FMA: Cerebral hemisphere - segment of telencephalon which has as its direct proper parts cerebral cortex and cerebral medulla.
One of two halves of the brain, divided along the midline in the sagittal plane
Need to look up whether this is only cortex
FMA: Brain - 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 of portion of neural tissue).
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.
Part of brain characterized by distinct cytoarchitectural layers, usually distinguishable in Nissl or myelin stains, e g., cerebellar cortex
Population of cells whose cell bodies may or may not be contained within a clearly defined nucleus but which are considered to be a functional grouping because they are believed to be of a common type and release the same neurotransmitter, e.g., dopaminergic cell group A8
Heimer, L. The Human Brain and Spinal Cord, 2nd ed, Spriner Verlag, 1995
Collection of fibers connecting similar areas on the two sides of the brain; note that Squire et al (pg 35) have commissures connecting cerebral cortical areas specifically. However, the habenular commissure is not cortical
Purves et al. Neuroscience. Sinauer, 1997, pg 5
Collection of neurons that are highly interconnected and process specific kinds of information
FMA: Segment of neural tree organ which has as its direct proper parts a nerve trunk and its branches; together with other nerves of the same tree it constitutes a neural tree.
Bundles of axons located in the peripheral nervous system
A set of connections made by neurons with their cell bodies in one parcel and their synaptic terminations in a different parcel.
Swanson, L. in Squire et al. Findamental Neuroscience, 3rd ed, Elsevier, 2008, pg 22.
toward the belly (ventrum) along the dorsal-ventral axis
I'm not sure why this is here? This is a functional term. (comment from JB, transducer is an entity, transduction is the function). Yes, but why would that be an upper level term for mammalian neuroanatomy? (MM). I guess it depends to what level people want to go-it does seem a bit out of place, do we know who added it, perhaps we could go to them for their thinking (JB)
One of 3 orthogonal cutting orientations for producing sections of brain or spinal cord, defined relative to the axes of the neuraxis or body.
Discussed issue of "Predominantly" - is this encoded in a relation? Sometimes just extra verbiage. Where not we want to get specific about what it is saying e.g. "more than 50%"
Predominantly gray lamina characterized by a predominance of fibers (dendrites, axons) and a paucity of cell bodies
A bundle of nerve fibers in the brainstem comprising ascending sensory fibers
Axis that extends along the length of the body from the rostrum (beak) to the cauda (tail)
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.
FMA: Synonym of Neuraxis - is an organ with organ cavity which has as its direct proper parts brain and spinal cord.
There's an issue on the question of the retina. There's contention about this issue. Jyl: From 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.
Maryann Martone, Onard Mejino, Paul Katz, David Osumi-Sutherland, Mihai Bota, Chris Mungall, Melissa Haendel, Laszlo Zaborszky, Doug Bowden, Alan, Ruttenberg, Jyl Boline
Brain, spinal cord and nerve cell layer of retina
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
"commonality of cytoarchitecture, chemoarchitecturel" how to capture that.
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.
toward the back (dorsum) along the dorsal-ventral axis
Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. // Structures containing a collection of nerve cell bodies.
Have some sort of epithelial capsule - is this true in mammals? Consider "sympathetic chain". Have ganglia and they are all connected. Maryanne's definition needs more. Predomimantly cell bodies. Onard: How do we distinguish ganglion with nucleus. Is the only differentia location? Functionally differetia? "discrete aggregate of neuron bodies". Note that the basal ganglion is not a ganglion in this sense. I've never heard the term "neural tree" before and I'm not sure it is useful (MM)
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.
Onard Mejino, Maryann Martone, David Osumi-Sutherland, Paul Katz, Jyl Boline
FMA: Set of neural tree organs directly connected to neuraxis.
FMA: Segment of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ).
A collection of neurons in the peripheral 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. 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.
Maryann Martone, Onard Mejino, Paul Katz, David Osumi-Sutherland, Mihai Bota, Jyl Boline
Toward the midline along the mediolateral axis
FMA: Segment of cerebral hemisphere which has as its direct proper parts cortical gray matter bounded by sulcal and surface fiat anatomical boundaries.
Raised convolutions or folds of gray matter in the cerebral cortex of gyrencephalic aimals
Swanson, L. in Squire et al. Findamental Neuroscience, 3rd ed, Elsevier, 2008, Figure 2.8
Plane perpendicular to the long axis of the body. This plane defines different planes of section in the brains of upright (e.g., human) and four-legged animals.
FMA: Meningeal cluster - organ cluster which has as its direct proper parts dura mater and leptomeningeal sac. (Leptomeningeal sac - organ with organ cavity which has as its direct proper parts arachnoid mater, pia mater and subarachnopid space.)
Uberon has two class: BBB, and endothelial BBB.Def for BBB: "Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions". Def for endothelial BBB: ""A blood brain barrier that is composed of endothelial cells."
Part of gray matter characterized by a dense intricate feltwork of interwoven fine glial processes, synaptic terminals, axons, and dendrites interspersed among the cell bodies of nerve cells (adapted from MESH)
FMA: Cell part cluster of neuraxis consisting of neurites confined to the gray matter.
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A large bundle of nerve fibers. A fasciculus may contain more than one tract
Axis that is vertical and runs from the dorsum (back) to the ventrum (belly)
Not sure we should have this in there. I think the definition will get tricky
FMA: 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.
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.
A collection of axons that largely arises from one central nervous system part and terminates in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus.
Elongated nuclei that are oriented along the rostral-caudal axis of the brain or spinal cord
Plane of section dividing the two sides of the neuraxis
Volumetric partition of the brain using bona fide and fiat anatomical boundaries based on sets of criteria.
a set of parcels occupying part or all of the brain that has been delineated using a common approach or set of criteria, often in a single study. A parcellation scheme for any given individual brain should not have overlapping parcels and may include gaps, transitional zones, or regions of uncertainty. A parcellation scheme derived from a set of individuals registered to a common target (atlas) may be probabilistic and include overlap of parcels in regions that reflect individual variability or imperfections in alignment.
FMA: Cerebral lobe - segment of cerebral hemisphere demarcated by both bonafide landmarks (sulci and fissures) and fiat boundaries.
Division of cerebral or cerebellar cortex the borders of which are sometimes defined by major sulci and/or general functional divisions
contiguous region of brain gray matter that is defined and delineated by methods based on one or another of the following approaches: architecture, function, pattern of connections (inputs and outputs), and/or topographic organization (mapping of a sensory sheet or a motor representation).
FMA: Cell part cluster which has as its direct proper parts predominantly somas of neurons in the brain and the spinal cord.
Part of neuraxis in which cell bodies and unmyelinated nerve processes predominate giving it a pinkish gray appearance in gross preparations, e.g., thalamic nucleus
Comments: Issue 1. Scope? - Nucleus of Neuraxis, of Spinal cord, of Brain. "direct part" in FMA is an issue. Most granular part for an object. Subcortical needs to be defined. Maybe not in the scope of CUMBO because it references cortex. Subcortical = part of the cerebral hemisphere but not part of the cortex. "sub" is not locational in this case it is functional. Onard: Medullary part. Maryanne - need to clarify the scope. "cytoarchitecture" correlates with "discrete aggregate of neuronal soma". See definition of CARO tissue for discussion related to cytoarchitecture and chemoarchitecture.
FMA: Nucleus of brain is a subcortical gray matter which has as its direct proper parts predominantly discrete aggregate of somas of neurons.
Group of cells that have commonality of cytoarchitecture chemoarchitecture and connections
A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in "subcortical" because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in "relatively compact" and "distiguishable by histology" because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
GO: A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma.
A collection of nerve fibers projecting towards a region in which it terminates
A collection of nerve fibers projecting away from the region in which it originates
Away from the midline along the mediolateral axis
FMA: Anatomical cranial point where the coronal and sagittal suture lines intersect.
A sulcus that is very deep, e.g., the lateral fissure
I don't think we should have actual structures in CUMBO
FMA: Cerebral ventricle - segment of ventricular system of brain which has as its direct proper parts wall of cerebral ventricle and cavity of cerebral ventricle.
Squire et al: Axon bundles (tracts or pathways) connecting very different structures ont he two sides of the CNS. pg 36
FMA: Anatomical junction in which two or more white matter structures intermingle.
FMA: Cell part cluster which has as its direct proper parts predominantly neurites in the brain and the spinal cord.
Part of neuraxis in which myelinated axons predominate giving it a white appearance in gross preparations
Axis that is horizontal and runs from the midline to the lateral margin of the animal
Toward the beak or nose of the animal along the rostrocaudal axis
Indentations or grooves in the cerebral cortex. Note that sulci are defined in lissencephalic animals as well as gyrencephalic, e.g., the rhinal sulcus
FMA: Subarachnoid sulcus - zone of subarachnoid space located between gyri.
Collection of circuits that serve broader functions, e.g., the visual system