[Ontology-editors] Action potential [was Re: Neurolex fixes]

[Jennifer Deegan (nee Clark)]

Hi Chris,

I am going to forward this on to Ian Paulson in case he has any thoughts 
on it. He is an electron tranport expert.

Jen

Chris Mungall wrote:

> 
> What kind of thing is an action potential and in which ontology would  
> we find it? Is it a wave? I'm not sure how bfo treats waves - as  
> processes? If so we'd expect to find action potential in GO.
> 
> In actual fact GO has regulation of action potential as a kind of  
> regulation of biological quality, so the change in PATO will need  
> coordinated in GO.
> 
> The GO def is: "Any process that modulates the frequency, rate or  
> extent of action potential creation, propagation or termination. An  
> action potential is a spike of membrane depolarization and  
> repolarization that travels along the membrane of a cell"
> 
> The supertype is:
> GO:0042391 ! regulation of membrane potential [DEF: "Any process that  
> modulates the establishment or extent of a membrane potential, the  
> electric potential existing across any membrane arising from charges  in 
> the membrane itself and from the charges present in the media on  either 
> side of the membrane."]
> 
> so I think something is not 100% correct in GO here. The change of  
> wording in the def between the term and its parent is suspect.  Membrane 
> potential appears to be a quality, but the action potential  is more 
> like a process in which a quality moves. I think RoAP in GO  may need 
> reclassified under RoBP.
> 
> we've done a lot of work on regulation of process and function in GO,  
> regulation of quality should be next, making sure we're consistent  with 
> PATO. This probably won't happen until after the GO mtg in March.
> 
> in the meantime, I tentatively support obsoletion of action potential  
> in PATO provided we can find some alternative home for it
> 
> 
> ------------------------------------------------------------------------
> 
> 
> 
> On Feb 2, 2009, at 2:19 PM, Maryann Martone wrote:
> 
>> Because we view PATO as being qualities.  In this case, the Action  
>> Potential would be the entity to which the quality is applied.
>>
>> On Feb 2, 2009, at 2:06 PM, Chris Mungall wrote:
>>
>>>
>>> Can you summarise the reasons for obsoletion?
>>>
>>> On Feb 2, 2009, at 1:28 PM, Stephen Larson wrote:
>>>
>>>> Great.  We should probably also let the PATO people know that  
>>>> "increased action potential" and "decreased action  potential" 
>>>> (PATO_0001661 and PATO_0001660) are questionable from  our 
>>>> perspective.  I'm CC-ing Chris Mungal and Suzanna Lewis on  that topic.
>>>>
>>>> --Stephen
>>>>
>>>> On Mon, Feb 2, 2009 at 1:23 PM, anita bandrowski  
>>>> <bandrow at gmail.com> wrote:
>>>> Thanks Stephen, it looks like the links work great as does deleting.
>>>> I just deleted increased action potential and decreased action
>>>> potential pages.  I can take out the duplicate dopamine receptors as
>>>> well.
>>>> anita
>>>>
>>>> On Mon, Feb 2, 2009 at 12:06 PM, Stephen Larson 
>>>> <slarson at ncmir.ucsd.edu > wrote:
>>>> > Wanted to let you know that the NIF query links in Neurolex  
>>>> should now all
>>>> > be pointing to the production site.  Additionally, I have  enabled 
>>>> delete
>>>> > access to any user that is logged in (decided not to give it to  
>>>> users who
>>>> > are not logged in).  Please let me know if you notice this not  
>>>> working.
>>>> >
>>>> > Thanks!
>>>> > --Stephen
>>>> >
>>>>
>>>>
>>>>
>>>> -- 
>>>> Anita Bandrowski, Ph.D.
>>>> NIF Project Curator
>>>> UCSD 858-822-3629
>>>>
>>>
>>
>>
> 
> 
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-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium