[Annotation] ligands, receptors, and signaling pathways

[Ruth Lovering]

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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