[go] Protein domain GO annotation

[Michael Ashburner]

I agree with Ben, this is not for the GO.
Michael

On 1 Nov 2007, at 14:49, Benjamin Hitz wrote:

>
> As resident protein structure expert, no.
> Not that what they are doing is wrong, or not important - but it's  
> not a biological process/function/component of the gene (product)  
> in question.
>
> What's next?  We annotate alpha helices?
>
> Ben
>
> On Nov 1, 2007, at 9:17 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).
>>
>> 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.
>> 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?).
>>
>> 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?
>>
>> 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
>> ************************************
>
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
> Consortium
> Stanford University ** hitz at genome.stanford.edu
>
>
>