Next definitions
Jyl Boline
We hadn't planned on defining these next terms, but realized that they
are necessary for the definitions of many other terms. Please send
your comments and suggestions on the definitions for neuraxis, brain
and spinal cord.
Neuraxis:
1) The neuraxis is the axis of the central nervous system. It denotes
the direction in which the central nervous system lies. During
embryological development, the neuraxis is bent by various flexures,
contributing to the mature structure of the brain and spinal cord.
2) The brain plus spinal cord
3) Same as CNS in the FMA
Brain:
1) The part of the central nervous system contained within the
cranium, comprising the prosencephalon, mesencephalon, and
rhombencephalon. It is derived from the anterior part of the embryonic
neural tube. Functions include muscle control and coordination,
sensory reception and integration, speech production, memory storage,
and the elaboration of thought and emotions.
2) Segment of neuraxis (central nervous system part) which consists
of portion of neural tissue arranged and subdivided into forebrain
(prosencephalon), midbrain (mesencephalon), and hindbrain,
(myelencephalon) and metencephalon), contained in cranial cavity,
surround cerebral ventricular system, continuous with and rostral to
spinal cord and demarcated from spinal cord by plane of foramen
magnum. (NOTE: The information on supporting neuroglial and vascular
networks are captured in the definition portion of neural tissue).
Spinal Cord:
1) Part of the central nervous system which is lodged in the
vertebral canal; it is composed of an inner core of gray matter in
which nerve cells predominate, and an outer layer of white matter in
which myelinated nerve fibers predominate; it is enclosed in three
protective membranes, the meninges.
2) Segment of neuraxis which consists of portion of neural tissue
continuous with and caudal to brain, surround central canal,
demarcated from brain by plane of foramen magnum and contained in
space of vertebral canal.
Best,
Jyl
Maryann Martone
excluding retina, I am assuming). I've run into many cases where I
need to denote this grouping (brain + spinal cord and not retina) in
defining other terms, e.g., tracts that run through spinal cord and
part of brain.
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Maryann Martone, Ph. D.
Professor-in-Residence
Department of Neuroscience
University of California, San Diego
San Diego, CA 92093-0446
Maryann Martone
decisions up to the ontologists as to what is required in the
definitions as this exercise is designed to create a set of upper
level terms needed to define other terms.
On Oct 21, 2010, at 4:53 PM, dmbo...@u.washington.edu wrote:
>
>
> Hi all,
>
> Here are comments on brain, neuraxis, and spinal cord definitions.
>
> Doug
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> <Definitions of brain & spinal cord.docx>
Jyl Boline
Thanks for the great comments, but just to clarify, there are multiple
definitions as they came from different sources and have slightly
different content and meaning. They're being presented to the group
to generate discussion and come up with a single consensus definition
for each.
Also, Doug's first paragraph brings up a good point. All these
definitions are specifically for the nervous system, and don't include
all the other parts that one would get in a dissection. Is this going
to be an issue as we move forward? Do we as Doug suggests need two
concepts for these different situations?
Best,
Jyl
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>> <Definitions of brain & spinal cord.docx>
>
> Maryann Martone, Ph. D.
> Professor-in-Residence
> Department of Neuroscience
> University of California, San Diego
> San Diego, CA 92093-0446
>
> 858-822-0745
>
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>
Jyl Boline
I've had a difficult time digesting this e-mail conversation and was
hoping some folks would step in to clarify, so I will give a synopsis
of where I think the discussion is at this point and potential
definitions and hope that you will help us make some decisions.
Please see http://pons.neurocommons.org/page/Common_Upper_Mammalian_Brain_Ontology_(Cumbo)
for other our current higher level definitions.
Best,
Jyl
DECISIONS:
• Retina is indeed part of the brain (if we have another definition
that excludes retina, what is it?)
• “tree-structure” stands in definition of nervous system
STILL OPEN QUESTIONS:
• Meninges either in or out of both spinal cord and brain definition
(I left them out here, what are people's preferences?)
• Use the Latin names for a developmental model, and English for a
classical (or dissection) model (proposed by Doug)
• Potentially have different definitions that includes everything
(CNS+other) one might find in a dissection…if we use the English
terms, as Doug suggests, we will likely need to also have two
different definitions of CNS that also have this separation (it
currently refers to only neural tissue).
DEFINITIONS:
Neuraxis: (currently two potential definitions, although they could
be combined)
1) brain + spinal cord (no retina)
2) the part of the embryonic brain that gives rise to the ‘central
nervous system’ of the mature brain
Brain:
The part of the central nervous system contained within the cranium,
comprising the forebrain, midbrain, hindbrain, and metencephalon. It
is derived from the anterior part of the embryonic neural tube (or the
encephalon). Functions include muscle control and coordination,
sensory reception and integration, speech production, memory storage,
and the elaboration of thought and emotions.
Encephalon:
The embryonic precursor of the brain and the set of mature brain
structures that derive from it.
Spinal cord:
Part of the central nervous system located in the vertebral canal
continuous with and caudal to the brain; demarcated from brain by
plane of foramen magnum. It is composed of an inner core of gray
matter in which nerve cells predominate, and an outer layer of white
matter in which myelinated nerve fibers predominate, and surrounds the
central canal.
Maryann Martone
On Nov 3, 2010, at 8:12 AM, Jyl Boline wrote:
> Hello All,
>
> I've had a difficult time digesting this e-mail conversation and was
> hoping some folks would step in to clarify, so I will give a synopsis
> of where I think the discussion is at this point and potential
> definitions and hope that you will help us make some decisions.
> Please see http://pons.neurocommons.org/page/Common_Upper_Mammalian_Brain_Ontology_(Cumbo)
> for other our current higher level definitions.
>
> Best,
> Jyl
>
>
> DECISIONS:
> • Retina is indeed part of the brain (if we have another definition
> that excludes retina, what is it?)
I thought we had put it as part of CNS but not part of brain
> • “tree-structure” stands in definition of nervous system
>
> STILL OPEN QUESTIONS:
> • Meninges either in or out of both spinal cord and brain definition
> (I left them out here, what are people's preferences?)
I don't think they should be included. It is easy to define them as a
separate structure.
> • Use the Latin names for a developmental model, and English for a
> classical (or dissection) model (proposed by Doug)
We can certainly propose this, although I think we will have a hard
time getting rid of telencephalon etc in the adult lexicon. But
anything that adds order to chaos is always worth tryig
> • Potentially have different definitions that includes everything
> (CNS+other) one might find in a dissection…if we use the English
> terms, as Doug suggests, we will likely need to also have two
> different definitions of CNS that also have this separation (it
> currently refers to only neural tissue).
A combinatorial nightmare! If we have the basic pieces down, we
should be able to build from them as necessary.
>
>
> DEFINITIONS:
> Neuraxis: (currently two potential definitions, although they could
> be combined)
> 1) brain + spinal cord (no retina)
> 2) the part of the embryonic brain that gives rise to the ‘central
> nervous system’ of the mature brain
This is a tough one. When I've been doing definitions in Neurolex,
I've been using the Neuraxis definition from FMA to define structures
that span brain and spinal cord. Bill Bug, when he set up Neurolex,
had established an "is a" structure that included classes like
"regional part of telencephalon". He established these categories
based on the part of hierarchy of Neuronames and carried the practice
to extreme. Part of the reason he did this, though, was the
difficulty in navigating part of trees in earlier versions of OWL/
Protege and our own inexperience with working with these constructs.
We've been removing many of the intermediate categories, but I still
find it useful to retain some for book keeping purposes. Also,
everything has to be a type of something. So "part of brain" and
"part of spinal cord" are very useful supercategories, but if
something like the ventricular system or certain tracts span both
subdivisions, then i want it to be "part of ?". I'd been using
neuraxis but, based on the definition of central nervous system, I
could use that instead. So this explanation is a very long winded way
of saying that if neuraxis has a definite meaning in the developmental
world, then I don't favor adding it to the adult. Rather, can we just
go with CNS for this purpose?
>
> Brain:
> The part of the central nervous system contained within the cranium,
> comprising the forebrain, midbrain, hindbrain, and metencephalon. It
> is derived from the anterior part of the embryonic neural tube (or the
> encephalon). Functions include muscle control and coordination,
> sensory reception and integration, speech production, memory storage,
> and the elaboration of thought and emotions.
>
> Encephalon:
> The embryonic precursor of the brain and the set of mature brain
> structures that derive from it.
>
> Spinal cord:
> Part of the central nervous system located in the vertebral canal
> continuous with and caudal to the brain; demarcated from brain by
> plane of foramen magnum. It is composed of an inner core of gray
> matter in which nerve cells predominate, and an outer layer of white
> matter in which myelinated nerve fibers predominate, and surrounds the
> central canal.
>
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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