[Annotation] ligands, receptors, and signaling pathways

[Jodi Hirschman]

We have done the same with the S. cerevisiae receptors that function  
in pheromone response, STE2 and STE3. They are annotated to
GO:750 pheromone-dependent signal transduction during conjugation  
with cellular fusion

which is a child term of G-protein coupled receptor signaling pathway

Because receptor binding is essential for signaling to occur, it  
seems to me that the receptor should be considered part of the pathway.

Jodi


On Jun 17, 2008, at 9:00 AM, Ruth Lovering wrote:

> Phew, Varsha and I have been doing this too
> Ruth
>
> On 17 Jun 2008, at 13:23, David Hill wrote:
>
>> I have always annotated both ligands and the receptors to the  
>> specific signaling pathways.
>>
>> David
>>
>> 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.
>>>>>
>>>>
>>>
>>>
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