[annotation] question about use of 'colocalizes with'

[Valerie Wood]

Hi Rama,

I don't think a qualifier is required in this case.
However, one of the current examples is a pombe example (clp1), and even 
in the example I don't know if it is really necessary. Do we need to use 
co-localizes to capture transient localization? I know I haven't done  
this consistently.

I have used it in cases like karyopherins (like sal3)
where authors report  a nuclear pore localization to indicate that this 
is not a 'component of' the nuclear pore. I think this is an example of the

"This qualifier may also be used in cases where the resolution of an 
assay is not accurate enough to say that the gene product is a bona fide 
component member"
type ?

I don't think that it was devised to capture the results of a 
'colocalization' experiment, when the component term which is indicated 
by the experiment is unambiguous.

My 2C,

(By the way, without the link the documentation for this is quite hard 
to find, I couldn't see it via the 'documentation' or 'Annotation Guide' 
links I'm not sure why 'Annotation Conventions' is separate from 'GO 
Annotation guide')





Val



Rama Balakrishnan wrote:

> reposting...
>
> rama
>
> On Dec 19, 2007, at 12:50 PM, Rama Balakrishnan wrote:
>
>>
>> Hi All,
>>
>> We have a question about the use of 'colocalizes with' qualifier.
>>
>> We are curating-
>>
>> PMID: 16713564
>>
>> Downregulation of PP2A(Cdc55) phosphatase by separase initiates
>> mitotic exit in budding yeast.  Queralt E, Lehane C, Novak B, Uhlmann
>> F. Cell. 2006 May 19;125(4):719-32.
>>
>> In the section titled " Separase-Dependent Downregulation of PP2ACdc55
>> at Anaphase Onset" the authors say that 'Colocalization with Net1
>> revealed nucleolar enrichment of Cdc55 in metaphase'....
>
>
>> The figure legend for
>> Fig 5A says 'Cdc55 localization in the nucleolus'.
>>
>> Should Cdc55 be annotated to 'nucleolus' directly or to 'colocalizes
>> with nucleolus'? The documentation on how to use this qualifier should
>> be updated with more examples.
>>
>>   http://www.geneontology.org/ 
>> GO.annotation.conventions.shtml#colocalizes_with
>>
>> Thanks for your help,
>>
>> Rama
>
>
>
>
>



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