Definitions

[Jyl Boline]

Hello All,

Members of the INCF PONS program are working on definitions for a
common upper mammalian brain ontology (or CUMBO) and since the
NeuroLex group is working on similar issues, Maryann has recommended
that we include all groups in these e-mail discussions. We plan to
start a regular "word or two a week" and we'd like to get your input
on developing consensus definitions.

We're going to start "easy" with the Central Nervous System and the
Peripheral Nervous System. From a recent PONS e-mail discussion on
retina, the consensus seemed to be that cranial nerves (I and 2)
(retina and bulbus olfactorius) are part of sensory organs that are
part of CNS, while cranial nerves III-XII are considered part of the
PNS, as are spinal nerves. In addition, there is the question of if
we want to go outside mammalian as well for these definitions.
Whatever our decisions, we will want to make this explicit and reflect
them in our definitions.

To start our discussions, we have a few straw definitions.

Below are three potential definitions for CNS:
1) Brain, spinal cord and nerve cell layer of retina

2) The central nervous system is the core nervous system that serves
an integrating and coordinating function. In vertebrates it consists
of the brain, spinal cord and **spinal nerves**. In those
invertebrates with a central nervous system it typically consists of a
brain, cerebral ganglia and a nerve cord

3) Synonym of Neuraxis - is an organ with organ cavity which has as
its direct proper parts brain and spinal cord.

Below are two potential definitions for PNS:
1) Set of neural tree organs directly connected to neuraxis.

2) PNS consists of the nerves and ganglia outside of the brain and
the spinal cord

Best Regards,
Jyl

[Jessica Turner]

Hi Jyl!! Good to hear from you!! Are you borrowing terms from FMA wherever reasonable? It's human but it generalizes--I thought Neurolex already incorporated it too. (http://sig.biostr.washington.edu/projects/fm/AboutFM.html)  Might save you some time and re-hashing, because they have done a lot of "part of" and "has part" relationships.  (It defines Neuraxis as a synonym of CNS and as #3 below, but already has the parts and other relationships laid out --I don't think you can infer that the retina is part of the CNS from it, though.)

 

Jess

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[Maryann Martone]

Yes, these terms come from FMA and Onard.  He's on the PONS project.

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Maryann Martone

Professor-In-Residence

Dept of Neurosciences

University of California, San Diego

San Diego, CA  92093-0446

Tel:  858 822 0745

Fax:  858 822 3610

[Maryann Martone]

See below:

On Oct 6, 2010, at 12:55 PM, Jyl Boline wrote:

>
> To start our discussions, we have a few straw definitions.
>
> Below are three potential definitions for CNS:
> 1) Brain, spinal cord and nerve cell layer of retina
>
> 2) The central nervous system is the core nervous system that serves
> an integrating and coordinating function.

That is not very well specified. What is an integrating and
coordinating function?

> In vertebrates it consists
> of the brain, spinal cord and **spinal nerves**.

Spinal nerves are not part of the central nervous system

> In those
> invertebrates with a central nervous system it typically consists of a
> brain, cerebral ganglia and a nerve cord
>
> 3) Synonym of Neuraxis - is an organ with organ cavity which has as
> its direct proper parts brain and spinal cord.

I'm not sure that non-mammalian vertebrate species have an organ
cavity in the brain in the adult

>
>
> Below are two potential definitions for PNS:
> 1) Set of neural tree organs directly connected to neuraxis.

What is a "neural tree" organ? I've never heard it before and because
it is similar to "dendritic tree", which is common, I do not favor its
use.

>
> 2) PNS consists of the nerves and ganglia outside of the brain and
> the spinal cord
>
>
> Best Regards,
> Jyl
>

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>

Maryann Martone
Professor-In-Residence
Dept of Neurosciences
University of California, San Diego
San Diego, CA 92093-0446
Tel: 858 822 0745

Fax: 858 246 0644

[Jyl Boline]

Hi Jess,

Good to hear from you too...hope you are well!

Looks like Maryann beat me to an answer, but thanks for the good suggestion.

Best,
Jyl

[Jessica Turner]

Well, you can count me as a +1 for the FMA definitions, generally speaking. Reduce, reuse, recycle--that's the way to go with ontologies.  :)

 

Can you explain what the difference will be between CUMBO and FMA? Is the scope the same, but you're looking specifically to make sure it's generic and not human-centric?

[Paul S. Katz]

What does the "upper" refer to in "common upper mammalian brain ontology (or CUMBO)"? 
Why is there a definition for CNS that includes invertebrates in a mammalian ontology?
Another possible definition of CNS is the portion of the nervous system that develops from the Neural Tube.
Best,
-Paul

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[Jyl Boline]

Hi Paul,

Thanks for your comments. The "upper" means that these are high level
terms used to describe structures or their location in the CNS such as
nucleus, pathway, sulcus, etc.

These definitions came from different sources (FMA, GO/Uberon, domain
expert), so I could have edited them before giving them to the group,
but decided to leave them as discussion items before forming a
consensus.

Best,
Jyl