Re: Definitions
Maryann Martone
Sorry I'm late on this.--
I can only speak for the FMA. The FMA definitions are derived from a structure-based ontology. There are strings of definitions that are transitively inherited from higher level anatomical classes as Chris pointed out (e.g. organ with organ cavity, anatomical structure, physical anatomical entity) and I believe you don't want this for CUMBO. The definitions I presented are examples of an exercise that the group may want to apply in defining high level CUMBO terms. Perhaps a good starting point is to come up with some "root" or primitive term such as "anatomical structure" or "nervous system part" from which the CUMBO terms can be defined.
Nervous system - anatomical structure which consists predominantly of aggregate of neurons arranged into a network of tree-like structures connected to a central axial body (or something like that). Then add other properties such as: -function, "it integrates, coordinates, regulates and controls bodily functions"
-development, "it develops from the neural tube"
-etc.
Therefore:
CNS- part of nervous system (nervous system part) which consists of the brain and the spinal cord (mammals). Then define "brain" as "part of CNS" which consists of ...
PNS- part of nervous system which consists of cranial nerves III - XII, spinal, peripheral and autonomic nerves and are connected to the CNS. (define in accord with what's true for mammalians). Then define cranial nerve as a "nerve" (nerve being defined as part of the nervous system which consists of an aggregate of neurons arranged into a tree-like structure, the somas of which are located in the CNS.)
Then add all other non-structural properties.
Hope this helps.
Onard
----- Original Message -----
From: "Chris Mungall" <CJMu...@lbl.gov>
To: "Maryann Martone" <mar...@ncmir.ucsd.edu>
Cc: "Jyl Boline" <jylb...@gmail.com>, neur...@googlegroups.com, structura...@googlegroups.com, pons-representati...@googlegroups.com
Sent: Wednesday, October 6, 2010 5:35:42 PM
Subject: Re: Definitions
On Oct 6, 2010, at 2:50 PM, Maryann Martone wrote:
> 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
Thought not, that's why I highlighted it with the ***s
(2) comes from GO - once we have a satisfactory CUMBO definition I
will feed it back to GO (via Uberon).
One consideration is that GO/Uberon go beyond vertebrates - this is
outside the scope of PONS. This is one reason the GO def is vague and
hand-wavy "integrating and coordinating function". Hopefully the CUMBO
def can be adapted to GO and Uberon easily. For example: "in organisms
with a spinal cord, the spinal cord is part of the CNS".
>> 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.
I'm neutral as to whether we adopt this FMA definition - however, as a
general principle, if CUMBO is to use this definition, then it must
first define "neural tree organ"
FMA has:
Nonparenchymatous organ which has as its parts an aggregate of neurons
(nuclei or ganglia) and their axons which are grouped into fasciculi
by connective tissue to form elongated, cable-like structures that are
arranged into a tree. Examples: vagus nerve, cervical spinal nerve, T2
spinal nerve (including the nuclei and ganglia of these nerves).
So again, we have to follow through and define "Nonparenchymatous
organ", "aggregate of neurons", fasiculus, conective tissue....
The FMA has done the work here. However, it's an open question as to
whether we want to adopt this directly or go for a simpler
representation, that doesn't require importing so many terms into CUMBO.
>> 2) PNS consists of the nerves and ganglia outside of the brain and
>> the spinal cord
>>
>>
>> Best Regards,
>> Jyl
>>
>> --
>> You received this message because you are subscribed to the Google
>> Groups "PONS Representation and Deployment" group.
>> To post to this group, send email to pons-representati...@googlegroups.com
>> .
>> To unsubscribe from this group, send email to pons-representation-and...@googlegroups.com
>> .
>> For more options, visit this group at http://groups.google.com/group/pons-representation-and-deployment?hl=en
>> .
>>
>
>
>
>
> 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
>
>
>
>
> --
> You received this message because you are subscribed to the Google
> Groups "PONS Representation and Deployment" group.
> To post to this group, send email to pons-representati...@googlegroups.com
> .
> To unsubscribe from this group, send email to pons-representation-and...@googlegroups.com
> .
> For more options, visit this group at http://groups.google.com/group/pons-representation-and-deployment?hl=en
> .
>
--
You received this message because you are subscribed to the Google Groups "PONS Representation and Deployment" group.
To post to this group, send email to pons-representati...@googlegroups.com.
To unsubscribe from this group, send email to pons-representation-and...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/pons-representation-and-deployment?hl=en.
You received this message because you are subscribed to the Google Groups "StructuralLexiconTF" group.
To post to this group, send email to structura...@googlegroups.com.
To unsubscribe from this group, send email to structurallexic...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/structurallexicontf?hl=en.
Jyl Boline
definitions. If people are happy with these we will add these to
CUMBO and move on to the next set of defintions.
The nervous system is an organ system containing predominantly neuron
and glial cells. In bilaterally symmetrical organism, it is arranged
in a network of tree-like structures connected to a central body.
The main functions of the nervous system are to regulate and control
body functions, and to receive sensory input, process this
information, and generate behavior.
The central nervous system (CNS) is the part of the nervous system
which includes the brain, spinal cord, and nerve cell layer of the
retina.
The peripheral nervous system (PNS) is the part of the nervous system
connected to the CNS which contains cranial nerves III - XII, spinal,
peripheral and autonomic nerves.
Best,
Jyl
Mihail Bota
The definition of Bullock & Horridge (1965, p. 6), is like this: "A nervous system may be defined as an organized constellation of cells (neurons) specialized for the repeated conduction of an excited state from receptor sites or from other neurons to effectors or to other neurons." To this, I think, one should add the glial cells and (those parts of) the circulatory system that directly communicates with it.
It's unclear to me what is an "organ system". A system made of many organs?
M.
Jyl Boline
Thanks for this input. An organ system is an organizational unit that
is grouped together based on function. e.g. cardiovascular system,
muscular system, endocrine system, etc. Given this, the circulatory
system is by definition not part of the nervous system.
Best,
Jyl
Maryann Martone
much to the definition. I don't believe that the enteric nervous
system in vertebrates is organized that way either.
On Oct 15, 2010, at 8:00 AM, Paul S. Katz wrote:
> David,
> (FYI) I am on the neurolex google group and the PONS group.
>
> I think that the CNS and PNS are structures that are only found in
> vertebrates. It would be like defining the hippocampus to include
> invertebrates. There are two camps regarding the issue of whether
> the nervous systems of bilateria are homologous: one led by Detlev
> Arendt says that based on gene expression, there is deep homology.
> I think that even if they are homologous, the current structures for
> the nervous systems of various phyla can have their own
> nomenclature. For example, in gastropod molluscs, we talk about the
> circumesophogeal ganglia that consist of the Cerebral, Pleural, and
> Pedal ganglia. If there were a CNS in gastropods, this would be it,
> but there are no equivalents to these ganglia in Arthropods,
> Annelids, or Vertebrates.
>
> This is not to say that there are not central and peripheral
> components to the nervous systems of molluscs, annelids, and
> arthropods. One could create a very general definition, but I'm not
> sure it's useful.
>
> I have somewhat of a disagreement with the broad definition of a
> nervous system:
> "The nervous system is an organ system containing predominantly
> neuron and glial cells. In bilaterally symmetrical organism, it is
> arranged in a network of tree-like structures connected to a central
> body."
> In the nematode, C. elegans the nervous system is not tree-like
> because the neurons do not branch out to muscles. The muscles have
> branches that go to the neurons. I would drop the tree-like
> structure because it does not help me understand what a nervous
> system is.
>
> -Paul
>
> Director of the Center for Neuromics
> Neuroscience Institute
> Georgia State University
> P.O. Box 5030
> Atlanta, GA 30302-5030
>
> Tel: 404-413-5398
> e-mail: pk...@gsu.edu
> http://neuroscience.gsu.edu/pkatz.html
>
>
>
>
> On 10/15/2010 5:30 AM, David Osumi-Sutherland wrote:
>> Hi all
>>
>> Sorry for not contributing to this earlier. Very busy.
>>
>> On 13 Oct 2010, at 13/Oct/2010 20:23:39, Jyl Boline wrote:
>>
>>> Thanks for everyone's input. Below is what I have so far as
>>> consensus
>>> definitions. If people are happy with these we will add these to
>>> CUMBO and move on to the next set of defintions.
>>>
>>> The nervous system is an organ system containing predominantly
>>> neuron
>>> and glial cells. In bilaterally symmetrical organism, it is arranged
>>> in a network of tree-like structures connected to a central body.
>>>
>>> The main functions of the nervous system are to regulate and control
>>> body functions, and to receive sensory input, process this
>>> information, and generate behavior.
>> This is fine.
>>
>>>
>>> The central nervous system (CNS) is the part of the nervous system
>>> which includes the brain, spinal cord, and nerve cell layer of the
>>> retina.
>>>
>>>
>>> The peripheral nervous system (PNS) is the part of the nervous
>>> system
>>> connected to the CNS which contains cranial nerves III - XII,
>>> spinal,
>>> peripheral and autonomic nerves.
>> So invertebrates have no CNS and no PNS???!!
>>
>>
>> If we are to have a definition that works more broadly, we will
>> have to avoid reference to structures that only vertebrates have.
>> I suspect the PNS definition references nerves that are, at best,
>> generalizable only to mammals. If that's the case, fish have no
>> PNS either by this definition.
>>
>> No time to discuss this more today. Will try to work on some
>> broader defs next week. Have cc'd Paul Katz (although he's likely
>> already on one of these lists) as he's probably the PONS person
>> best qualified to suggest sufficiently broad definitions.
>>
>> Cheers,
>>
>> David
>>>>>> to pons-representation-and-deployment
>>>>>> +unsub...@googlegroups.com
>>>> at http://groups.google.com/group/pons-representation-and-deployment?hl=en
>>>> .
>>>>
>>>> --
>>>> You received this message because you are subscribed to the
>>>> Google Groups
>>>> "StructuralLexiconTF" group.
>>>> To post to this group, send email to structura...@googlegroups.com
>>>> .
>>>> To unsubscribe from this group, send email
>>>> to structurallexic...@googlegroups.com.
>>>> For more options, visit this group
>>>> at http://groups.google.com/group/structurallexicontf?hl=en.
>>>>
>>>> Maryann Martone, Ph. D.
>>>> Professor-in-Residence
>>>> Department of Neuroscience
>>>> University of California, San Diego
>>>> San Diego, CA 92093-0446
>>>> 858-822-0745
>>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "PONS Representation and Deployment" group.
>>> To post to this group, send email to pons-representati...@googlegroups.com
>>> .
>>> To unsubscribe from this group, send email to pons-representation-and...@googlegroups.com
>>> .
>>> For more options, visit this group at http://groups.google.com/group/pons-representation-and-deployment?hl=en
>>> .
>>>
>> David Osumi-Sutherland, PhD
>> Curator/ Ontologist
>> FlyBase / Virtual Fly Brain
>> Department of Genetics,
>> University of Cambridge,
>> Downing Street,
>> Cambridge, CB2 3EH, UK
>> Tel: +44 (0)1223 333 963
>> Fax: +44 (0)1223 766 732
>>
>
> --
> You received this message because you are subscribed to the Google
> Groups "PONS Representation and Deployment" group.
> To post to this group, send email to pons-representati...@googlegroups.com
> .
> To unsubscribe from this group, send email to pons-representation-and...@googlegroups.com
> .
> For more options, visit this group at http://groups.google.com/group/pons-representation-and-deployment?hl=en
> .
>
Maryann Martone, Ph. D.
Mihail Bota
Is this "organ system" expression used somewhere? It's for the first time when I encounter it. If it's not used, then maybe body system can replace it, since it makes more sense: "nervous system is one of the body systems (systems of the body) that etc., etc.". To me, at least, it makes more sense.
Regarding the general approach in defining these general terms, I think one first use what is already published; it doesn't make any sense to use definitions found in different places, without no reference information. CUMBO is not by itself, but should be linked, or related, to already existent definitions. This is why I proposed Bullock's definition as a start. Of courrse there may be better definitions in the literature.
Going further with your definition, "The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior.", maybe this definition can be arranged a little bit: "receive input, process it, and generate...". Also the control of body functions is overlapping with the "generate behavior".
Onard, enteric nervous system is found in mammals. Is involved in the control of the gastrointestinal system.
M.
Maryann Martone
Hi Mihai,
I'm not questioning whether mammalians have ENS. I'm just asking what the forum is for, for CUMBO or for a more general or broader scope which includes invertebrates? The definitions presented and proposed were for mammalians. Are we now considering pan-vertebrate or even broader, including invertebrates?
Maryann Martone
Hi Maryann,
I know you're very familiar with the FMA but I'd like to address those in the group who are not. The "tree-like" description in the FMA is applied at different granularity levels. The nervous system in its entirety can be described as tree-like, just like the vascular trees (in humans, and perhaps in all mammals?) A cranial nerve or a spinal nerve or its branch fits the same description as well, so does a neuron with its neurites. I'm not very familiar with ENS but myenteric and submucosal plexuses seem to be more spatially related to trees than any other structural shape. The textual definitions we provide in the FMA are rooted in the structural ontology. Because components of the nervous system largely deal with spatial properties such as branching, ramifications and multiple connectivity relationships at different levels of granularity, we can best describe them textually as trees. But this is more than just a textual definition for human consumption, the spatio-structural attributes of being a"tree" that are captured in the ontology are computable. I just want to provide some background information on our rationale for the tree description. This may or may not be important or required for CUMBO, especially if the focus is on function and at the level of neurons, as illustrated in Mihai's example and if the goal is simply to provide human readable textual definitions.
Jyl Boline
First to address Mihai's comments.
-An organ system is a fundamental tenant of biology and physiology
so we should use that term
-Any starting definitions are welcome, we should see what the rest
of the group thinks of the definition you proposed. Personally, I
think there are several parts that lead to confusion, but we can try
to incorporate some components from it.
-The differentiation between "controls body functions" and
"generate behavior" was meant to acknowledge the different roles of
the autonomic nervous system and what most of this group thinks of
when we think of the nervous system.
It seems the following decisions have been made:
1) stick to vertebrates
2) keep the tree-like structure component-does this need to be
edited in some way?
Finally, as of now, it seems the original definitions still stand.
Please provide additional comments on if you feel any of the
components of Mihai's proposed definition (below) or additional
clarification should be incorporated.
From Mihai-"The definition of Bullock & Horridge (1965, p. 6), is like
this: "A nervous system may be defined as an organized constellation
of cells (neurons) specialized for the repeated conduction of an
excited state from receptor sites or from other neurons to effectors
or to other neurons." To this, I think, one should add the glial cells
and (those parts of) the circulatory system that directly communicates
with it."
Thanks much!
Best,
Jyl
Maryann Martone
our ontology groups that the definition for human consumption and that
for logical consumption are not always the same.
>>>>>> , pons-representati...@googlegroups.com
>>>>>> to pons-representation-and...@googlegroups.com
>>>>>> .
>>>>>> For more options, visit this group
>>>>>>
>>>>>>
>>>>>> at http://groups.google.com/group/pons-representation-and-deployment?hl=en
>>>>>> .
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the
>>>>>> Google
>>>>>> Groups
>> .
>> To unsubscribe from this group, send email to
>> structurallexic...@googlegroups.com.
>> For more options, visit this group at
>> http://groups.google.com/group/structurallexicontf?hl=en.
>>
>
> --
> You received this message because you are subscribed to the Google
> Groups "PONS Representation and Deployment" group.
> To post to this group, send email to pons-representati...@googlegroups.com
> .
> To unsubscribe from this group, send email to pons-representation-and...@googlegroups.com
> .
> For more options, visit this group at http://groups.google.com/group/pons-representation-and-deployment?hl=en
> .
>
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
Paul S. Katz
(FYI) I am on the neurolex google group and the PONS group.
I think that the CNS and PNS are structures that are only found in
vertebrates. It would be like defining the hippocampus to include
invertebrates. There are two camps regarding the issue of whether the
nervous systems of bilateria are homologous: one led by Detlev Arendt
says that based on gene expression, there is deep homology. I think
that even if they are homologous, the current structures for the nervous
systems of various phyla can have their own nomenclature. For example,
in gastropod molluscs, we talk about the circumesophogeal ganglia that
consist of the Cerebral, Pleural, and Pedal ganglia. If there were a
CNS in gastropods, this would be it, but there are no equivalents to
these ganglia in Arthropods, Annelids, or Vertebrates.
This is not to say that there are not central and peripheral components
to the nervous systems of molluscs, annelids, and arthropods. One could
create a very general definition, but I'm not sure it's useful.
I have somewhat of a disagreement with the broad definition of a nervous
system:
"The nervous system is an organ system containing predominantly neuron
and glial cells. In bilaterally symmetrical organism, it is arranged in
a network of tree-like structures connected to a central body."
In the nematode, C. elegans the nervous system is not tree-like because
the neurons do not branch out to muscles. The muscles have branches
that go to the neurons. I would drop the tree-like structure because it
does not help me understand what a nervous system is.
-Paul
Director of the Center for Neuromics
Neuroscience Institute
Georgia State University
P.O. Box 5030
Atlanta, GA 30302-5030
On 10/15/2010 5:30 AM, David Osumi-Sutherland wrote:
> Hi all
>
> Sorry for not contributing to this earlier. Very busy.
>
> On 13 Oct 2010, at 13/Oct/2010 20:23:39, Jyl Boline wrote:
>
>> Thanks for everyone's input. Below is what I have so far as consensus
>> definitions. If people are happy with these we will add these to
>> CUMBO and move on to the next set of defintions.
>>
>> The nervous system is an organ system containing predominantly neuron
>> and glial cells. In bilaterally symmetrical organism, it is arranged
>> in a network of tree-like structures connected to a central body.
>>
>> The main functions of the nervous system are to regulate and control
>> body functions, and to receive sensory input, process this
>> information, and generate behavior.
> This is fine.
>
>>
>> The central nervous system (CNS) is the part of the nervous system
>> which includes the brain, spinal cord, and nerve cell layer of the
>> retina.
>>
>>
>> The peripheral nervous system (PNS) is the part of the nervous system
>> connected to the CNS which contains cranial nerves III - XII, spinal,
>> peripheral and autonomic nerves.
> So invertebrates have no CNS and no PNS???!!
>
>
> If we are to have a definition that works more broadly, we will have to avoid reference to structures that only vertebrates have. I suspect the PNS definition references nerves that are, at best, generalizable only to mammals. If that's the case, fish have no PNS either by this definition.
>
> No time to discuss this more today. Will try to work on some broader defs next week. Have cc'd Paul Katz (although he's likely already on one of these lists) as he's probably the PONS person best qualified to suggest sufficiently broad definitions.
>
> Cheers,
>
> David
>
>