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

[anita bandrowski]

Chris,

I am not an ontologist, but my reasons for asking to obsolete
increased action potential and decreased action potential (not action
potential itself) is because the concepts have a really obscure basis
in neurophysiology.

An action potential is an action, as the term suggests.
The action has properties of being a wave, propagating, etc as you suggest.
Importantly, it also has the quality of being a digital signal (so
that it is only important whether or not it has occurred not how big
it is to 99% of the neuroscience literature).  Modifying action
potential frequency is highly important to neuroscience and many
volumes of publications are still being created on it, but the size
(or amplitude) does not matter.

While technically knowing the time and length constants one can
calculate the exact amplitude of the action potential at any given
distance and time, the calculation is only relevant to a very small
subset of the total knowledge of action potentials.  Furthermore, it
is confusing as it may be interpreted as a frequency of action
potential rate, which it does not seem to mean.

Perhaps it would be best to add frequency of action potential firing
as a quality and then you can have two modifiers of increased and
decreased action potential firing?  Just a thought.

The GO definition that you gave points to 'action potential
regulation' as the appropriate label for the term. - "Any process that
modulates the frequency, rate or extent of action potential creation,
propagation or termination."

Note: rate and frequency are synonyms
There may be some problems in extracting the definition of action
potential out of this regulation of action potential.

anita



>
> 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."]



On Mon, Feb 2, 2009 at 2:41 PM, Chris Mungall <cjm at berkeleybop.org> 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
>>>>
>>>
>>
>>
>
>
>



-- 
Anita Bandrowski, Ph.D.
NIF Project Curator
UCSD 858-822-3629