Release Notes: 1.1 - 05/28/2007 Added definitions Modified Non-neuronal cell types, especially glial types Simplified properties Did a lot of work cleaning up restrictions 1.2 - 07/06/2007 Restructured cell class hierarchy for glia and epithelial cells Converted SAO class names into SAO ids Made SAO OWL-DL compliant Checked and corrected consistency and satisfiability issues
Maryann Martone, Lisa Fong, Stephen D. Larson, Lily Chen, and Amarnath Gupta
Ontology for the subcellular anatomy of the nervous system
The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a post-synaptic potential responsible of the muscle contraction (Gene Ontology).
Protein based machines that are involved in or cause movement such as the rotary devices (flagellar motor and the F1 ATPase) or the devices whose movement is directed along cytoskeletal filaments (myosin, kinesin and dynein motor families) (MSH).
These relationships are modeled after the spatial relationships contained in the FMA.
A type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm (Gene Ontology).
Progression through prophase, the first stage of chromosome segregation in the cell cycle. Canonically, chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell (Gene Ontology).
From Reactime: Regions within compact myelin in which the cytoplasmic faces of the enveloping myelin sheath are not tightly juxtaposed, and include cytoplasm from the cell responsible for making the myelin. Schmidt-Lanterman clefts occur in the compact myelin internode, while lateral loops are analogous structures found in the paranodal region adjacent to the nodes of Ranvier.
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle (Gene Ontology).
Type of synapse characterized by an electron-dense ribbon, lamella (bar) or spherical body in the presynaptic process cytoplasm (Sjostrand, 1953; Ladman, 1958; Gray and Pease, 1971). It usually sits in or just above an evaginated ridge of the terminal membrane..." - Dowling (1987)
A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes (Gene Ontolgoy).
A synthetic enzyme that catalyzes the formation of acetylcholine from acetyl-CoA and choline. EC 2.3.1.6 (MSH).
Family of transmembrane heparan sulfate proteoglycans (CSP - Bonfire).
Indicates that two entities share a continuous space but that the continuity is formed through a specialized junctional component, e.g., gap junction.
Interfascicular oligodendrocyte which can support myelin volumes of approximately 30,000 cubic microns (up to 150,000 cubic microns) and is associated with large diameter axons.
Two entities are considered to be adjacent if they have no overlapping (shared) boundaries and parts and not other anatomical entity is interposed between them. The adjacency relationship is symmetrical (adapted from FMA).
Filamentous proteins that are the main constituent of the thin filaments of muscle fibers. The filaments (known also as filamentous or F-actin) can be dissociated into their globular subunits; each subunit is composed of a single polypeptide 375 amino acids long. This is known as globular or G-actin. In conjunction with MYOSINS, actin is responsible for the contraction and relaxation of muscle (MSH).
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology).
Electron dense structure anchored to the presynaptic membrane closely associated with large numbers of synaptic vesicles, which appear to be tethered to the dense body by several short filaments (from Parsons and Sterling, 2003).
Refers to a specialized arrangements of a cellular component or other structure that is characteristic of a given region, e.g., bundled microtubules.
Progression through metaphase, the second stage of chromosome segregation in the cell cycle. Canonically, chromosomes become aligned on the equatorial plate of the cell (Gene Ontology).
A small, migratory, phagocytic, interstitial cell of hematopoietic origin found in the central nervous system. Microglial cells are of various forms and may have slender branched processes.
The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology).
Refers to the ability of structures to move about the cell.
Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster).
Minimum diameter of a cross section through structure.
Refers to the morphological type of a spine.
Pyramidal neuron from the cerebral cortex (not including hippocampus).
Calcium pump found in the membrane of the smooth endoplasmic reticulum.
Indicates that a feature was described in intact tissue.
Inner Mitochondrial Compartment (from Peters, Palay, and Webster)
Interior portion of mitochondrion bounded by the inner mitochondrial membrane and cristae membranes and containing the mitochondrial matrix. Does not include the crista or crista lumen.
Smaller branches of an axon that emanate from the main axon cylinder.
Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology).
Classic ligand-gated ion channel receptor type, where binding of ligand (acetylcholine) to transmembrane protein oligomer causes channel to open, permitting ion (sodium and potassium) flux and depolarization (CSP).
Differentiates among different functional states of a cell or cell component, e.g., activated microglia, interphase nucleus, orthodox mitochondria.
A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology).
Indicates that the feature exists in isolation, e.g., single filaments as opposed to bundled filaments.
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope (Gene Ontology).
Generally round shape where minimum diameter and maximum diameter are roughly the same
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals which are the site of storage and release of neurotransmitter (Gene Ontology).
Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA)
The largest class of organic compounds, including starches, glycogens, cellulose, gums, and simple sugars. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n (MSH).
Schwann cell that forms compact myelin sheath around axons.
Refers to the average distance between features.
A stack of flattened vesicles that functions in posttranslational processing and sorting of proteins, receiving them from the RER and directing them to secretory vesicles, lysosomes, or the cell membrane. The movement of proteins takes place by transfer vesicles that bud off from the rough endoplasmic reticulum or Golgi apparatus and fuse with the Golgi, lysosomes or cell membrane. (From Glick, Glossary of Biochemistry and Molecular Biology, 1990) (MSH)
Type of VIP containing neuron found in the visiual cortex.
Definition was modified from that in Wikipedia by MM
Neurons located in the olfactory bulb in the mammalian central nervous system. They receive information from the axons of olfactory receptor neurons, forming synapses in neuropils called glomeruli. Axons of the mitral cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, and amygdala.
Cone shaped elevation from which the axon originates; in Nissl stained preparations, the axon hillock usually can be identified as a region of the perikaryon that is distinguished by a deficiency of Nissl substance (Peters, Palay and Webster, 1991).
Category of non-SER vesicle described by Clooney et al. (2002) in dendrites, categorized by smooth membranes, electron-lucent interiors and irregular shapes. Sometimes occurrs in clumps. These vesicles contained gold taken up from the extracellular space, suggesting that they may be part of the endosomal pathway.
Generally rounded shape, where the minimum and maximum dimensions produce a roughly egg-shape.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane (Gene Ontology).
Non-striated, elongated, spindle-shaped cells found lining the digestive tract, uterus, and blood vessels. They are derived from specialized myoblasts (myoblasts, smooth muscle) (MSH).
Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin.
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the ER to the Golgi, between Golgi cisternae, and to destinations within or outside the cell (Gene Ontolgoy).
Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells.
Definition modified from Wikipedia by MM. According to Reichenbach and Wolberg the Bergmann glia should be considered a type of radial astrocyte but some do not consider this a type of astrocyte
Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses.
A short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum that is similar in structure to a centriole. The basal body serves as a nucleation site for axoneme growth (Gene Ontology).
Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004).
Mechanoreceptor cells in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea. (MSH)
Contact site between adjacent cells in cardiac muscle fibers. When observing tissue through a microscope, this is an identifying feature of cardiac muscle.It holds the myofibrils together and permits easy transfer of excitation (depolarization).
Large neuron found in the molecular layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters into a complex arrangement witht he mossy fiber terminal-granule cell dendrite in the cerebellar glomerulus.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine) (MSH).
Portion of myelin-forming Schwann cell consisting of terminal cytoplasmic extensions adhered to the axon at the beginning and end of the myelin sheath.
Process of astrocyte that extends to the surface of the central nervous system. Together, they form the glial limiting membrane or glial limitans.
Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH).
A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter (MSH).
A group of enzymes removing the serine- or threonine-bound phosphate groups from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. (Enzyme Nomenclature, 1992) EC 3.1.3.16. (MSH)
The plasma membrane of an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness (Gene Ontology).
A class of ionotropic glutamate receptors characterized by affinity for N-methyl-D-aspartate. NMDA receptors have an allosteric binding site for glycine which must be occupied for the channel to open efficiently and a site within the channel itself to which magnesium ions bind in a voltage-dependent manner. The positive voltage dependence of channel conductance and the high permeability of the conducting channel to calcium ions (as well as to monovalent cations) are important in excitotoxicity and neuronal plasticity (MSH).
Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins.
Mechanoreceptors located in the organ of Corti that are sensitive to auditory stimuli and in the vestibular apparatus that are sensitive to movement of the head. In each case the accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system (MSH).
Cells that line the inner and outer surfaces of the body (MSH).
The shape of the nucleus, e.g., round, lobulated, indented
The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes (Gene Ontology).
A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle (Gene Ontology).
Anatomical location which specifies the relationship between one or more physical anatomical entities in terms of...
A mononuclear phagocyte which differentiates from monocytes, is typically resident in a particular tissue, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells (Cell Ontology).
According to some, synantocytes are equivalent to NG2 cells. According to others, they are the predominant NG2 cell found in the post-natal animal, but are distinct from bipolar progenitory cells.
NG2 positive glial cell characterized by a stellate appearance and a large process arborization. They have a centrally placed cell body from which extend numerous primary processes that pass radially and bifurcate three or more times to form a process field of approximately 100 nanometers in diameter ((Butt et al., 2004; PMID: 16367797).
NG2 cell characterized by a differentiated, stellate appearance that lack expression of most differentiated glial cell-type specific markers.
A type of astrocyte with a radial orientation commonly found in spinal cord and brain of lower vertebrates and sometimes in the optic nerve of mammals. One process abuts the pial surface and the other extends through significant thicknesses of neural tissue. (Reichenbach and Wolberg)
Cell membrane glycoproteins that are selectively permeable to potassium ions. At least eight major groups of K channels exist and they are made up of dozens of different subunits (MSH).
Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies.
A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2) (Gene Ontology).
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid (Gene Ontology).
Cytoskeletal protein present in Z lines of muscle fibrils and at sites of non-muscle cell contact with a substrate (CSP).
Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003).
Multivesicular bodies surrounded by and connected with multiple tubular compartments with associated vesicles. MVB-tubule complexes are posited by Clooney et al. (2002) to correspond to sorting endosomes.
Astrocytes that are virtually devoid of neuron contacting processes that form extensive endfoot contacts to blood vessels. They have been found in rabbit and human retina but also occur elsewhere in the brain. (Reichenbach and Wolberg)
The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology).
Need to define property with "reference point"
Specialized ribosome-free subdomains of synthetic endoplasmic reticulum where cargo is concentrated into vesicles tha bud from the endoplasmic reticulum for tranport to the Golgi (Horton and Ehlers, 2004).
Fingerlike evaginations that extend from the dendrite that are filled with fluffy filamentous material, characteristic of some neurons like motor neurons (Peters, Palay and Webster, 1991).
Any specialized areas of the plasma membranes of adjacent cells where the membranes are 2-4 nm apart and penetrated by a connexon (Gene Ontology).
Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology).
Refers to the transport of a structure via microtubules and microtubule-associated motors.
Cell surface proteins that bind acetylcholine with high affinity and trigger intracellular changes influencing the behavior of cells. Cholinergic receptors are divided into two major classes, muscarinic and nicotinic, based originally on their affinity for nicotine and muscarine. Each group is further subdivided based on pharmacology, location, mode of action, and/or molecular biology (MSH).
A group of functionally related glycoproteins responsible for the calcium-dependent cell-to-cell adhesion mechanism. They are divided into subclasses E-, P-, and N-cadherins, which are distinct in immunological specificity and tissue distribution. They promote cell adhesion via a homophilic mechanism. These compounds play a role in the construction of tissues and of the whole animal body (MSH).
Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle
We still don't know if the synapse, in the sense that it is typically used, belongs here or whether large, multicontact synapses like the neuromuscular junction and the calycl synapse of Held, belong here and not simple synapses
A multifunctional protein that is found primarily within membrane-bound organelles. In the endoplasmic reticulum it binds to specific N-linked oligosaccharides found on newly-synthesized proteins and functions as a molecular chaperone that may play a role in protein folding or retention and degradation of misfolded proteins. In addition calreticulin is a major storage form for calcium and functions as a calcium-signaling molecule that can regulate intracellular calcium homeostasis (MSH).
Characterized by the length being greater than the diameter of the neck, with the diameter of the head being similar to that of the neck (Harris et. al 1992).
Electrotonic synapses are gap junctions that allow the passage of ions directly from cell to cell. Ultrastructurally, it can be recognized as a 7 layered structure with 4 dense lines, two from each of the plasma membranes, alternating with 3 lighter lines. Electrotonic synapses are generally symmetric and display little or no dense material associated with the cytoplasmic face of the plasma membrane (Peters, Palay and Webster, 1991).
The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology).
Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets.
Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA).
Subcompartmentalization of cellular structures such as organelles.
Neurons which activate muscle cells (MSH).
Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974).
Synaptic vesicle that is fused to the pre-synaptic membrane, forming the characteristic omega profile.
Progression through anaphase, the third stage of chromosome segregation in the cell cycle. Canonically, sister chromatids (or homologous chromosomes) separate and migrate towards the poles of the spindle (Gene Ontology).
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology).
large lower motor neurons of the brainstem and spinal cord. They innervate extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. Alpha motor neurons are distinct from gamma motor neurons, which innervate intrafusal muscle fibers of muscle spindles.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane (Gene Ontology).
We are unclear why this is causing an inconsistency error.
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached) (Gene Ontology).
Characterized by two or more heads (Harris et. al 1992) that emerge from the same origin (Sorra KE and Harris KM, 2000).
Membrane associated dimeric protein (240 and 220 kDa) of erythrocytes. Forms a complex with ankyrin, actin and probably other components of the membrane cytoskeleton, so that there is a mesh of proteins underlying the plasma membrane, potentially restricting the lateral mobility of integral proteins (Gene Ontology).
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins (Gene Ontology).
A transient cell present only in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration (Cell Ontology).
Refers to dendrites arising from another dendrite.
A large family of monomeric GTP-binding proteins that are involved in regulation of actin organization, gene expression and cell cycle progression. EC 3.6.1.- (MSH).
A non-pyramidal neuron class found primarily in layer IV of mammalian neocortex characterized by a high density of dendritic spines (While and Rock, 1980).
Abbreviation for gamma amino butyric acid, the major inhibitory neurotransmitter in the mammalian central nervous system.
Indicates that the feature was observed in the living animal.
Terminal process of astrocyte abutting non-neuronal surfaces in the brain.
One of two globular polypeptides forming microtubules.
High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages (MSH).
Paranodal terminations of Schwann cells that do not directly contact the paranodal axon membane. Usually found in thicker myelin. (Sosinsky et al., 2005)
Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward (Gene Ontology)
Supracellular structure formed by the descending axon collaterals of several cerebellar basket cells that wrap around the Purkinje cell initial segment. Although the axons contain many vesicles and form terminal endings, most do not synapse directly on the Purkinje cell initial segment but rather end blindly.
Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface (Gene Ontology). Appears as small, electron dense particles 20-40 nm in diameter. Glycogen is difficult to fix in vivo so amounts may be underestimated (Peters, Palay and Webster).
Ending of a process closest to the cell soma.
Region of axon immediately adjacent to the paranode.
The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane (Gene Ontology).
"Occurrent" refers to processual entities (e.g. events, actions, procedures, happenings) which unfold over a period of time from their beginning to their ending. Such entities depend on corresponding continuants (Rosse C et a., 2005).
A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack) (Gene Ontology).
Electron dense material observed coating the cytoplasmic face of the plasma membrane in certain regions of a neuron, e.g., the axon initial segment; the nodal membrane at the Node of Ranvier
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed) (MSH)
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins (MSH).
Refers to any specialized coating present on a vesicle membrane, e.g., clathrin.
A cell specialized to detect and transduce light (MESH).
Enzymes that hydrolyze GTP to GDP. EC 3.6.1.- (MSH).
Spaces defined by the inner and outer mitochondrial membranes
Microtubule-associated proteins that are mainly expressed in neurons. Tau proteins constitute several isoforms and play an important role in the assembly of tubulin monomers into microtubules and in maintaining the cytoskeleton and axonal transport. Aggregation of specific sets of tau proteins in filamentous inclusions is the common feature of intraneuronal and glial fibrillar lesions (neurofibrilllary tangles; neuropil threads) in numerous neurodegenerative disorders (alzheimer disease; tauopathies) (MSH).
A non-pyramidal neuron class found primarily in layer IV of mammalian neocortex characterized by relatively smooth dendrites (While and Rock, 1980).
Cellular inclusion found in the nucleus.
Axon collateral that ramifies in the area of the soma of the cell of origin.
An electron dense body, some of which contain granules (Peters, Palay and Webster (1991)
Not clear if this should be described as an organelle or an inclusion.
Nucleolar compartment consisting of large numbers of small, extremely dense granules 150-300 A in diameter, suspended in a matting of fine filaments (Palay and Chan-Palay, 1974).
Terminal pre-synaptic ending of an axon or axon collateral.
A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it.
Characterized by a high density of dendritic spines.
We have adopted the more neutral "part" rather than "compartment" which carries a functional connotation. This distinction may not matter in the long run, because we believe them to be synonymous.
A protoplasmic astrocyte with extremely thin veil-like (vellous) processes.
Any vesicles associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell (Gene Ontology).
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial genome is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins (MSH).
Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991).
Characterized by numerous swellings or varicosities along their length.
A class of nuclear body measuring 20-25 nm in diameter and distributed throughout the interchromatin space, linked together by thin fibrils. They are believed to be storage centers for various snRNAs, snRNPs, serine/arginine-rich proteins and RNA polymerase II. A typical mammalian cell contains 25-50 clusters of interchromatin granules. Interchromatin granule clusters do not contain the heterogeneous nuclear RNA-binding proteins (hnRNPs) (Gene Ontology).
Neurofilament protein with molecular weight approximately 68 kd.
Cellular inclusions found in cytoplasm that resemble nuclioli and stain with basophilic stains. They are ball-like structures about .9 microns in diameter and lack a limiting membrane. Structurally, they are composed of tightly packed fine filaments attached to them by means of fine filaments that radiate from their periphery. They were first discribed by Grillo in 1970. (from Peters, Palay, Webster)
Part of axon located at the gaps between adjacent myelin sheaths characterized by a slightly larger diameter than paranodal axon and the presence of a dense coating on the axolemma.
A dense intricate feltwork of interwoven fine glial processes, fibrils, synaptic terminals, axons, and dendrites interspersed among the nerve cells in the gray matter of the central nervous system (MSH).
Nucleus with smooth membrane and no large folds or lobules.
Refers to the "entities of reference" (FMA). Location may be defined by qualitative coodrinates or absolute coordinates.
The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology). The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology).
Characterized by the diameter of the neck being similar to that of the head (Harris et. al 1992).
Integral membrane proteins that transport molecules or ions into or out of the cell or compartment.
A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated.(MSH)
Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment.
Portion of a cell soma closest to the point where the apical dendrite emerges.
Small excitatory neuron located in the granule cell layer of the cerebellar cortex. The axon of the granule cell ascends into the molecular layer where it bifurcates and runs parallel to the long axis of the folium, contacting Purkinje cell dendrites. This portion of the granule cell axon is known as a parallel fiber.
Region of the spine within several hundred nanometers of the post synaptic specialization characterized by the presence of coated pits. It is believed that this zone may be specialized for endocytosis. These coated pits are never observed in membrane associated with the post synaptic specialization (Blanpied and Ehlers, 2004).
Quiescent Oligodendrocyte Precursor Cell
A configuration of somatic spines found on ciliary ganglion neurons in the embryonic and adult brain consisting of patches of closely spaced spines lying flat against the soma. (Shoop et al., 2000).
SAO classifies Schwann cells as a type of macroglia; Cell Type Ontology includes only astrocytes and oligodendroglia
Cellular inclusion found in the cytoplasm.
Dendritic specialization that is typically long and has a darker cytoplasm than spines. Additionally, filopodia usually end in a pointy rather than a bulbous head, and can be much longer than mature dendritic spines.
Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions (Gene Ontology).
Indicates that the feature was observed in fixed tissue.
Secretory organelles, some 50 nm in diameter, of pre-synaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the 'active zone' of the pre-synaptic plasma membrane (Gene Ontology).
Acidic protein found in sarcoplamic reticulum that binds calcium to the extent of 700-900 nmoles/mg. It plays the role of sequestering calcium transported to the interior of the intracellular vesicle (MSH).
A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane (Gene Ontology).
Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002).
Neurofilmanet protein with molecular weight 150 kd.
Elongated shape that tapers at both ends
Indicates that the feature was observed in tissue prepared by chemical fixation.
Nucleus with one or more indentations in the nuclear membrane.
Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope.
A compact and highly condensed form of chromatin (Gene Ontology).
A configuration of ER found in Purkinje cells in the cerebellum and in axons in the lateral vestibular nucleus, consisting of a number of parallel and interconnecting tubules whose outer surfaces are covered by particles or ringlike structures (Peters, Palay and Webster, 1991).
Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes.
A naturally occurring lipid pigment with histochemical characteristics similar to ceroid. It accumulates in various normal tissues and apparently increases in quantity with age (MSH).
Mobility that is mediated by the actin cytoskeleton.
A membrane-bounded organelle of eukaryotic cells that contains the chromosomes. It is the primary site of DNA replication and RNA synthesis in the cell (Gene Ontology).
Site of contact between the inner and outer mitochondrial membrane found in neuronal mitochondria; may play a role in maintaining the structural integrity of the inner and outer boundary membranes (Perkins and Ellisman, 2005).
Generally triangular-shaped soma with a dendrite emerging from the apical pole and basilar dendrites emerging from two or more basal poles
Refers to a bundle of closely apposed microtubules running parallel to each other.
Min-Lin Chang, Ching-Hsiang Wu, Ya-Fen Jiang-Shieh, Jeng-Yung Shieh, Chen-Yuan Wen (2007) Reactive changes of retinal astrocytes and Muller glial cells in kainate-induced neuroexcitotoxicity Journal of Anatomy 210 (1), 54.65. doi:10.1111/j.1469-7580.2006.00671.x
Specialized glial cell of the retina that extends from the inner limiting membrane to the outer limiting membrane
We classify this differently from the cell type ontology, as a type of radial glia rather than as a type of astrocyte. We need to look at this again.
A real boundary corresponds to its surface and designates a discontinuity between constitutional parts of anatomical entities (FMA: Mejino and Cornelius, ???)
Membranous inclusions composed of stacks of unperforated cisternae derived from the granular endoplasmic reticulum. Cisternae are spaced at intervals of about 30-40 nm (Peters, Palay and Webster, 1991).
Multipolar neuron found in cerebellar molecular layer.
Need to determine what is the proper relationships between an electrotonic synapse and a gap junction
An intercellular junction recognized in electron micrographs as a 7 layered structure with 4 dense lines, two from each of the plasma membranes, alternating with 3 lighter lines. The plaque is composed of multiple intercellular gap junction channels.
A type of NG2 positive cell that resemble oligodendrocyte precursors
A distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: keratin filaments of mammalian epithelial cells; desmin filaments found in cells of muscles of all types; vimentin filaments found in mesenchymal cells; neurofilaments of neurons; and glial filaments found in all types of glial cells (Gene Ontology).
A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology).
Cell residing in the inner third of the molecular layer of the cerebellar cortex. Axons extend laterally, transverse to the folium, and densely innervate the somata of Purkinje neurons. Axon collaterals of the basket cell axon form the specialized terminal plexus, the "pinceau", around the Purkinje cell axon initial segment.
An enzyme that catalyzes the hydrolysis of acetylcholine to choline and acetate. In the CNS, this enzyme plays a role in the function of peripheral neuromuscular junctions. EC 3.1.1.7. (MSH)
PDZ containing proteins with F-actin binding protein activity.
Schwann cell that forms a simple ensheathment around axons.
Refers to dendrites emanating from the cell soma.
Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle.
Assembly of 6 connexins into a hemichannel that forms one half of a gap junction. In some cells, the hemichannel is active as a conduit between the cytoplasm and the extracellular space.
There is some discussion about whether all marginal glia are astrocytes.
Astrocytes lying close to the pia mater that may form several layers of endfeet. They also extend several smooth long processes into the neuropil. They are located on the borders between neuronal and non-neuronal tissue
Large dense cored vesicles, up to 150-200 nm in diameter found in neurosecretory cells in the hypothalamus. The electron dense appearance is dependent upon fixation (Peters, Palay and Webster, 1991).
The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells.
The Cell_Cell_Contact_Zone and the Intercellular_Junction are not the same. The junction only refers to the bridging complex and not the larger region where the junction resides. The intercellular_Junction is part of a larger cell-cell contact zone. The cell-cell contact zone may also contain additional junctions and cellular machinery related to the function of the junction.
G-protein coupled surface receptor that mediates acetylcholine action on smooth and cardiac muscle and in CNS; may be linked to a potassium channel (membrane polarization) or second messenger systems (CSP).
Characterized by a flattened shape in glutaraldehyde fixed tissue.
The major component of glia-specific intermediate filament primarily found in astrocytes and Bergmann glia.
Diverse group of viral, prokaryotic, and eukaryotic proteins which interact with specific sites on DNA or its associated proteins to initiate or inhibit transcription; not all are DNA binding proteins per se, although that is a BT (CSP).
Refers to the terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance.
A mechanoreceptor cell located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem.
A family of synaptic vesicle-associated proteins involved in the short-term regulation of neurotransmitter release. Synapsin I (Protein I), the predominant member of this family, links synaptic vesicles to actin filaments in the presynaptic nerve terminal. These interactions are modulated by the reversible phosphorylation of synapsin I through various signal transduction pathways. The protein is also a substrate for cAMP- and calcium-calmodulin-dependent protein kinases. It is believed that these functional properties are also shared by synapsin II (Protein III) (MSH).
The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology).
A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology).
The space bounded by the cristae membrane
Sodium dependent transport protein, located on presynaptic terminals, involved in the uptake of dopamine; site at which cocaine exerts rewarding/ reinforcing effects (CSP).
Type of inhibitory cortical interneuron that provides inhibitory innervation of pyramidal neurons. Most commonly described in primates; may be absent in rodent (DeFelipe et al., 2001).
The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology).
A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH).
Synaptic vesicle docked at the pre-synaptic active zone.
Transport in the direction away from the cell soma.
Contact between endothelial cell and pericyte consisting of membrane invaginations extending from either cell type, which contain tight-, gap-, and adherence junctions (Armulik et al., Circ Res 97: 512, 2005).
Indicates that feature was described in tissue prepared by fast freezing followed by freeze substitution.
Cilia arising from neurons have been described in many different regions of the nervous system. Neuronal cilia have a "9+0" pattern, that is, they are missing the central pair of microtubules that characterizes most cilia (Peters, Palay and Webster, 1991).
Generally star shaped multipoloar cell shpae with spherically extending processes
Activated Oligodendrocyte Precursor Cell
Potassium channels whose activation is dependent on intracellular calcium concentrations (MSH).
Junctional complex consisting of two connexons that come together to form a communicating pore between two cells
Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004).
Implies that a morphologically identified synapse exists between two cell components where release of transmitter from cell influences cell B.
A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology).
Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004).
Family of polypeptide growth factors produced by peripheral target tissues as well as the nervous system, which are critical to neuronal growth, regeneration, survival, and differentiation (CSP).
Refers to the bundled configuration of microtubules in the axon hillock and initial segment.
Motor neurons which activate the contractile regions of intrafusal muscle fibers, thus adjusting the sensitivity of the muscle spindles to stretch. Gamma motor neurons may be "static" or "dynamic" according to which aspect of responsiveness (or which fiber types) they regulate. The alpha and gamma motor neurons are often activated together (alpha gamma coactivation) which allows the spindles to contribute to the control of movement trajectories despite changes in muscle length (MSH).
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes (Gene Ontology).
Transport in the direction towards the cell soma.
The portion of the myelin sheath in which layers of cell membrane are tightly juxtaposed, completely excluding cytoplasm. The juxtaposed cytoplasmic surfaces form the major dense line, while the juxtaposed extracellular surfaces form the interperiod line visible in electron micrographs (Gene Ontology).
Morphological state characterized by a contracted matrix and expanded intracristal space; observed experimentally when added ADP is used up (Mannella et al., 2001).
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration (Gene Ontology).
Morphological state characterized by an expanded matrix space and contracted intracristal space; observed experimentally when ADP is added (Mannella et al., 2001).
Synaptic arrangement where the axon courses orthogonal to and forms a synapse with a portion of dendrite.
Peptides released by neurons as intercellular messengers. Many neuropeptides are also hormones released by non-neuronal cells (MSH).
A family of high molecular weight GTP phosphohydrolases that play a direct role in vesicle transport. They associate with microtubule bundles (microtubules) and are believed to produce mechanical force via a process linked to GTP hydrolysis (MSH).
The narrow gap that separates the presynaptic and postsynaptic membranes, into which a neurotransmitter is released (Gene Ontology).
What is the right property to relate these to Cell_Cell_Contact_Zone ? We are not sure that Regional_Part is the right term for this.
Conceptual anatomical entity which describes the structural and transformation relationships between physical anatomical entities. Example: class subsumption relationship, structural relationship, anatomical tranformation relationship (FMA).
Want to organize this more carefully in the next version of the SAo
Protrusion from a dendrite. Spines are specialised subcellular compartments involved in the synaptic transmission. They are linked to the dendritic shaft by a restriction. Because of their bulb shape, they function as a biochemical and an electrical compartment. Spine remodeling is though to be involved in synaptic plasticity (Gene Ontology).
The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane (Gene Ontology).
Meshwork of extremely fine filaments composed of polypeptides called lamins that run parallel with the inner surface of the nuclear envelope (Peters, Palay and Webster, 1991).
Characterized by the diameter of the head being much greater than that of the neck (Harris et. al 1992).
Astrocytes characterized by high content of intermediate filaments and few vellous processes; often found in white matter.
Synaptic contact characterized by both electrical and chemical synaptic junctions.
Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991).
Major protein of the polyhedral coat of coated pits and vesicles (EMBL-EBI).
A network of membrane compartments, located at the cytoplasmic side of the golgi apparatus, where proteins and lipids are sorted for transport to various locations in the cell or cell membrane (MSH).
Shape descriptors that have been applied to the cell soma of nerve cells. The shape generally does not take into account processes extending from the soma.
Cell surface proteins that bind glutamate and directly gate ion channels in cell membranes. AMPA receptors were originally discriminated from other glutamate receptors by their affinity for the agonist AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid). They are probably the most common mediators of fast excitatory synaptic transmission in the central nervous system. Several subtypes have been cloned, and for some types the traditional distinction from kainate receptors may not apply (MSH).
The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes concerned with fatty-acid oxidation and enzymes of the tricarboxylic acid cycle (Gene Ontology).
Large astrocyte that forms a layer that lies beneath the ependymal layer.
Characterized by a low density of dendritic spines.
Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH).
A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes (Gene Ontology).
A lysosome before it has fused with a vesicle or vacuole (Gene Ontology).
The smooth ER has no ribosomes attached to it. The smooth is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER (Gene Ontology).
Specialization of the hypolemmal cisterna consisting of either single profiles or closely apposed stacks of ER in which the lumen is obliterated, lying 10-20 nm beneath the plasma membrane (Peters, Palay and Webster, 1991).
Refers to the morphology of mitochondria.
Refers to crisate with a roughly circular profile in cross section.
A neurotransmitter. Acetylcholine in vertebrates is the major transmitter at neuromuscular junctions, autonomic ganglia, parasympathetic effector junctions, a subset of sympathetic effector junctions, and at many sites in the central nervous system. It is generally not used as an administered drug because it is broken down very rapidly by cholinesterases, but it is useful in some ophthalmological applications (MSH).
Cell adhesion molecule expressed at neuronal surface.
Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain.
This comes from derouiche et al. J. Physol. Paris 2002 96:177 PubMedID:12445894
It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet
Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain. These processes are characterized by few glial filiments or organelles and high concentrations of the actin-binding protein ezrin.
A belt-like region of very close contact between the plasma membranes of adjacent cells so that the intercellular space is completely occluded. They occur in epithelia and brain endothelia (Gene Ontology).
Portion of the axon proximal to the neuronal cell body, at the level of the axon hillock. The action potentials that propagate along the axon are generated at the level of this initial segment (Gene Ontology).
Macromolecular organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and usually, sulfur. These macromolecules (proteins) form an intricate meshwork in which cells are embedded to construct tissues. Variations in the relative types of macromolecules and their organization determine the type of extracellular matrix, each adapted to the functional requirements of the tissue. The two main classes of macromolecules that form the extracellular matrix are: glycosaminoglycans, usually linked to proteins (proteoglycans), and fibrous proteins (e.g., collagen, elastin, fibronectins, and laminin). (MSH)
The rough (or granular) ER has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae (Gene Ontology).
A two-stranded helical polymer of the protein actin. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. Reference(s): ISBN:0198506732 PMID:10666339 (GO)
Parts of a supracellular object, e.g., synapse.
We have not yet decided whether they are regional parts of some other sort. So for now, they are just parts.
Mature contractile cells, commonly known as myocytes, that form one of three kinds of muscle. The three types of muscle cells are skeletal (muscle fibers), cardiac (myocytes, cardiac), and smooth (myocytes, smooth muscle). They are derived from embryonic (precursor) muscle cells called myoblasts (MSH).
Indicates that the feature was observed in cells in culture or in isolated subcellular fractions.
Interfascicular oligodendrocyte which can support myelin volumes of approximately 500 cubic microns and is associated with small diameter axons
"Continuant" refers to the participants of occurrent processes and are entities that endure during the period of their existence (Rosse C et a., 2005).
Potassium channel whose permeability to ions is extremely sensitive to the transmembrane potential difference. The opening of these channels is induced by the membrane depolarization of the action potential (MSH).
A sodium channel in a cell membrane whose opening is governed by the membrane potential (Gene Ontology).
A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from "star" cells) are irregularly shaped with many long processes, including those with "end feet" which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and "reactive astrocytes" (along with microglia) respond to injury (MSH).
The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system (MSH).
A dispersed and relatively uncompacted form of chromatin (Gene Ontology).
An intercellular junction found in invertebrate epithelia that is characterised by a ladder like appearance in electron micrographs. Thought to provide structural strength and to provide a barrier to diffusion of solutes through the intercellular space. Occur widely in transporting epithelia and are controversially considered analogous to tight junctions (zonula occludens) Biology-online.org
Cell surface receptors that bind signalling molecules released by neurons and convert these signals into intracellular changes influencing the behavior of cells. Neurotransmitter is used here in its most general sense, including not only messengers that act to regulate ion channels, but also those which act on second messenger systems and those which may act at a distance from their release sites. Included are receptors for neuromodulators, neuroregulators, neuromediators, and neurohumors, whether or not located at synapses (MSH).
An adherens plaque attached by filamentous strands to mitochondrion found in large synaptic terminals in the calyc of Held. The peripheral membrane facing the plaque is flattened and faces the synaptic presynaptic membrane (Perkins and Ellisman, 2005).
Do spines only have a post synaptic density
With the restrictions we are trying to say that if you are a spine, you may have one or more of the following parts, a head, a neck or a spinule. If you have one of these parts then you are likely a spine.
Cellular inclusions associated with pathological conditions.
The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology).
Cytoplasmic pockets, or as they appear in thin sections "loops" formed by the Schwann cell in the paranodal region. These pockets are actually part of a continuous helical structure providing cytoplasmic continuity from the inntermost to the outermost layers of the myelin sheath through the cytoplasmic channel formed by the loop. Most are directly apposed to the paranodal axonal membrane
An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system (Gene Ontology).
A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO).
A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles.
Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings.
The space between the inner and outer nuclear membranes
We need to figure out how to relate these to their corresponding properties, and whether it is necessary to do so, what that gains us.
Located in the sub-retinal space, these cells form the sub-retinal blood-brain barrier and contain light-absorbing melanin pigment granules
There is a visual pigment cell in the cell type ontology but we are not sure if this is the same cell
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) (MSH)
Pyramidal neuron whose cell soma resides in layer 5 or whose connectivity patterns resemble layer 5 neurons.
A biochemical messenger and regulator, synthesized from the essential amino acid L-tryptophan. In humans it is found primarily in the central nervous system, gastrointestinal tract, and blood platelets. Serotonin mediates several important physiological functions including neurotransmission, gastrointestinal motility, hemostasis, and cardiovascular integrity. Multiple receptor families (receptors, serotonin) explain the broad physiological actions and distribution of this biochemical mediator (MSH).
Extracellular tissue protease that degrades a wide spectrum of extracellular matrix proteins.
A specialization of the endomembrane system found in some classes of spines consisting of two or more closely apposed lamellae with interspersed dense material.
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating.
Serum glycoprotein produced by activated macrophages and other mammalian mononuclear leukocytes. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share two receptors (MSH).
A class of large neuroglial (macroglial) cells in the central nervous system. Oligodendroglia may be called interfascicular, perivascular, or perineuronal (not the same as satellite cells, perineuronal of ganglia) according to their location. They form the insulating myelin sheath of axons in the central nervous system (MSH).
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome (Gene Ontology).
Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991).
Signal molecules that are involved in the control of cell growth and differentiation (MSH).
Maximum diameter of a cross section through structure, assumed to be the maximum diameter in the case of spherical structures like vesicles. Use this field when entering only a single cross section value where the structure is assumed to be spherical.
Region of nodal complex adjacent to the paranode
Part of nodal complex located underneath the compact myelin in between nodes of Ranvier
Astrocyte characterized by spongy appearance and many vellous processes; often found in gray matter.
A diverse superfamily of proteins that function as translocating proteins. They share the common characteristics of being able to bind ACTINS and hydrolyse MgATP. Myosins generally consist of heavy chains which are involved in locomotion, and light chains which are are involve in regulation. Within the structure of myosin heavy chain are three domains: the head, the neck and the tail. The head region of the heavy chain contains the actin binding domain and MgATPase domain which provides energy for locomotion. The neck region is involved in binding the light-chains. The tail region provides the anchoring point that maintains the position of the heavy chain. The superfamily of myosins is organized into structural classes based upon the type and arrangement of the subunits they contain (MSH).
The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology).
A group of homologous proteins which form the intermembrane channels of gap junctions. The connexins are the products of an identified gene family which has both highly conserved and highly divergent regions. The variety contributes to the wide range of functional properties of gap junctions (MSH).
Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode
Cardiac muscle cell comprising the ventricles
A group of 7 proteins produced from a single gene by alternate splicing found in central and peripheral nervous system myelin. The major basic protein (MBP) has long been of interest because it is the antigen, that, when injected into an animal, elicits a cellular immune response that produces the CNS autoimmune disease called experimental allergic encephalomyelitis (encephalomyelitis, allergic). In the peripheral nervous system, myelin basic protein 18.5 kD is often referred to as the P1 protein. (From Siegel et al., Basic Neurochemistry, 5th ed, p130, 133) (MSH)
Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum.
A 43 kD peptide which is a member of the connexin family of gap junction proteins. Connexin 43 is a product of a gene in the alpha class of connexin genes (the alpha-1 gene). It was first isolated from mammalian heart, but is widespread in the body including the brain (MSH).
Equivalent to "regional part" in the FMA--a primary partition that spatially subdivides an anatomical structure into sets of diverse constiutional parts that share a given location within the whole; i.d., the partition is spatial instead of compositional (Mejino JLV et al., 2003).
Endosomal component consisting of cylindrical shaped tubues, ~50 nm in diameter, with smooth outer membranes an dark, grainy interiors (Clooney et al., 2002). Clathrin-like protein coats occur at the ends of some tubular compartments.
Type of spine characterized by a narrow neck of varying length attached to an expanded head (Jones and Powell 1969). It appears from the definition given by these authors that the thin and mushroom shaped categories are both included as subclasses of pedunculated.
May need to do more reading to determine whether this should be a parent of mushroom and thin.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm (MSH).
Arrangement of pre- and post-synaptic components.
A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).
Large branching neurons of the middle layer of cerebellar cortex, characterized by vast arrays of dendrites; involved in controlling complex movements (CSP).
A soluble factor produced by monocytes, macrophages, and other cells which activates T-lymphocytes and potentiates their response to mitogens or antigens. IL-1 consists of two distinct forms, IL-1 alpha and IL-1 beta which perform the same functions but are distinct proteins. The biological effects of IL-1 include the ability to replace macrophage requirements for T-cell activation. The factor is distinct from INTERLEUKIN-2 (MSH).
Cell adhesion molecule involved in a diverse range of contact-mediated interactions among neurons, astrocytes, oligodendrocytes, and myotubes. It is widely but transiently expressed in many tissues early in embryogenesis. Four main isoforms exist, including CD56; (ANTIGENS, CD56); but there are many other variants resulting from alternative splicing and post-translational modifications. (From Pigott & Power, The Adhesion Molecule FactsBook, 1993, pp115-119) (MSH)
Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane
The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS).
A virtual boundary does not represent a structural discontinuity between entities but corresponds to an imaginary boundary between functional compartments, e.g., soma and dendrite (adapted from FMA).
Category for vesicles observed in electron micrographs with unknown function.
White matter oligodendrocytes that may be aligned in rows (Peters, Palay and Webster, 1991).
Cellular inclusion containing filamentous structures.
Small membrane-bounded organelle formed by pinching off of a coated region of membrane. Some coats are made of clathrin, whereas others are made from other proteins (Gene Ontology).
One of the catecholamine neurotransmitters in the brain. It is derived from tyrosine and is the precursor to norepinephrine and epinephrin. Dopamine is a major transmitter in the extrapyramidal system of the brain, and important in regulating movement. A family of receptors (receptors, dopamine) mediate its action (MSH).
Elongated portion of the tanycyte that sticks into the periventricular layer of neuropil where it appears to contact a blood vessel; characterized by numerous cytoplasmic extensions (Peters, Palay and Webster, 1991).
Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology).
Characterization based on high or low density of classical spines on dendrites.
Synaptic component; electron dense cytoskeletal specialization located on the post synaptic membrane at the site of synaptic contact. The PSD is particularly prominent in glutamatergic synapses, giving the synapse an asymmetrical appearance. This type of PSD is often referred to as "asymmetrical" or Gray's Type 1 (Maryann Martone, from the CCDB Dictionary).
A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).
Neurofilament protein with molecular weight 200 kd.
Refers to the morphology of mitochondrial cristae.
Membrane proteins which facilitate the passage of water. They are members of the family of membrane channel proteins which includes the lens major intrinsic protein and bacterial glycerol transporters (MSH).
The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches.
A small version of the zonula adharens type junction, characterized by a symmetrical adherent point between two cells.
The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology).
A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) (MSH).
Glial cell type unique to primates which extend long processes throughout cortical lamina forming pallisades.
We need to create an object property that allows us to assign taxonomy information to classes that are only seen in certain taxa
A type of nerve cell characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space. (Reichenbach and Wolburg, 2nd edition, 2005)
Major constituent of the cytoskeleton found in the cytoplasm of eukaryotic cells. They form a flexible framework for the cell, provide attachment points for organelles and formed bodies, and make communication between parts of the cell possible (MSH).
A non-material physical anatomical entity of two or fewer dimensions that delimits or demarcates anatomical entities from one another that are of one dimension higher than the bounding entity (FMA).
Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991).
Nucleus with heavily indented nuclear membrane, giving the appearance of one or more lobes.
Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003).
The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology).
I'm having difficulty deciding whether this is a regional part of a mitochondrion or whether it is a site; today it is a regional part.
The region between the inner and outer lipid bilayers of the mitochondrial envelope. (Gene Ontology).
Projection neurons in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region (MSH).
Refers to integral membrane proteins carried via the vesicle membrane.
A dendrite characterized by few or no recognizable dendritic spines.
Pyramidal neuron whose cell soma resides in layer 3 of neocortex.
Microtubules are characterized by a + and a - end and may be oriented with respect to the soma (origin) in either + to - or - to +.
Cellular inclusion found in cytoplasm of giant cells of Dieters in lateral vestibular nucleus of the rat consisting of circular areas filled with fine slender filaments about 10 nanometers in diameter, delimited by a wall of varying complexity either a single continuous membrane or a tubular network consisting of a fine filamentous material giving the wall a honeycomb appearance. Similar structures have been discribed in the ventral cochlear nucleus, spinal cord, substantia nigra. First described by Sitelo and Palay, 1968. (from Peters, Palay, and Webster)
40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991).
Shaw-like family of voltage gated potassium channels.
Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction
Cuboidal shaped epithelial cell forming one of the components of the choroid plexus (Peters, Palay and Webster, 1991).
A protein that speeds up chemical reactions in the body (PDQ).
Refers to cristae with a flattened, extended appearance.
A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter (Gene Ontology).
Protein complexes that mediate the release of calcium from the sarcoplasmic reticulum in both skeletal and cardiac muscle cells by forming tetrametric complexes. These complexes each then act as a calcium channel. There are three isoforms of the RyR: RyR1, RyR2, and RyR3. RyR1 is specifically expressed in skeletal muscles and RyR2 in cardiac muscles. RyR3 is yet another isoform found in non-muscle cells such as neuronal cells. (From Yonsei Med J 1996;37(1):72-80) (MSH)
Elongated process, devoid of cytoplasmic extensions, that courses through the hypothalamic nucleis to form small endfoot processes that terminate either on blood vessels or at the pial surface of the brain (Peters, Palay and Webster, 1991).
The volume enclosed by the membranes of an endosome (Gene Ontology).
Refers to processes of astrocytes extending from the cell soma that wrap around neurons and conform to cellular components in the neuropil.
Large cell located in the dorsal root ganglion with a single process that extends into the periphery and into the spinal cord. These neurons convey sensory information from the body.
Characterized by many shapes in glutaraldehyde fixed tissue.
This needs to be extensively investigated
Ramification of basket cell axon surrounding cell bodies, forming the characteristic peri-cellular baskets from which the cell class derives its name.
see example at: http://synapse-web.org/anatomy/chemical/asymh.htm
Type of chemical synapse characterized by a pronounced and relatively thick post-synaptic density compared to the pre-synaptic specialization giving the junction an asymmetrical appearance. This type of synapse is also characterized by round, clear vesicles in the pre-synaptic terminal.
Cell membrane glycoproteins selective for sodium ions. Fast sodium current is associated with the action potential in neural membranes (MSH).
Voltage-dependent cell membrane glycoproteins selectively permeable to calcium ions. They are categorized as L-, T-, N-, P-, Q-, and R-types based on the activation and inactivation kinetics, ion specificity, and sensitivity to drugs and toxins. The L- and T-types are present throughout the cardiovascular and central nervous systems and the N-, P-, Q-, & R-types are located in neuronal tissue (MSH).
One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision.
Small finger-like extension of the Schwann cell that contact the nodal membrane but are not closely apposed to each other like the paranodal lops (Sosinsky et al., 2005)
Proteins found in the microtubules (MSH).
A specialized glial cell in the pectin oculi of avians, located at the interface between the optic nerve head and the vitreous body. These cells produce pectin.
Schwann cell that apposes or encapsulates neuronal perikarya (Peters, Palay and Webster, 1991).
Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000).
All experimental entities will be ported into a separate ontology based on OBI
Indicates the experimental conditions under which a feature was observed.
A flattened, or elongated, stellate-shaped solitary cell with multiple cytoplasmic processes encircling the capillary endothelium and contacting a large abluminal vessel area. It may be equivalent to the vascular smooth muscle cell, although this identify has not been conclusively determined yet (Armulik et al., Circ Res 97: 512, 2005).
One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. (MSH)
Refers to the process of the Schwann cell that surrounds an unmyelinated axon or cell soma.
Specializations associated with intracellular membrane systems, e.g. lamellar bodies. Membranes of subcellular structures. (MSH)
Used to refer to the main axonal trunk, as opposed to the collaterals.
Molecule-sized pores in biomembranes that permit the passage of hydrophilic solutes such as inorganic ions, and the proteins that form such pores and control their permeability (CSP).
Spatial association relationship which describes the containment, adjacency, and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate (FMA).
Giant pyramidal neuron found in primate motor cortex.
Diverse family of cytoskeletal proteins which bind actin, thereby stabilizing or destabilizing microfilaments, anchoring them to other cell structure, or subserving intracellular translocation and motility (CSP).
Cell-surface proteins that bind glutamate and trigger changes which influence the behavior of cells. Glutamate receptors include ionotropic receptors (AMPA, kainate, and N-methyl-D-aspartate receptors), which directly control ion channels, and metabotropic receptors which act through second messenger systems. Glutamate receptors are the most common mediators of fast excitatory synaptic transmission in the central nervous system. They have also been implicated in the mechanisms of memory and of many diseases (MSH).
Type of chemical synapse characterized by a thin post-synaptic density relatively equal in density to the pre-synaptic specialization giving the junction a symmetric appearance. This type of synapse is also characterized by flattened or pleiomorphic vesicles in the pre-synaptic terminal when fixed with aldehydes.
see example at: http://synapse-web.org/anatomy/chemical/symh.htm
Embryonic cell that develops into a neuron (CSP).
Site located at the gaps in the myelin sheaths of myelinated axons. Axon diameter is generally decreased in the nodal region, compared to the internode. Ranvier's nodes allow saltatory conduction, that is, jumping of impulses from node to node, which is faster and more energetically favorable than continuous conduction (MSH).
Transports adenine nucleotides (AMP, ADP, and ATP) across membranes (Gene Ontology).
An enzyme that catalyzes the conversion of L-tyrosine, tetrahydrobiopterin, and oxygen to 3,4-dihydroxy-L-phenylalanine, dihydrobiopterin, and water. EC 1.14.16.2 (MSH).
Large cholinergic interneuron in the caudate nucleus, putamen and nucleus accumbens.
Mitogenic peptide growth hormone carried in the alpha-granules of platelets. It is released when platelets adhere to traumatized tissues. Connective tissue cells near the traumatized region respond by initiating the process of replication (MSH).
Distance, usually in linear microns, from soma where a feature is observed.
Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner (MSH).
Ending of a process furthest from the cell soma.
It is unclear to us whether perineuronal oligodendrocytes should be considered a separate class.
Oligodendrocyte found in gray matter in close association with neurons (Peters, Palay and Webster, 1991).
Progression through interphase, the stage of cell cycle between successive rounds of chromosome segregation. Canonically, interphase is the stage of the cell cycle during which the biochemical and physiologic functions of the cell are performed and replication of chromatin occurs (Gene Ontology).
A branching protoplasmic process of a neuron that receive and integrate signals coming from axons of other neurons, and convey the resulting signal to the body of the cell (Gene Ontology).
One of several similar processes that issue from the perikaryon of a neuron, generally specialized for receiving synaptic input from other neurons or transduction of signals from the environment.
NG2 cells are central nervous system (CNS) glial cells defined by their expression of the chondroitin sulfate proteoglycan, NG2, which is also known as Cspg4 or AN2
Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined (Gene Ontology).
Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology)
Specialized part of the smooth endoplasmic reticulum that closely underlies the plasma membrane, usually within 60 nm or closer (Peters, Palay and Webster, 1991).
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology).
Need to determine whether this should be a part of a vesicle; I think it shouldn't be
Refers to the contents contained in the vesicle.
Refers to the fine, veil-like terminal processes of protoplasmic astrocytes.
is this the same as what is now termed the peripheral astrocyte process?
Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA).
Equivalent to "constitutional part" in the FMA--a primary partition of an anatomical structure into its compositionally distinct anatomical elements. In the context of the whole, an element is any relatively simple component of which a larger, more complex anatomical structure is compounded; i.e., teh partition is compositional rather than spatial (Mejino JLV et al., 2003).
This cell class is not contained in the Cell Type Ontology
Type of cortical interneuron characterized by a bitufted appearance, with groups of dendrites extending from the upper and lower poles of an elongate cell body, but some cells have a more multipolar configuration.
Anatomical space occurring within a cell, usually formed by intracellular membranes.
Oligodendrocyte that forms compact myelin sheath.
Characterized by a nuclear membrane with no indentations.
Note that the cell type ontology does not consider Schwann Cells to be macroglia
Neuroglial cells of the peripheral nervous system which form the insulating myelin sheaths of peripheral axons (MSH).
Region of nodal complex adjacent to the nodal region
Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974).
Portion of a cell soma closest to the point where the basilar dendrite emerges.
A heterodimer of tubulins alpha and beta that constitutes the protomer for microtubule assembly (Gene Ontology).
Properties derived from Gersdorff and Borst (2002).
Principal Cells Medial Nucleus Trapezoid Body
A hexagonal array of electron dense particles attched to the cyotplasmic face of the presynaptic membrane, revealed by staining with ethanolic phosphotungstic acid (Peters, Palay and Webster, 1991).
That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology).
An epithelial cell lining the walls of the ventricles of the brain and central canal of the spinal cord that secret cerebral spinal fluid. (Peters, Palay and Webster, 1991).
A neurectoderm derived cell that lines the neural lumen (Cell Ontology).
We are not sure whether ependymal cells should be considered a type of ependymoglial cell
The distal terminations of axons which are specialized for the release of neurotransmitters. Also included are varicosities along the course of axons which have similar specializations and also release transmitters. Presynaptic terminals in both the central and peripheral nervous systems are included (MSH).
When several members of a class occur tightly apposed to one another or attached to one another in identifiable bundles.
Portion of the ensheathing process (either myelin or non-myelin) where the enveloping lips of the ensheathing cell come together so that their apposed plasma membranes run parallel to each other, separated by a cleft 12 nm wide (Peters, Palay and Webster, 1991).
Refers to a structure that defines the boundary of a given structure
refers to a set of property classes that reflect unique aspects of a given structure, e.g., orientation, stability
Used to describe a physical relationship between two or more cellular components
This idea was adopted from FMA but possibly needs reconsideration.
Cellular element derived from another cell associated with a compartment, e.g., myelin
is Intercellular Junction Compartment Of
Indicates that there is a spatial relationship other than containment or parthood between cellular regional parts or components (e.g. microtuble associates with mitochondria)
Neurotransmitter associated with neuronal class
Refers to the cellular component with which a feature is associated, e.g., ion receptor is associated with the plasma membrane
Refers to the specific location of an instance of a cell
participates in one or more types of intercellular junctions
Classification of synaptic type according to Gray, except using the symmetrical (Gray's Type 2) and asymmetrical (Gray's Type 1) designations
This property is temporarily defined as a datatype property. We anticipate that the locations of cells and cell parts will be drawn from a neuroanatomical brain region ontology in a future version.
General description of the anatomical location assigned to the cell class, regardless of whether parts of the cell are located elsewhere. For neurons, this would be the location of the cell soma
Indicates under what conditions the observation was made
Indicates the point at which a described measurement was taken
Describes general morphology of the post synaptic density (PSD), where it is classified as macular if the thickening is continuous, or perforated when the PSD is interrupted by electron-lucent regions (Harris KM et al., 1992).
Used to denote the presence or absence of a feature. "Found" indicates that the feature described was observed in this instance. "Found" is always assumed to be the default. "Not found" indicates that a feature was looked for and specifically not found, e.g. microtubules were not found in dendritic spines. This value should not be used if the feature was merely not described.
This property should be updated when we switch to OBR relations to the "lacks" relationship
A continuant is an entity that endures through time. If true, then entity is a continuant; if false, then entity is an occurrent. An occurrent is defined as a process, event or happening, e.g., a dividing cell.
Cellular components found in typical cells.
Describes whether the reported values are averages, estimates, ranges, or absolute values
Refers to the minimum number of primary dendrites arising from the cell soma
Refers to the maximum branch order of the dendritic tree
Coordiante along the anteior-posterior axis
Indicates the species of organism from which an observation derives
Coordinate along the medial-lateral axis
Denotes whether a neuron or dendrite is characterized by at least one spine.
Indicates that the structure forms the boundary for another structure, e.g., membrane of endoplasmic reticulum is boundary of lumen of endoplasmic reticulum
Refers to the maximum number of primary dendrites generally seen in a particulary neuronal class
Cumulative length of all dendrites in the dendritic tree
Indicates the sex of the animal in which the observation was made.
Indicates the age of the animal in which the observation was made
Refers to the number of axons arising from the cell soma or primary dendrite. Usually is "1", but may be "0" for some neuron types. In rare cases in mammalian neurons, may be more than 1.
Name and edition of atlas used to derive coordinates
Describes the general morphology of a class of neurons with respect to the number of processes extending from the cell soma
functional categorization of cell, e.g., motor, sensory, secretory, myelinating
Differentiates between cells and processes that are located in the central nervous system (CNS) vs peripheral nervous system (PNS). Does not refer to embyrological origin.
Used to describe whether properties are derived from a single, identified object or represent a summary derived from multiple instances of the object. For example, if a source described the properties of a single filled dendrites, this would not be a population object. If a source described the general attributes of all dendrites from a single neuron, then this would be a population object because the properties represent a summary of all dendrites lumped together. The number field can be used to specify the number of objects on which the descriptions is based.
Reference point of the coordinate system used, e.g., bregma
Element with reference to which orientation is defined
Unique identifier of an instance found in the CCDB.
A property of branching structures such as axons and dendrites
Location of a cell in a specific coordinate system
Need to determine whether this property is useful in conjunction with intercellular junctions, i.e., in order for two things to be attached, there must be a junction of some sort
Indicates an intimate contact between two anatomical entities, each with their own real boundaries
Used to describe generic shape of a component or compartment
Used to describe the method by which the parent cell to a subcellular part is identified. "Identified cell" means that some sort of interacellular label was used to identify the parent cell with some degree of certainty; "asserted" refers to the use of morphological and anatomical criteria to assign identity to a parent.
Coordinate along the dorsal ventral axis