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

[Maryann Martone]

I would support it being in biological process as the very name  
"action" implies an active process that leads to the change in  
membrane potential.  At the very least, GO needs a "generation of  
action potential" or something like that.


On Feb 2, 2009, at 2:41 PM, 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
>
> <RoAP.png>
>
> 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
>>>>
>>>
>>
>>
>