[Annotation] ligands, receptors, and signaling pathways

[Jennifer Deegan (nee Clark)]

Hi,

If you all have little things that you have noticed about the signaling 
terms I'd really appreciate if you would note them on this page of the wiki:

http://wiki.geneontology.org/index.php/Signaling_-_pointers_from_the_community

I am trying to figure out which parts are the highest priority to be 
fixed and any information that you can give me, no matter how vague, is 
really helpful. Even if you can say 'X set of terms is very unclear and 
causes me a lot of problems' then that is a huge help as it gives me the 
annotators view, which is always incredibly instructive.

Thanks,

Jen


Valerie Wood wrote:

> 
> 
> Hi Doug,
> 
> I have annotated receptors  to signal transduction (or one of its 
> children) but not to the signaling pathway itself. I'd also like to know 
> if this is correct.
> I seem to remember that this was a previous consensus, but I find it 
> documented anywhere.
> 
> Val
> 
> 
> 
> Jennifer Deegan (nee Clark) wrote:
> 
>> Hi Doug,
>>
>> I'm starting to overhaul the signaling terms just now. I'll make a 
>> note of this for when I get down that far.
>>
>> Thanks,
>>
>> Jen
>>
>> Doug howe wrote:
>>
>>> Is it correct to annotate receptors with signaling pathway terms?  
>>> For example if a BMP receptor mutant is shown to have reduced bmp 
>>> signaling, should the receptor gene be annotated with the term 'BMP 
>>> signaling pathway', or are receptors themselves not part of the 
>>> pathway?  Ditto for ligands.
>>>
>>> The current def of 'BMP signaling pathway' is: A series of molecular 
>>> signals generated as a consequence of any member of the BMP (bone 
>>> morphogenetic protein) family binding to a cell surface receptor."
>>>
>>> This def makes it seem like the signaling pathway initiates with 
>>> things downstream of (and excluding) the receptor itself?
>>>
>>> Whatever the policy is on this, it might be a useful curatorial note 
>>> to include on such terms so curators can see the info right in term 
>>> browsers.
>>>
>>
> 
> 

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium