[Annotation] ligands, receptors, and signaling pathways

[David Hill]

Hi Doug,
> Perhaps the signaling pathway terms would benefit from definitions 
> that more clearly include the starting and ending points of the 
> pathway.  It sounds like pathways start generally with the ligand and 
> receptor interacting (and these are included in the  pathway).
Yup, this is one of the things we hope to do in the signal transduction 
overhaul. The ligand-receptor interaction will certainly be the 
beginning of the pathways.
> Where do signaling pathways end?  That is perhaps a harder question 
> with a greater variety of answers.  
Yup, the idea is to find an end point to them all and relate them to the 
appropriate cellular processes with a regulates relationship.
> Making an effort to define the pathway end point would also be helpful 
> in clarifying if a gene product should be annotated with these types 
> of terms.
>
> Thanks for the clarification, sounds like we have majority agreement.
>
> -Doug
>
> David Hill wrote:
>> 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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>