[Annotation] phenotype or GO-still struggling

[Julie Park]

Hi Doug,

SGD's practice on this is that if it is known that what is being  
observed is a secondary/downstream effect, then we only capture it via  
phenotypes and not as a GO process.  However, if the gene product in  
question is not well characterized or there is a conflict in the  
literature about whether it is a direct or indirect involvement then  
we would give it a GO annotation.

We've made a decision to use GO to try and capture the primary role of  
a gene product as much as possible and to reduce the duplication of  
effort required to capture data both in GO and as phenotypes.

Just our take on things.

Regards,
-Julie


On Jul 3, 2008, at 3:16 PM, Doug howe wrote:

> Hi David,
> It still seems like there is a line that has to be drawn somewhere.
> We've talked in the past about the scope of a process...when does it
> start and when does it end?  A gene that has as it's primary role
> regulation of transcription (perhaps binds DNA etc. etc.) may have a
> secondary effect upon eye morphogenesis.  However, the process of eye
> morphogenesis does not start with the binding of such a gene to a
> regulatory sequence...it is a downstream consequence....and perhaps it
> is the gene who's expression is being regulated that is really  
> involved
> in the downstream process.  It seems like there is a significant  
> amount
> of redundant curation work to do if we always annotate both GO and
> phenotype using the same GO process terms.  I'm not strongly opposed  
> to
> such annotations, I just want to revisit the discussion and see if
> anyone has other views on the issue.
> -Doug
>
> David Hill wrote:
>> Doug,
>>
>> I do this all the time. I just finished systematically doing all  
>> the homeobox genes in mouse. Many of them are annotated to things  
>> like pattern specification. I think in the future, it will be very  
>> nice to know these are playing roles in regulating transcription  
>> but that regulation is fundamental in other processes as well.
>>
>> David
>>
>> Doug howe wrote:
>>> I'm still struggling with the issue of whether to make a GO  
>>> annotation (processes in particular) or only phenotype  
>>> annotation.  The zebrafish literature is replete with mutant  
>>> papers that often describe phenotypes involving eyes, otic  
>>> vesicles, or pharyngeal arches, organ development etc.   Often,  
>>> the IEA annotations for a gene seems to indicate that the gene is  
>>> binding DNA, and may be some sort of transcriptional regulator.   
>>> Should such a gene be annotated with GO terms like 'otic vesicle  
>>> development', or 'eye morphogenesis', or should that be left for  
>>> phenotype annotations?
>>>
>>
>
> -- 
> Doug Howe, Ph.D.
> ZFIN Scientific Curator
> Zebrafish Nomenclature Coordinator
>
>
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