[annotation] question about use of 'colocalizes with'

[E Dimmer]

Hi,

Like Val, I wouldn't use the colocalizes_with qualifier as a matter of 
course for results obtained from colocalization experiments, as results 
often provides a clear indication of the proteins location. However we 
do use colocalizes_with when a protein has been shown to be transiently 
associated with subcellular component (e.g. shuttling between nucleus 
and cytoplasm) or peripherally  with a complex.  

I think that the page must have been removed from the GO web site's 
menus at some point, I agree with Val that (once rewritten) the page 
should included in or at the very least linked to from the Annotation 
Guide page.

Emily

Valerie Wood wrote:
> 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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    Emily Dimmer
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    EMBL-EBI
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