[go] Protein domain GO annotation

[Jim Hu]

Hi Emily,

Here are my thoughts:

On Nov 1, 2007, at 11:17 AM, E Dimmer wrote:

> Hi,
>
> Could I please ask people's opinion on the functional annotation of  
> protein domains/regions to the GO?
>
> I have been contacted by a group who would like to annotate GO  
> functions to identified disordered regions in proteins.
>
> The thought so far is that they would annotate to a  
> 'disordered_region' SO term, along with sequence co-ordinates, and  
> then also attach a GO term with a reference and evidence code.
> (I have spoken with Gabby Reeves from BioSapiens, who would be  
> happy to add 'disordered_region' terms to the BioSapiens protein  
> feature ontology section of SO).

This clearly would need to go in all of SO, not just BioSapiens

>
> For an annotation example: protein LEF-1 (Q9QXN1) has a disordered  
> region corresponding to residues 296 - 397. This domain has been  
> found to act to bend DNA, as reported in a experiment in PMID:  
> 7651541.
> In the normal course of GO annotation I would of course happily to  
> annotate the whole protein (Q9QXN1) to the DNA bending term (DNA  
> bending activity, GO:0008301), and while I might read about the  
> discrete region in the protein that is responsible for this  
> function I would not capture this data.

I don't think GO should capture the protein region coordinates  
directly, but it should be possible to find coordinates if they exist  
via something linked.

> However the IUP(Intrinsically Unstructured Protein) curators would  
> include the aa residue information in their annotations and want to  
> describe the individual functions that a protein's multiple domains  
> might have.
>
> So I assume that for these kinds of annotations, where an  
> equivalent GO term exists, a GOC annotation group could integrate  
> this group's annotations and relate it up to the whole protein/gene  
> product (and possibly being able to keep the SO term in the new  
> cross-reference column 16? but not the aa residue location?).

I don't recall how column 16 works, but wouldn't it point to a SO  
annotation for the protein that captures the residue locations.   
Isn't that also better from a normalization POV? i.e. if the gene  
model changes we have to change the GO annotation?

>
> While the majority of the function terms that the IUP community are  
> interested in applying to their domains do map quite straight- 
> forwardly to GO terms, there are some new ones which would need to  
> be requested. And some of these new terms seem to describe more  
> domain-specific, intra-protein function. For example, for some of  
> the function terms used in the DisProt database:
>
> flexible linker/spacer
> Provides separation and permits movement between adjacent domains
>
> entropic brisle
> A disordered region that creates a zone of exclusion by its  
> entropic movement
>
> entropic spring
> Provides a restoring force resulting from randomization of bond  
> torsion angles that become restricted upon stretching.
>
> (see: http://www.disprot.org/view_function_subclass.php)
>
> So, would GO be willing to add these types of terms? And how much  
> of the IUP communities annotation data would GOC groups be happy to  
> incorporate into their own annotation sets?

Consider the reductio - should GO annotate individual residues in an  
active site?  I think not, even though there is a lot of information  
of that kind in the literature and people find it useful.  So, I'd be  
opposed.  Not for GO.  Yes for SO or some other domain/feature  
ontology if SO is not quite appropriate.

Jim

>
> Thanks,
> Emily
>
>
> -- 
> ************************************
>    Emily Dimmer
>    GOA Coordinator
>    EMBL-EBI
>    Wellcome Trust Genome Campus
>    Hinxton
>    Cambridge CB10 1SD, U.K.
>    Tel:     +44 1223 494654
>    Fax:    +44 1223 494468
>    email:  edimmer at ebi.ac.uk
> ************************************
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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