[Annotation] phenotype or GO-still struggling

[Doug howe]

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