[Annotation] ligands, receptors, and signaling pathways

[David Hill]

The receptor and the ligand are certainly parts of the pathway. However, 
things that control the concentration or availability of the ligand are not.


David

Jodi Hirschman wrote:
> 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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