.org/index.php/Annotation_Conf._Call_November_26,_2013#Discussion

Histone kinase issue:

    Creating amino acid position specific terms in this case can lead to incorrect annotations. These terms should be evaluated and removed by the ontology group leaving the higher level term
    Curators should request PRO IDs for the modified/specific phosphorylated form of the histone and include that ID in col-16 with has_output relation. 

The minutes state that terms such as GO:0034649 will be removed. This wasn't quite my recollection of the meeting. However, the terms as-is need some kind of refactoring as it positions may vary across taxa. My suggestion was to punt this to PRO to come up with the recommended strategy for genericising modified proteins

Original comment by: cmungall

[gocentral]

I realised that you did not write the question after I added the comment ;)

I know we don't usually have specific residues modified in GO terms (or even gene products), and histone modifications are a special case. I think it is useful if we had some way of keeping the "equivalent residues in different species" notation at the ontology level. So we can preserve the information in the histone code

Original comment by: ValWood

[gocentral]

Actually is the suggestion that ALL of these histone modifiying terms are obsoleted? Nooooo. They are a special case but because the different modifications have such different and major consequences they are really useful as explicit terms in GO to make process links.

Original comment by: ValWood

[gocentral]

I'm the owner of this ticket but probably won't have the time to take this forward for a while.

Original comment by: cmungall

[gocentral]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,3 @@
-
 I'm working with Alan Ruttenberg to see what kinds of information we can associate with PRO. We're looking at protein modifications (phosphorylation, methylation, and so on). One route is to look at the GO functions corresponding to the modifications. An example is 'histone H3-monomethyl-K4' (GO:0034649). We understand that the proteins annotated to this term act as the catalyst, but couldn't find any links to the target of this activity (the target seems to be methylated SETD7).

 I would like to request axioms that link functions corresponding to modifications like this to their targets.

• status: open --> open-later

Original comment by: paolaroncaglia

[gocentral]

• Priority: 5 --> 4

Original comment by: cmungall

[gocentral]

We should axiomatize these classes. Had no time to do so. Also still awaiting advice on homology of sites

Original comment by: cmungall

[pgaudet]

@hdrabkin as a PRO representative - do you see what the action could be here ?

[hdrabkin]

This seems more like an annotation issue; A phosphorylated protein would get a set a specific annotations whereas it's unphosphorylated form would not; PRO would have ids for each of the two forms.

[pgaudet]

So it looks like there's nothing to do - I'll close.

@cmungall if we misread this please reopen.

Thanks, Pascale