[Annotation] phenotype or GO-still struggling

[Karen Christie]

Hi Doug,

Another thing we've talked about at SGD, is whether or not a given gene, 
is specifically involved in a process or not. So for transcription 
factors, if a transcription factor is a regulatory factor that 
specifically affects transcription of phosphate metabolic genes, but does 
not affect transcription of most genes, then we would go ahead and give a 
GO annotation to the the relevant term for "phosphate metabolic process". 
However, if a transcription factor was a general transcription factor that 
affects (Pol II) transcription globally, we would only do GO process 
annotations to high level terms like "transcription from Pol II promoter", 
but not to more specific terms, like "phosphate metabolic process".

-Karen


On Thu, 3 Jul 2008, Julie Park wrote:

> 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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