However there are quite a number of GO function terms which occur on
discrete portions of a protein sequence, for instance many of the child
terms of 'binding' (GO:0005488) (protein, ATP, lipid, co-factor etc)
and simple catalytic domains.
I feel that there could be a mid-way point - there are GO terms that can
be annotated to a specific region of a sequence where it is also
appropriate for the function to be 'inherited' by the whole protein.
But also there there are domain terms which are not appropriate for a
whole protein - then these should go into another ontology, which could
be a composite of GO terms and domain-specific terms.
So while protein domain function annotators and and gene-product
annotators will need to work from a different term set and add different
parameters to their annotations, where a domain has been annotated to a
GO term e.g. 'DNA binding' IDA , then we could consider including these
into GO.
Would this suggestion be more acceptable to GO folk?
Emily
Michael Ashburner wrote:
> 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
>>
>>
>>
--
************************************
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
************************************