[Annotation] ligands, receptors, and signaling pathways

[Doug howe]

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).  Where do 
signaling pathways end?  That is perhaps a harder question with a 
greater variety of answers.  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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-- 
Doug Howe, Ph.D.
ZFIN Scientific Curator
Zebrafish Nomenclature Coordinator