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

[Chris Mungall]

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

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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
>>>
>>
>
>