is Regional Part Of
is Regional Part Of
sao1239937685
associated Cell Component
Used to describe a physical relationship between two or more cellular components
associated Cell Component
sao1356746816
is Component Of
is Component Of
sao138767806
has Regional Part
has Regional Part
sao1434436507
continuous With Centrifugal
continuous With Centrifugal
sao1454173298
has Neurotransmitter
Neurotransmitter associated with neuronal class
has Neurotransmitter
sao1490541696
has Molecular Constituent
has Molecular Constituent
sao152994059
continuous With Centripetal
continuous With Centripetal
sao158083006
Anatomical location: atlas
anatomical Location Atlas
Location of a cell in a specific coordinate system
anatomical Location Atlas
sao1597912566
has Component
Cellular components found in typical cells.
has Component
sao1623809261
associated Cellular Element
Cellular element derived from another cell associated with a compartment, e.g., myelin
associated Cellular Element
sao180517057
has Boundary
Refers to a structure that defines the boundary of a given structure
has Boundary
sao1844377738
continuous With
Physical continuity between structures
This idea was adopted from FMA but possibly needs reconsideration.
continuous With
graph position temporary
sao1896217670
attached To
Indicates an intimate contact between two anatomical entities, each with their own real boundaries
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
attached To
sao1896476612
is Molecular Constituent Of
is Molecular Constituent Of
sao1939689633
associated With
Indicates that there is a spatial relationship other than containment or parthood between cellular regional parts or components (e.g. microtuble associates with mitochondria)
associated With
sao2047323768
has Property
has Property
refers to a set of property classes that reflect unique aspects of a given structure, e.g., orientation, stability
sao2103390115
is Aggregate Part of
is Aggregate Part of
sao2422696582
location Component
Refers to the cellular component with which a feature is associated, e.g., ion receptor is associated with the plasma membrane
location Component
sao333215121
is Morphological Type Of
is Morphological Type Of
sao3610809721
has Vesicle Component
has Vesicle Component
sao3762365186
has Morphological Type
has Morphological Type
sao3931558608
located in
located in
sao4245285112
is Intercellular Junction Compartment Of
is Intercellular Junction Compartment Of
sao45720944
anatomical Location Specific
Refers to the specific location of an instance of a cell
anatomical Location Specific
sao548011359
contains Site
contains Site
sao554204175
has Part
has Part
sao5598458770
anatomical Location
anatomical Location
sao7122682114
inverse of has Component 6
inverse of has Component 6
sao7291254923
intercellular Junction Compartment
intercellular Junction Compartment
participates in one or more types of intercellular junctions
sao733319732
morphometrics
Measurement associated with compartment
morphometrics
sao872346836
has Aggregate Part
has Aggregate Part
sao8839644583
boundary Of
Indicates that the structure forms the boundary for another structure, e.g., membrane of endoplasmic reticulum is boundary of lumen of endoplasmic reticulum
boundary Of
sao923422536
is Neurotransmitter Of
is Neurotransmitter Of
sao924725934
has Location Of
has Location Of
sao9371595441
is Part Of
is Part Of
sao9906015852
PSD morphology
psd Morphology
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).
psd Morphology
sao1056822429
asymmetric
macular
perforated
symmetric
anatomical Location General
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
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.
anatomical Location General
graph position temporary
sao1065676773
has Mass
has Mass
sao1077517916
false
true
location CNS PNS
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.
location CNS PNS
sao1130665397
CNS
PNS
species
Indicates the species of organism from which an observation derives
sao1185641609
species
molecular Weight
molecular weight
molecular Weight
sao1220772118
has Inherent 3D Shape
has Inherent 3D Shape
sao1254683799
false
true
isoform
isoform
sao1267375031
Number of Axons
number Of Axons
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.
number Of Axons
sao1384659949
population Object
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.
population Object
sao1428515021
No
Yes
observation Conditions
Indicates under what conditions the observation was made
observation Conditions
sao1429489883
functional Type
functional Type
functional categorization of cell, e.g., motor, sensory, secretory, myelinating
sao1608074544
excitatory
inhibitory
modulatory
standard Error
Standard error (+/-)
sao1620782974
standard Error
shape
Used to describe generic shape of a component or compartment
sao166035570
shape
concave
convex
cylindrical
elliptical
flat
round
spherical
spindle-shaped
point Of Measurement
Indicates the point at which a described measurement was taken
point Of Measurement
sao1669593695
distal
proximal
number Of Branches
number Of Branches
sao1746944408
is Continuant
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.
is Continuant
sao1798215493
false
true
Atlas Coordinate M-L
atlas Coordinate M-L
Coordinate along the medial-lateral axis
atlas Coordinate M-L
sao1804901442
is Spiny
is spiny
Denotes whether a neuron or dendrite is characterized by at least one spine.
is Spiny
sao1863785805
number Primary Dendrites Max
Refers to the maximum number of primary dendrites generally seen in a particulary neuronal class
number Primary Dendrites Max
sao1936650489
Atlas reference point
atlas Reference Point
Reference point of the coordinate system used, e.g., bregma
atlas Reference Point
sao1945565347
circuit Type
circuit Type
sao1967171150
local circuit neuron
projection neuron
Cell ID
parent Cell Identity
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.
parent Cell Identity
sao1981606713
Asserted
abstract
concrete
Atlas Coordinate A-P
atlas Coordinate A-P
Coordiante along the anteior-posterior axis
atlas Coordinate A-P
sao2048509857
orientation Reference To
Element with reference to which orientation is defined
orientation Reference To
sao2110623092
Age of Animal
age Of Animal
Indicates the age of the animal in which the observation was made
age Of Animal
sao2134236783
presence
This property should be updated when we switch to OBR relations to the "lacks" relationship
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.
graph position temporary
presence
sao2372462654
not found
Atlas Reference
atlas Reference
Name and edition of atlas used to derive coordinates
atlas Reference
sao244654816
number
number
sao267012610
value Type
Describes whether the reported values are averages, estimates, ranges, or absolute values
sao375065056
value Type
absolute
average
direct
estimate
greater than
greater than or equal to
less than
less than or equal to
range
density
density
sao382106499
sex Of Animal
Indicates the sex of the animal in which the observation was made.
sao392224970
sex Of Animal
Female
Male
Unspecified
maximum
maximum
maximum value in a range
sao395752640
unit
sao40919963
unit
unit of measurement
angstroms
cubic microns
microns
microns squared
spines per micron
polarity Reference To
Reference to which polarity is defined
polarity Reference To
sao431495567
total Dendritic Length
Cumulative length of all dendrites in the dendritic tree
sao528500906
total Dendritic Length
minimum
Minimum value in a range
minimum
sao643761283
value
measurement value
sao655061336
value
ccdb ID
Unique identifier of an instance found in the CCDB.
ccdb ID
sao796296921
Atlas Coordinate D-V
atlas Coordinate D-V
Coordinate along the dorsal ventral axis
atlas Coordinate D-V
sao833783433
process Number
Describes the general morphology of a class of neurons with respect to the number of processes extending from the cell soma
process Number
sao841626191
bipolar
multipolar
unipolar
maximum Branch Order
Refers to the maximum branch order of the dendritic tree
maximum Branch Order
sao925977276
Number of Primary Dendrites
number Primary Dendrites Min
Refers to the minimum number of primary dendrites arising from the cell soma
number Primary Dendrites Min
sao950829914
branch Order
A property of branching structures such as axons and dendrites
branch Order
sao996727841
2
3
>2
>3
synapse Type
Classification of synaptic type according to Gray, except using the symmetrical (Gray's Type 2) and asymmetrical (Gray's Type 1) designations
sao99760531
synapse Type
asymmetrical
symmetrical
Filopodium
0030175
Filopodium
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)
sao-1046371754
uncurated
Schwann Cell Paranodal Termination
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
Schwann Cell Paranodal Termination
sao-1067215520
uncurated
Schwann Cell Compact Myelin
Schwann Cell Compact Myelin
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).
sao-1123256993
uncurated
Soma Type
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.
Soma Type
sao-1126011106
Interlaminar Astrocyte
Eric Bushong
Glial cell type unique to primates which extend long processes throughout cortical lamina forming pallisades.
Interlaminar Astrocyte
We need to create an object property that allows us to assign taxonomy information to classes that are only seen in certain taxa
sao-1220620412
true
Branch Point Of Dendrite
Branch Point Of Dendrite
sao-1348591767
uncurated
Mitochondrial Site
Mitochondrial Site
sao-1367457321
Pyramidal
Generally triangular-shaped soma with a dendrite emerging from the apical pole and basilar dendrites emerging from two or more basal poles
Pyramidal
curation complete
sao-1465673360
Pre-synaptic Ribbon
Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster).
Pre-synaptic Ribbon
sao-1488888179
Regional Part Of Mitochondrial Membrane
Regional Part Of Mitochondrial Membrane
sao-1686050947
uncurated
Intercellular Gap Junction Channel
Intercellular Gap Junction Channel
Junctional complex consisting of two connexons that come together to form a communicating pore between two cells
Maryann Martone
sao-1778046445
Regional Part Of Cell Component
Regional Part Of Cell Component
sao-1819020575
uncurated
Cell Process
Cell Process
sao-1828894864
uncurated
Glial Filament
Glial Filament
sao-1863852493
uncurated
Marginal Astrocyte
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
Marginal Astrocyte
There is some discussion about whether all marginal glia are astrocytes.
graph position temporary
sao-1865064409
true
Node Of Ranvier Axon
Node Of Ranvier Axon
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.
sao-188049490
uncurated
Mitochondrial Lumen
0031980
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.
Mitochondrial Lumen
sao-1899375636
true
uncurated
Internode
Internode
Part of nodal complex located underneath the compact myelin in between nodes of Ranvier
sao-206157942
Paranode
Paranode
Region of nodal complex adjacent to the nodal region
sao-234066064
Pectin Glial Cell
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.
Need to associate this with avians
Pecten_Glial_Cell
Pectin Glial Cell
graph position temporary
sao-243744138
true
Neuron Protrusion
Neuron Protrusion
sao-250931889
uncurated
Basal
Basal
sao-282380853
uncurated
Junction Complex
Junction Complex
sao-301233507
Type I II Oligodendrocyte
Type I/II Oligodendrocyte
Interfascicular oligodendrocyte which can support myelin volumes of approximately 500 cubic microns and is associated with small diameter axons
Type I II Oligodendrocyte
definition incomplete
sao-32901633
true
Mitochondrial Space
Mitochondrial Space
Spaces defined by the inner and outer mitochondrial membranes
sao-343550527
true
Synantocyte
2007-01-13
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 cell characterized by a differentiated, stellate appearance that lack expression of most differentiated glial cell-type specific markers.
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).
Synantocyte
graph position temporary
sao-408886955
true
Regional Part Of Neuron Process
Regional Part Of Neuron Process
sao-420949334
uncurated
Pigment Epithelial Cell
Located in the sub-retinal space, these cells form the sub-retinal blood-brain barrier and contain light-absorbing melanin pigment granules
Pigment Epithelial Cell
There is a visual pigment cell in the cell type ontology but we are not sure if this is the same cell
sao-423426544
true
Schwann Cell Myelin Sheath
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).
Schwann Cell Myelin Sheath
sao-593830697
uncurated
Node Related Site
Node Related Site
Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode
sao-596411490
Regional Part Of SER
Regional Part Of SER
sao-699412220
uncurated
Regional Part Of Neuron Protrusion
Regional Part Of Neuron Protrusion
sao-750951932
uncurated
Pyramidal Neuronal Cell Body
Pyramidal Neuronal Cell Body
sao-820130069
uncurated
Cell Protrusion
Cell Protrusion
sao-82111036
uncurated
Anatomical Coordinate
Anatomical Coordinate
Anatomical location which specifies the relationship between one or more physical anatomical entities in terms of...
FMA
FMA
sao-843826795
uncurated
Neuron Process
Neuron Process
sao-867568886
Mushroom Dendritic Spine
Mushroom Dendritic Spine
sao-876577163
uncurated
Obsolete class
Obsolete class
sao-943768255
Synaptic Site
Synaptic Site
sao-946766835
Excrescence
Excrescence
sao-961694769
uncurated
Branched Dendritic Spine
Branched Dendritic Spine
sao-965204139
uncurated
Pituicyte
C0229545
CL:0000645
Pituicyte
sao1004082033
true
uncurated
Dense Material
Dense Material
sao1004601938
uncurated
Ventricular Cardiac Muscle Cell
Cardiac muscle cell comprising the ventricles
Ventricular Cardiac Muscle Cell
sao1011026882
uncurated
ventricular myocyte
SERCA2
C0916183
SERCA2
sao1016012060
uncurated
Cytosol
0005829
C0010854
Cytosol
The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS).
sao101633890
uncurated
S100 beta
C0654870
S100 beta
sao1022370595
uncurated
Sorting Endosome
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.
Sorting Endosome
sao1028571114
uncurated
Endoplasmic Reticulum
0005783
C0014239
Endoplasmic Reticulum
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).
sao1036339110
uncurated
Membrane Cargo
Membrane Cargo
Refers to integral membrane proteins carried via the vesicle membrane.
sao1037637579
Polyribosome
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).
C0032592
Polyribosome
sao1038025871
uncurated
Dendritic Segment
Dendritic Segment
Refers to dendrites emanating from the cell soma.
sao1039042901
uncurated
Trans Face
0005802
The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology).
Trans Face
sao1039242387
uncurated
Neuronal Cell Body
C0599444
Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA).
Neuronal Cell Body
sao1044911821
soma
uncurated
Mitochondrial Membrane
Mitochondrial Membrane
sao1045389829
uncurated
Tyrosine Kinase Receptor
A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH).
C0206364
Tyrosine Kinase Receptor
sao1048004962
uncurated
Cell Adhesion Molecule
Cell Adhesion Molecule
sao1048879260
uncurated
Interchromatin Granule
0035061
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).
C0230547
Interchromatin Granule
sao1049471211
uncurated
Regional Part Of Neuronal Cell Body
Regional Part Of Neuronal Cell Body
sao1049717962
uncurated
Morphological Type
Morphological Type
sao1057800815
uncurated
Axocruciform
Axocruciform
Synaptic arrangement where the axon courses orthogonal to and forms a synapse with a portion of dendrite.
sao1062287912
uncurated
Biological Occurrent
"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).
Biological Occurrent
sao1070274187
uncurated
Synaptic Vesicle
0008021
C0039065
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).
Synaptic Vesicle
sao1071221672
uncurated
Microtubule Polarity
Microtubule Polarity
Microtubules are characterized by a + and a - end and may be oriented with respect to the soma (origin) in either + to - or - to +.
sao107236050
uncurated
Post-synaptic Site
Post-synaptic Site
sao1074198261
Tau
C0085401
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).
Tau
sao1077731745
uncurated
Trunk
Trunk
sao1078172392
uncurated
Basilar Dendrite
Basal Dendrite
Basilar Dendrite
sao1079900774
uncurated
Glycogen Granule
0042587
C0017911
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).
Glycogen Granule
sao1081228141
uncurated
Connexin 43
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).
C0110613
Connexin 43
sao1089608116
uncurated
Boundary
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).
Boundary
sao1090974305
uncurated
SERCA2b
SERCA2b
sao1091808058
uncurated
Membrane Pump
Membrane Pump
sao1091882528
uncurated
Neurofilament Protein
Neurofilament Protein
sao1093009192
uncurated
Pinceau Fiber
Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment.
Pinceau Fiber
sao109906988
uncurated
Retinal Cone Cell
C0206428
CL:0000573
Cone cell
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)
Retinal Cone Cell
UMLS
sao1103104164
true
uncurated
Dendritic Microtubule
Dendritic Microtubule
sao110773650
uncurated
Pre-synaptic Dense Body
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).
Pre-synaptic Dense Body
ribbon
sao1111202255
Regional Part Of
Regional Part Of
definition incomplete
sao1120063482
Kv3
Kv3
Shaw-like family of voltage gated potassium channels.
sao1120423785
uncurated
Sidekick
Sidekick
sao1121590138
uncurated
Layer 3 Pyramidal Neuron
Layer 3 Pyramidal Neuron
Pyramidal neuron whose cell soma resides in layer 3 of neocortex.
sao1123695773
true
uncurated
Neuromuscular Junction
0031594
Neuromuscular Junction
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).
sao1124888485
uncurated
SERCA3
C0916181
SERCA3
sao1127560844
uncurated
Regional Part Of Nucleolus
Regional Part Of Nucleolus
sao113580911
uncurated
Free Ribosome
Free Ribosome
sao1139385046
uncurated
Primary Lysosome
0005766
A lysosome before it has fused with a vesicle or vacuole (Gene Ontology).
C0230814
Primary Lysosome
sao1140587416
uncurated
Filopodial
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.
Filopodial
sao1141340175
uncurated
Random
No particular orientation.
Random
sao1143221302
uncurated
Spine
Do spines only have a post synaptic density
Spine
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.
sao1145756102
uncurated
Tanycyte
CNS
C0926518
CL:0000643
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.
Stretch cells
Tanycyte
sao1149261773
true
uncurated
Condensed
Condensed
Morphological state characterized by a contracted matrix and expanded intracristal space; observed experimentally when added ADP is used up (Mannella et al., 2001).
sao1152497626
uncurated
Intercalated Disk
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).
Intercalated Disk
sao1152983960
uncurated
Vesicle Membrane
0012506
C1167317
The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology).
Vesicle Membrane
sao1153182838
uncurated
Alpha Motor Neuron
Alpha Motor Neuron
Wikipedia
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.
lower motor neuron
sao1154704263
true
uncurated
Glutamate Receptor
C0061465
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).
Glutamate Receptor
sao1164727693
uncurated
MRNA
C0035696
MRNA
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).
sao116515730
uncurated
Transporter Protein
Integral membrane proteins that transport molecules or ions into or out of the cell or compartment.
Transporter Protein
sao1165516281
uncurated
Neurexin
Neurexin
sao1172124127
uncurated
Microtubule Associated Protein
C0026042
Microtubule Associated Protein
Proteins found in the microtubules (MSH).
sao1174532162
uncurated
Vesicle Coat
0030120
C1166749
Refers to any specialized coating present on a vesicle membrane, e.g., clathrin.
Vesicle Coat
sao1177708494
Attachment
Attachment
C0923872
sao1179195262
uncurated
Subcellular Fraction
Subcellular Fraction
sao1180716477
Anatomical Relationship
Anatomical Relationship
Conceptual anatomical entity which describes the structural and transformation relationships between physical anatomical entities. Example: class subsumption relationship, structural relationship, anatomical tranformation relationship (FMA).
FMA
FMA
FMAID:54723
sao1184653804
uncurated
Gap Junction
0005921
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).
C0206117
Gap Junction
sao118541872
uncurated
Mitochondrial Chromosome
0000262
A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology).
C1166687
Mitochondrial Chromosome
sao1186327184
uncurated
Oligodendrocyte Compact Myelin
0043218
Oligodendrocyte Compact Myelin
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).
sao1186642361
uncurated
Basal Pole Of Neuron
Basal Pole Of Neuron
Portion of a cell soma closest to the point where the basilar dendrite emerges.
sao1186862860
uncurated
Vellous Process
Refers to the fine, veil-like terminal processes of protoplasmic astrocytes.
Vellous Process
graph position temporary
is this the same as what is now termed the peripheral astrocyte process?
sao1189060993
uncurated
Mitochondrial Intermembrane Space
0005758
C1166886
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.
Mitochondrial Intermembrane Space
The region between the inner and outer lipid bilayers of the mitochondrial envelope. (Gene Ontology).
graph position temporary
sao118944228
true
Bouton Type
Bouton Type
Refers to the morphology of a bouton.
sao1189513296
uncurated
Juxta Paranode Axon
Juxta Paranode Axon
Region of axon immediately adjacent to the paranode.
sao1191319089
uncurated
Post-synaptic Density
0014069
BF_C000103
Post-synaptic Density
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).
sao1196688972
Basal Body
0005932
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).
Basal Body
C0230744
sao11978067
uncurated
Neurofilament 200kd
200 kd
Neurofilament 200kd
Neurofilament protein with molecular weight 200 kd.
sao1200165704
uncurated
Beta Tubulin
Beta Tubulin
C0005290
One of two globular polypeptides forming microtubules.
sao1202564066
uncurated
Phosphatase
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)
C0031686
Phosphatase
sao1202737159
uncurated
Cellular Inclusion
Cellular Inclusion
Cellular inclusion found in the cytoplasm.
sao120573470
uncurated
Lumenal Surface
Lumenal Surface
sao120818728
uncurated
Myelinating Schwann Cell
Myelinating Schwann Cell
Schwann cell that forms compact myelin sheath around axons.
sao1209655615
uncurated
Nucleolus-associated Heterochromatin
Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974).
Nucleolus-associated Heterochromatin
sao1210952635
uncurated
Dendrite
0030425
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).
C0011305
Dendrite
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.
sao1211023249
uncurated
Connectivity
C0925206
Connectivity
sao1211239798
uncurated
Oligodendrocyte Precursor Cell
OPC
Oligodendrocyte Precursor Cell
sao1213292244
uncurated
Length
Length
sao1217691568
uncurated
Pars Granulosa
C0230580
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).
Pars Granulosa
sao1217793903
uncurated
Nerve Cell
CL:0000710
Nerve Cell
Neuroepithelial cell
sao1224657022
uncurated
Pigment
Pigment
sao1231384859
uncurated
SAP90
C0213974
SAP90
sao1232021729
uncurated
Thin Dendritic Spine
Thin Dendritic Spine
sao1232858786
uncurated
Photoreceptor Cell
A cell specialized to detect and transduce light (MESH).
CL:0000210
Photoreceptor Cell
sao1233810115
true
uncurated
Cortical Spiny Stellate Cell
true
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).
BF_T0000036
Cortical Spiny Stellate Cell
sao1236796660
true
uncurated
Perivascular Astrocyte
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)
Perivascular Astrocyte
graph position temporary
sao1239389
true
Large Vesicle
Large Vesicle
Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating.
sao1241866791
uncurated
Clathrin Coated Endocytic Vesicle
0045334
A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).
Clathrin Coated Endocytic Vesicle
sao1243595998
uncurated
Endoplasmic Reticulum Exit Site
Endoplasmic Reticulum Exit Site
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).
sao124393998
uncurated
Perivascular Macrophage
Perivascular Macrophage
sao1245187339
uncurated
Half Life
Half Life
Measure of turnover.
sao124571525
uncurated
Synthetic Enzyme
C0597548
Synthetic Enzyme
sao1246280606
uncurated
Glial Subcompartment
Glial Subcompartment
sao1253297813
uncurated
Chandelier Cell
cerebral cortex
false
Chandelier Cell
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.
sao1267578530
true
uncurated
Indented Nucleus
Indented Nucleus
Nucleus with one or more indentations in the nuclear membrane.
sao1277586470
uncurated
Cell Morphological Type
Cell Morphological Type
sao1278200674
Oligodendrocyte Myelin Sheath
0043209
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).
C0026973
Oligodendrocyte Myelin Sheath
sao1279474730
uncurated
Scaffolding Protein
Scaffolding Protein
sao1280179455
uncurated
Fused Vesicle
Fused Vesicle
Omega profile
Synaptic vesicle that is fused to the pre-synaptic membrane, forming the characteristic omega profile.
sao128105491
uncurated
Actin Bundling Protein
Actin Bundling Protein
sao1281431356
uncurated
Sub-surface Cisternae
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).
Sub-surface Cisternae
sao128470897
uncurated
Aspiny
A dendrite characterized by few or no recognizable dendritic spines.
Aspiny
sao128827344
uncurated
Sparsely Spiny
Characterized by a low density of dendritic spines.
Sparsely Spiny
sao1288413465
uncurated
Cellular Space
false
Anatomical space occurring within a cell, usually formed by intracellular membranes.
Cellular Space
sao1289190043
uncurated
Synaptic Configuration
Arrangement of pre- and post-synaptic components.
Synaptic Configuration
sao1289583168
uncurated
Mitochondrial Membrane Outer
0005741
C0230839
Mitochondrial Membrane Outer
The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology).
sao1289741256
uncurated
Cell Cyle Phase
Cell Cyle Phase
sao1290101869
Membrane Bound Ribosome
A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it.
Membrane Bound Ribosome
sao1291545653
uncurated
Bergmann Glia
CNS
Bergmann Glia
C0228088
CL:0000644
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.
Wikipedia
graph position temporary
radial epithelial cell
sao1299495391
true
Cell Cell Contact Zone
Cell Cell Contact Zone
Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle
Maryann Martone
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
sao1299635018
uncurated
Microtubule Mediated Motility
Microtubule Mediated Motility
Refers to the transport of a structure via microtubules and microtubule-associated motors.
sao1301290450
Velate Astrocyte
A protoplasmic astrocyte with extremely thin veil-like (vellous) processes.
C0926509
Velate Astrocyte
sao1309473597
true
uncurated
Electrotonic Synapse
Electrical Synapse
Electrotonic Synapse
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).
sao1311109124
uncurated
Hippocampal Pyramidal Neuron
Hippocampal Pyramidal Neuron
sao131261273
true
uncurated
Neurofilament
0005883
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).
C0027834
Neurofilament
sao1316272517
uncurated
Synapse Associated Protein
Synapse Associated Protein
sao1319795695
uncurated
GluR1
GluR1
sao1322219701
uncurated
Membrane Surface
Membrane Surface
sao1329750433
uncurated
Motility
Motility
Refers to the ability of structures to move about the cell.
sao1330317521
Cellular Component
0005575
Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA).
Cellular Component
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).
sao1337158144
uncurated
Tuft
Refers to the terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance.
Tuft
sao1340260079
uncurated
Quiescent Oligodendrocyte Precursor Cell
Quiescent Oligodendrocyte Precursor Cell
sao1352451787
uncurated
Perineuronal Oligodendrocyte
C0949376
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).
Perineuronal Oligodendrocyte
graph position temporary
sao1353298471
true
Oligodendrocyte Paranodal Termination
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
Oligodendrocyte Paranodal Termination
Paranodal loop
sao1354781919
uncurated
Pericyte
bipolar
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).
C0598800
CL:0000184
Mural Cell
Pericyte
Rouget Cell
sao1355908696
uncurated
Endocytic Vesicle
0030139
A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).
C0887883
Endocytic Vesicle
sao1362520468
uncurated
Ciliary Ganglion Neuron
unipolar
0
projection neuron
ciliary ganglion
C0229060
Ciliary Ganglion Neuron
sao1366775348
true
uncurated
Cross Section Diameter Minor
Cross Section Diameter Minor
Minimum diameter of a cross section through structure.
sao136816674
uncurated
Mitochondrial Membrane Inner
0005743
C0230840
Mitochondrial Membrane Inner
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).
sao1371347282
uncurated
Junctional Continuity
Indicates that two entities share a continuous space but that the continuity is formed through a specialized junctional component, e.g., gap junction.
Junctional Continuity
sao1374293695
uncurated
Ensheathing Process
Ensheathing Process
Refers to the process of the Schwann cell that surrounds an unmyelinated axon or cell soma.
sao1376748732
uncurated
Organismal Occurrent
"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).
Organismal Occurrent
sao1379576571
Lamellar Body
0042599
Lamellar Body
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).
sao1379604862
uncurated
Vesicular Component
Vesicular Component
sao138219748
uncurated
Inter-Golgi Transport Vesicle
0030143
A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack) (Gene Ontology).
Inter-Golgi Transport Vesicle
sao1382918459
uncurated
Nematosome
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)
Nematosome
sao138430598
uncurated
Alpha 7 Acetylcholine Receptor
Alpha 7 Acetylcholine Receptor
sao138926812
uncurated
GluR2
C0536483
GluR2
sao1390810994
uncurated
Junctional Connectivity
Junctional Connectivity
sao1392266325
uncurated
Astrocyte
CNS
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).
Astrocyte
C0004112
CL:0000127
sao1394521419
true
uncurated
Intercellular Junction
Intercellular Junction
sao1395777368
Basal Lamina
0005605
A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology).
Basal Lamina
C0242195
sao1397492660
uncurated
Glutamate Transporter
C0061467
Glutamate Transporter
sao1399894198
uncurated
Zonula Adhaerens
Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991).
Zonula Adhaerens
fascia adhaerens
sao1400623473
uncurated
Cerebellar Golgi Cell
local circuit neuron
cerebellar cortex
Cerebellar Golgi Cell
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.
sao1415726815
true
uncurated
Syndecan
C0075691
Family of transmembrane heparan sulfate proteoglycans (CSP - Bonfire).
Syndecan
sao1417256224
uncurated
Neuron
C0027882
CL:0000540
Neuron
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).
sao1417703748
true
uncurated
Junctional Part
Junctional Part
sao1423758634
uncurated
Extracellular Space
0005616
Extracellular Space
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid (Gene Ontology).
sao1425028079
uncurated
Anatomical Location
Anatomical Location
Spatial association relationship which describes the containment, adjacency, and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate (FMA).
sao1426984192
uncurated
Ribosome
0005840
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).
C0035553
Ribosome
sao1429207766
uncurated
Monoamines
Monoamines
sao1430127373
Spine Type
Refers to the morphological type of a spine.
Spine Type
sao1436578787
uncurated
Gamma Motor Neuron
C0026610
CL:0000717
Gamma Motor Neuron
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).
fusimotor neuron
sao1438006234
true
uncurated
Neurotransmitter Associated Protein
Neurotransmitter Associated Protein
sao1440704204
uncurated
Extracellular Matrix Protein
C0079323
Extracellular Matrix Protein
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)
sao1442185587
uncurated
Pial Endfoot
Pial Endfoot
sao1447478620
uncurated
Reactive Microglia
Reactive Microglia
sao1448451779
uncurated
Vesicle Subcomponent
Vesicle Subcomponent
sao1455064842
Nuclear Lamina
0005652
C1136039
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).
Nuclear Lamina
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).
sao1455996588
uncurated
Non Membrane Bound Organelle
0043228
Non Membrane Bound Organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes (Gene Ontology).
sao1456184038
uncurated
Retinal Rod Cell
retinal rod cell
C0206427
CL:0000604
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.
Retinal Rod Cell
rod cell
sao1458938856
true
uncurated
Motor Neuron
C0026609
CL:0000100
Motor Neuron
Neurons which activate muscle cells (MSH).
UMLS
sao1460710779
true
uncurated
Cadherin
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).
C0006631
Cadherin
sao1463925374
uncurated
Active Zone Cytomatrix
Active Zone Cytomatrix
Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004).
sao1470121605
uncurated
Axon Collateral
Axon Collateral
Smaller branches of an axon that emanate from the main axon cylinder.
sao1470140754
uncurated
Neurotrophin
C0132298
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).
Neurotrophin
sao1473913158
uncurated
Clustered
Clustered
sao1475145503
uncurated
Kv3.2
C0906849
Kv3.2
sao1482557638
uncurated
Spherical Bushy Cell
anterior ventral cochlear nucleus
Spherical Bushy Cell
sao1482618768
true
uncurated
Clathrin Coated Vesicle
0030136
A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes (Gene Ontolgoy).
C0887885
Clathrin Coated Vesicle
sao148845161
uncurated
Vesicle Cargo
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.
Vesicle Cargo
sao1490223249
Bipolar Progenitor Cell
A type of NG2 positive cell that resemble oligodendrocyte precursors
Bipolar Progenitor Cell
Ligon et al PNAS 2006, PMID: 16682644
sao1492258085
true
Calcium Activated Potassium Channel
C0949653
Calcium Activated Potassium Channel
Potassium channels whose activation is dependent on intracellular calcium concentrations (MSH).
sao1494484467
uncurated
Beta Neurexin
Beta Neurexin
sao149790201
uncurated
Nuclear Subcomponent
Nuclear Subcomponent
sao1499850686
uncurated
GlurR3
C0536486
GlurR3
sao1501064039
uncurated
Syndecan-2
C0174307
Syndecan-2
fibroglycan
sao1504920769
uncurated
Mixed Synapse
Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991).
Mixed Synapse
Synaptic contact characterized by both electrical and chemical synaptic junctions.
sao1506103497
uncurated
Post-synaptic Component
Post-synaptic Component
sao1507566336
Calsequestrin
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).
C0006787
Calsequestrin
sao1508721375
uncurated
Density
Density
sao1510923311
uncurated
Amino Acid
Amino Acid
C0002520
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).
sao1511566913
uncurated
Cytoplasmic Surface
Cytoplasmic Surface
sao1514682949
uncurated
General Cell Subcompartment
General Cell Subcompartment
Subcompartmentalization of cellular structures such as organelles.
sao1515819812
uncurated
Contactin
C0056257
Contactin
sao1517449491
uncurated
Junctional Site
Junctional Site
sao1524397168
Amorphous Vesicle
Amorphous Vesicle
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.
sao1531915298
uncurated
NeurabinI
NeurabinI
PDZ containing proteins with F-actin binding protein activity.
sao1535366556
uncurated
Sessile Dendritic Spine
Sessile Dendritic Spine
sao1536532595
uncurated
Organelle
0043226
C0029219
Organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane (Gene Ontology).
sao1539965131
uncurated
Capillary Endothelial Cell
Capillary Endothelial Cell
sao1540081501
uncurated
Choroid Epithelial Cell
Choroid Epithelial Cell
Cuboidal shaped epithelial cell forming one of the components of the choroid plexus (Peters, Palay and Webster, 1991).
sao1541570510
true
uncurated
Vascular Endothelial Cell
This cell class is not contained in the Cell Type Ontology
Vascular Endothelial Cell
sao1543450574
uncurated
Regional Part Of Golgi
Regional Part Of Golgi
sao1546288504
uncurated
Endosomal Lumen
0031904
Endosomal Lumen
The volume enclosed by the membranes of an endosome (Gene Ontology).
endosome lumen
sao1547508851
uncurated
Aquaporin 4
AQP4
Aquaporin 4
C0292777
sao1548226791
uncurated
Secondary Lysosome
0005767
C0230815
Secondary Lysosome
Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology).
sao1549842807
uncurated
Chemical Fixation
Chemical Fixation
Indicates that the feature was observed in tissue prepared by chemical fixation.
sao1554187262
Mitochondrial Type
Mitochondrial Type
Refers to the morphology of mitochondria.
sao1562245920
uncurated
Dynamin
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).
C0058836
Dynamin
sao1565708461
uncurated
Tubular Endosome
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.
Tubular Endosome
sao1570660411
uncurated
Barr Body
Barr Body
sao1571698684
uncurated
Peripheral Astrocyte Process
It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet
Peripheral Astrocyte Process
Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain.
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.
This comes from derouiche et al. J. Physol. Paris 2002 96:177 PubMedID:12445894
graph position temporary
sao1573004591
Cell Interior
Cell Interior
sao1579007712
uncurated
Cochlear Outer Hair Cell
C0206513
CL:0000601
Cochlear Outer Hair Cell
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)
sao1582628662
true
uncurated
Symmetrical
Gray's Type 2
Symmetrical
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.
curation complete
sao1583093969
see example at: http://synapse-web.org/anatomy/chemical/symh.htm
EAAT2
EAAT2
sao1585306176
uncurated
Regional Part Of Basket Cell Axon
Regional Part Of Basket Cell Axon
Terminal pre-synaptic ending of an axon or axon collateral.
sao1586851177
uncurated
Actin Filament
0005884
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).
Actin Filament
C0025979
sao1588493326
uncurated
Regional Part Of Spiny Dendrite
Regional Part Of Spiny Dendrite
sao1590928667
uncurated
Cytoskeletal Protein
C0010852
Cytoskeletal Protein
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).
sao1593305396
uncurated
Dendritic Growth Cone
Dendritic Growth Cone
sao1594955670
uncurated
Oval
Generally rounded shape, where the minimum and maximum dimensions produce a roughly egg-shape.
Oval
definition incomplete
sao1595237779
SER Membrane
0030868
SER Membrane
The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology).
sao1596955044
uncurated
Organotypic Slice
Organotypic Slice
sao1596955138
Main Axon
Main Axon
Used to refer to the main axonal trunk, as opposed to the collaterals.
sao1596975044
uncurated
Post-synaptic Part
Post-synaptic Part
Post-synaptic compartment
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.
sao1607047124
uncurated
Cytokine
C0079189
Cytokine
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).
sao1611333173
uncurated
Nuclear Inner Membrane
0005637
Nuclear Inner Membrane
The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology).
sao1612527463
uncurated
Muller Cell
CL:0000636
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
Muller Cell
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.
graph position temporary
sao1615912903
true
Chromatin
0000785
C0008546
Chromatin
The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology).
sao1615953555
uncurated
Nuclear Outer Membrane
0005640
Nuclear Outer Membrane
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).
sao1617136075
uncurated
SER Subcompartment
SER Subcompartment
sao1619512288
uncurated
Vesicle Binding Protein
Vesicle Binding Protein
sao1624466407
uncurated
SERCA
Calcium pump found in the membrane of the smooth endoplasmic reticulum.
SERCA
sao163038736
uncurated
Astrocyte Process
Astrocyte Process
Refers to processes of astrocytes extending from the cell soma that wrap around neurons and conform to cellular components in the neuropil.
sao1630537580
uncurated
Hypolemmal Cisternae
Hypolemmal Cisternae
Specialized part of the smooth endoplasmic reticulum that closely underlies the plasma membrane, usually within 60 nm or closer (Peters, Palay and Webster, 1991).
sao1634374950
uncurated
Cytoskeletal Element
Cytoskeletal Element
sao1635329413
uncurated
Recurrent Collateral
Axon collateral that ramifies in the area of the soma of the cell of origin.
Recurrent Collateral
sao1642494436
uncurated
Spine Neck
Spine Neck
neck
pedicle
sao1642908940
uncurated
Thin
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).
Thin
sao1643644091
uncurated
Cortical Stellate Cell
cerebral cortex
local circuit neuron
CL:0000122
Cortical Stellate Cell
sao164665273
true
uncurated
In Vitro
In Vitro
Indicates that the feature was observed in cells in culture or in isolated subcellular fractions.
sao1649728317
Alpha Actinin
Alpha Actinin
C0917705
Cytoskeletal protein present in Z lines of muscle fibrils and at sites of non-muscle cell contact with a substrate (CSP).
sao1659393491
uncurated
Plasma Membrane
0005886
C0007603
Plasma Membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology).
cell membrane
sao1663586795
uncurated
Growth Factor
C0018284
Growth Factor
Signal molecules that are involved in the control of cell growth and differentiation (MSH).
sao1671627152
uncurated
Regional Part Of Spine Apparatus
Regional Part Of Spine Apparatus
sao1682692988
uncurated
Endosomal Subcomponent
Endosomal Subcomponent
sao1683772610
uncurated
Calyx Of Held
Calyx Of Held
sao1684283879
uncurated
Nuclear Membrane
0031965
C0028584
Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology).
Nuclear Membrane
sao1687101204
uncurated
Fast Frozen Freeze Substituted
Fast Frozen Freeze Substituted
Indicates that feature was described in tissue prepared by fast freezing followed by freeze substitution.
sao1693353776
Living Animal
Indicates that the feature was observed in the living animal.
Living Animal
sao1694199019
Acetylcholine Receptor
Acetylcholine Receptor
C0034792
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).
sao1700719022
uncurated
Olig2
C0912988
Olig2
sao1701066619
uncurated
Nucleus
0005634
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).
C0007610
Nucleus
sao1702920020
uncurated
Apical
Apical
sao1703115805
uncurated
Varicose Dendrite
Characterized by numerous swellings or varicosities along their length.
Varicose Dendrite
sao1706854098
uncurated
MAP2
C0024773
MAP2
sao1707694834
uncurated
Ependymal Cell
A neurectoderm derived cell that lines the neural lumen (Cell 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).
C0228092
CL:0000065
Ependymal Cell
We are not sure whether ependymal cells should be considered a type of ependymoglial cell
graph position temporary
sao1714094301
true
Endosome
0005768
A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO).
C0034850
Endosome
sao1720343330
uncurated
Dendritic Tree
BF_C000102
Dendritic Tree
The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches.
sao172297168
uncurated
Resting Microglia
Resting Microglia
sao172764364
uncurated
Intracellular Calcium Channel
Intracellular Calcium Channel
sao1728785226
uncurated
Pre-synaptic Grid
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).
Pre-synaptic Grid
sao1730664005
uncurated
Cerebellar Granule Cell
1
cerebellar cortex
BF_C000108
Cerebellar Granule Cell
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.
sao1736323572
true
uncurated
Skeletal Muscle Cell
CL:0000188
Skeletal Muscle Cell
sao1741889714
uncurated
Glutamate
C0220839
Glutamate
sao1744435799
uncurated
Chemical Synapse Type
Chemical Synapse Type
definition incomplete
sao1746643703
Varicose Axon
Varicose Axon
sao1746802704
Orthogonal Array
Orthogonal Array
Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins.
sao1747012216
square array
uncurated
Tail Portion
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).
Tail Portion
sao1749953771
uncurated
Terminal Bouton
Terminal Bouton
sao1757774791
uncurated
Nicotinic Acetylcholine Receptor
C0034830
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).
Nicotinic Acetylcholine Receptor
sao1767745398
uncurated
Axon
0030424
Axon
C0004461
Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA)
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).
sao1770195789
uncurated
Distance From Soma
Distance From Soma
Distance, usually in linear microns, from soma where a feature is observed.
sao1779606731
uncurated
Synaptic Component
Synaptic Component
sao1784069613
Nuclear DNA
Nuclear DNA
sao1785015039
uncurated
Actin Binding Protein
Actin Binding Protein
C0001239
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).
sao1785445428
uncurated
Flattened
Characterized by a flattened shape in glutaraldehyde fixed tissue.
Flattened
sao1785495506
uncurated
Spinal Motor Neuron
multipolar
Spinal Motor Neuron
anterior horn cell
sao1785599611
uncurated
Stubby
Characterized by the diameter of the neck being similar to that of the head (Harris et. al 1992).
Stubby
sao1786354232
uncurated
Real Boundary
A real boundary corresponds to its surface and designates a discontinuity between constitutional parts of anatomical entities (FMA: Mejino and Cornelius, ???)
Real Boundary
sao1786656680
uncurated
Surface Area
Surface Area
sao1788621392
uncurated
Regional Part Of Myelinated Axon
Regional Part Of Myelinated Axon
sao1791490892
uncurated
ATP Synthase
ATP Synthase
sao1794895660
uncurated
Sodium Channel
C0037492
Cell membrane glycoproteins selective for sodium ions. Fast sodium current is associated with the action potential in neural membranes (MSH).
Sodium Channel
sao1797800540
uncurated
RIM1
C0171438
RIM1
sao1798128207
uncurated
Dendritic Spine
0043197
C0872341
Dendritic Spine
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).
sao1799103720
uncurated
Functional State
Differentiates among different functional states of a cell or cell component, e.g., activated microglia, interphase nucleus, orthodox mitochondria.
Functional State
sao1802798922
Mitochondrial Matrix
0005759
C0230843
Mitochondrial Matrix
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).
sao1804523077
uncurated
Cytoplasmic Vesicle
0031410
A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology).
Cytoplasmic Vesicle
sao180601769
uncurated
Myosin
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).
C0027096
Myosin
sao1810043179
uncurated
Cell
0005623
CL:0000000
Cell
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).
sao1813327414
uncurated
Glial Limiting Endfoot
Glial Limiting Endfoot
Process of astrocyte that extends to the surface of the central nervous system. Together, they form the glial limiting membrane or glial limitans.
sao181458425
uncurated
RER Lumen
0048237
RER Lumen
The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology).
rough endoplasmic reticulum lumen
sao1819509473
uncurated
Nucleolus
0005730
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).
C0007609
Nucleolus
sao1820400233
uncurated
Axonal Spine
Axonal Spine
Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991).
sao18239917
uncurated
Virtual Boundary
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).
Virtual Boundary
sao1825296048
uncurated
Crista Junction
Crista Junction
Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003).
sao1825845900
uncurated
Subregional Part Of Neuron Process
Subcompartment of a compartment.
Subregional Part Of Neuron Process
sao183270081
uncurated
Fixed Tissue
Fixed Tissue
Indicates that the feature was observed in fixed tissue.
sao1833377695
Pars Fibrosa
C0230581
Pars Fibrosa
Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974).
sao1841764412
uncurated
SER Subcomponent
SER Subcomponent
sao1842028314
uncurated
Acetylcholinesterase
Acetylcholinesterase
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)
C0001044
sao1842089031
uncurated
Cristae Type
Cristae Type
Refers to the morphology of mitochondrial cristae.
sao1843037539
uncurated
RNA
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)
C0035668
RNA
sao1843715402
uncurated
Non Neural Cell Compartment
Non Neural Cell Compartment
sao1843719868
uncurated
Smooth Membrane
Characterized by a nuclear membrane with no indentations.
Smooth Membrane
sao1845602529
uncurated
Neurofilament 150kd
150 kd
Neurofilament 150kd
Neurofilmanet protein with molecular weight 150 kd.
sao1845865352
uncurated
Inner Bounding Mitochondrial Membrane
Inner Bounding Mitochondrial Membrane
Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane
sao18461326
uncurated
Integrin
C0021701
Integrin
sao1846292151
uncurated
Microtubule
0005874
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).
C0026046
Microtubule
sao1846835077
uncurated
Calcium Channel
C0006685
Calcium Channel
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).
sao1846985919
uncurated
Meninges Cell
Cell that comprises the meninges
Meninges Cell
This needs to be extensively investigated
sao1847837612
uncurated
Acetylcholine
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).
Acetylcholine
C0001041
sao185580330
uncurated
Prophase
0051324
C0033464
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).
Prophase
sao1856556831
Macrophage
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).
CL:0000235
Macrophage
sao185843373
uncurated
Bridge Contact Site
Bridge Contact Site
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).
sao1858501007
uncurated
Mitochondrion
0005739
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).
C0026237
Mitochondrion
sao1860313010
uncurated
Organismal Continuant
"Continuant" refers to the participants of occurrent processes and are entities that endure during the period of their existence (Rosse C et a., 2005).
Organismal Continuant
sao1863115908
uncurated
Vesicle Type
Refers to the morphology of a vesicle.
Vesicle Type
sao1863391630
uncurated
Cholinergic Striatal Neuron
false
Cholinergic Striatal Neuron
Large cholinergic interneuron in the caudate nucleus, putamen and nucleus accumbens.
sao1866881837
true
uncurated
Configuration
Configuration
Refers to a specialized arrangements of a cellular component or other structure that is characteristic of a given region, e.g., bundled microtubules.
sao18717211
uncurated
Microtubule Fascicle
Microtubule Fascicle
Refers to a bundle of closely apposed microtubules running parallel to each other.
sao1872343973
uncurated
Synaptic Bouton
Synaptic Bouton
Terminal pre-synaptic ending of an axon or axon collateral.
sao187426937
uncurated
Apical Pole Of Neuron
Apical Pole Of Neuron
Portion of a cell soma closest to the point where the apical dendrite emerges.
sao1877927224
uncurated
Rough Endoplasmic Reticulum
0005791
C0230779
Nissl substance
Rough Endoplasmic Reticulum
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).
sao1881364067
uncurated
Ribbon Synapse
Ribbon Synapse
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)
sao1884931180
uncurated
Schwann Cell Microvillus
Schwann Cell Microvillus
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)
sao1890444066
uncurated
Neurofascin
C0068587
Neurofascin
sao189141251
uncurated
Macroglia
C0228087
CL:0000126
Macroglia
SAO classifies Schwann cells as a type of macroglia; Cell Type Ontology includes only astrocytes and oligodendroglia
macroglial cell
sao1895605722
true
uncurated
Intranuclear Membrane Space
Intranuclear Membrane Space
The space between the inner and outer nuclear membranes
sao1908934319
uncurated
Pre-synaptic Active Zone Component
Pre-synaptic Active Zone Component
sao1911631652
uncurated
Principal Cells Medial Nucleus Trapezoid Body
multipolar
medial nucleus of the trapezoid body
CNS
1
Principal Cells Medial Nucleus Trapezoid Body
Properties derived from Gersdorff and Borst (2002).
sao1918137235
true
uncurated
Dorsal Root Ganglion Cell
unipolar
Doral root ganglion
Dorsal Root Ganglion Cell
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.
sao1919499702
true
uncurated
IP3R Type 2
IP3R Type 2
sao1920358312
uncurated
Intercellular Junction Site
0005911
Intercellular Junction Site
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.
The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells.
definition incomplete
sao1922892319
Pinocytic Vesicle
Pinocytic Vesicle
sao1925368674
uncurated
Brainstem Motor Neuron
Brainstem Motor Neuron
sao1928362432
uncurated
Mitochondrial Adhaerens Complex
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).
Mitochondrial Adhaerens Complex
sao1933817066
uncurated
Subplasmalemmal Coating
2007-02-23
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
Subplasmalemmal Coating
definition incomplete
sao1938587839
Zonula Occludens
0005923
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).
Zonula Occludens
sao1939999134
tight junction
uncurated
Peg And Socket Contact
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).
Peg And Socket Contact
sao1943947957
uncurated
Biological Continuant
"Continuant" refers to the participants of occurrent processes and are entities that endure during the period of their existence (Rosse C et a., 2005).
Biological Continuant
sao1950472752
uncurated
Schaffer Collateral
Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum.
Schaffer Collateral
sao1950673097
uncurated
Endoplasmin
C0059259
Endoplasmin
sao1951490568
uncurated
Regional Part Of Schwann Cell
Regional Part Of Schwann Cell
sao195217619
uncurated
Interfascicular Oligodendrocyte
C0205867
Interfascicular Oligodendrocyte
White matter oligodendrocytes that may be aligned in rows (Peters, Palay and Webster, 1991).
sao1952867392
true
uncurated
Golgi Lumen
Golgi Lumen
sao1956231674
uncurated
Macular Adhaerentia
Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction
Macular Adhaerentia
sao1956738165
uncurated
Dendrite Type
Characterization based on high or low density of classical spines on dendrites.
Dendrite Type
sao1959705051
uncurated
Experimental Condition
All experimental entities will be ported into a separate ontology based on OBI
Experimental Condition
Indicates the experimental conditions under which a feature was observed.
sao1960697157
uncurated
Anatomical Part
Anatomical Part
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.
sao1968590282
uncurated
Coated Pit
C0009143
Coated Pit
Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003).
sao1969557946
uncurated
Volume
Volume
sao196989303
uncurated
Glycogen
C0017911
Glycogen
sao196990275
uncurated
Cell Regional Part Aggregate Object
Cell Regional Part Aggregate Object
sao1970895398
Vascular Cell
C0225336
Cells that line the inner and outer surfaces of the body (MSH).
Vascular Cell
sao197110912
uncurated
Regional Part Of Epithelial Cell
C0932419
Regional Part Of Epithelial Cell
sao1974433376
uncurated
Mushroom
Characterized by the diameter of the head being much greater than that of the neck (Harris et. al 1992).
Mushroom
sao1983595164
uncurated
Coated Vesicle
0030135
C0242915
Coated Vesicle
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).
sao1985096626
uncurated
Lamellar
Lamellar
Refers to cristae with a flattened, extended appearance.
sao1995010823
uncurated
Neuromelanin
C0068608
Neuromelanin
sao1996310556
uncurated
IP3R Type 3
IP3R Type 3
sao2003006393
uncurated
Microfilament
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)
C0025979
Microfilament
sao2006047981
uncurated
Axon Terminal
Axon Terminal
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).
sao2007137787
uncurated
Dentate Gyrus Granule Cell
CNS
dentate gyrus
true
local circuit neuron
1
Dentate Gyrus Granule Cell
sao2007319345
true
uncurated
EAAT1
EAAT1
sao2016979058
uncurated
Age Associated
Age Associated
sao2017162875
uncurated
Regional Part Of RER
Regional Part Of RER
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).
sao2019617624
uncurated
Modified Astrocyte
Modified Astrocyte
sao2022412481
true
uncurated
Spinophliln
Spinophliln
neurabinII
sao2023460124
uncurated
Cell Cell Contact
Cell Cell Contact
sao2023779072
Neurosecretory Vesicle
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).
Neurosecretory Vesicle
sao2031592629
uncurated
Dendritic Shaft
0043198
BF_C000106
Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology).
Dendritic Shaft
sao2034472720
uncurated
Active Zone Plasma Membrane
Active Zone Plasma Membrane
Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004).
sao2038461087
uncurated
Axonal Growth Cone
Axonal Growth Cone
sao203987954
uncurated
Pre-synaptic Part
Pre-synaptic Part
Pre-synaptic compartment
sao2044996357
uncurated
Pedunculated
May need to do more reading to determine whether this should be a parent of mushroom and thin.
Pedunculated
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.
graph position temporary
sao2045795635
Multivesicular Body
0005771
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).
C0230825
Multivesicular Body
sao2045955158
uncurated
Hair Cell
hair cell
C0018496
CL:0000202
Hair Cell
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).
sao2046464388
true
uncurated
Cerebellar Stellate Cell
CNS
Cerebellar Stellate Cell
Multipolar neuron found in cerebellar molecular layer.
sao2046525601
true
uncurated
Asymmetrical
Asymmetrical
Gray's Type 1
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.
curation complete
sao2047438300
see example at: http://synapse-web.org/anatomy/chemical/asymh.htm
Somatic Spine
Somatic Spine
Spine emanating from the cell soma.
sao2048514053
uncurated
Perivascular Endfoot
Perivascular Endfoot
We are unclear why this is causing an inconsistency error.
sao2048701763
uncurated
Dopamine
C0013030
Dopamine
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).
sao2050279787
uncurated
Atlas Location
Atlas Location
graph position temporary
sao2052625281
Neuropil
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).
C0228081
Neuropil
sao205380252
uncurated
Connexin
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).
C0110611
Connexin
sao2056711309
uncurated
Calreticulin
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).
C0054543
Calreticulin
sao2060855807
uncurated
Muscarinic Acetylcholine Receptor
C0034826
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).
Muscarinic Acetylcholine Receptor
sao2062447305
uncurated
Vascular Endfoot
Vascular Endfoot
sao2064469343
uncurated
Adenine Nucleotide Transporter
0000295
Adenine Nucleotide Transporter
C1153655
Transports adenine nucleotides (AMP, ADP, and ATP) across membranes (Gene Ontology).
sao2077117136
uncurated
Radial
Radial
sao2077793822
uncurated
Fibrous Astrocyte
Astrocytes characterized by high content of intermediate filaments and few vellous processes; often found in white matter.
C0228090
Fibrous Astrocyte
sao2078084673
true
uncurated
Regional Part Of Cell Cell Contact Zone
Regional Part Of Cell Cell Contact Zone
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.
graph position temporary
sao2081625415
Filamentous Inclusion
Cellular inclusion containing filamentous structures.
Filamentous Inclusion
sao2081684219
uncurated
Rosette
Rosette
sao2082026326
uncurated
Axon Type
Axon Type
Refers to the morphology of an axon.
sao2088691397
uncurated
Cytoplasmic Inclusion
Cellular inclusion found in the cytoplasm.
Cytoplasmic Inclusion
sao2092254444
uncurated
Speed
Speed
sao2102170307
uncurated
Neuropeptide
C0027895
Neuropeptide
Peptides released by neurons as intercellular messengers. Many neuropeptides are also hormones released by non-neuronal cells (MSH).
sao2106486330
uncurated
Pre-synaptic Site
Pre-synaptic Site
sao2108323256
Tubular
Refers to crisate with a roughly circular profile in cross section.
Tubular
sao2110170574
uncurated
Ribosomal RNA
0003735
C0035701
Ribosomal RNA
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)
sao2114723559
uncurated
Membrane Stack
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).
Membrane Stack
sao2114874506
uncurated
Inositol 1 4 5 Trisphosphate Receptor
C0063592
Inositol 1 4 5 Trisphosphate Receptor
sao2115096416
uncurated
Supra-organismal Occurrent
Supra-organismal Occurrent
sao211804939
Spacing
Refers to the average distance between features.
Spacing
sao2126482353
uncurated
Mesaxon
Mesaxon
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).
sao2127666702
uncurated
Random Cell
multipolar
Random Cell
created for testing purposes only
sao2127763636
Spine Mat
2007-02-09
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).
Maryann Martone
Spine Mat
sao2128156969
Cortical Pyramidal Neuron
Cortical Pyramidal Neuron
Pyramidal neuron from the cerebral cortex (not including hippocampus).
sao2128417084
true
uncurated
Extracellular Surface
Extracellular Surface
sao2135015805
uncurated
Calcium Binding Protein
Calcium Binding Protein
sao2138417829
uncurated
Plus To Minus
Plus To Minus
sao2139310701
uncurated
Synapsin
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).
C0085252
Synapsin
sao2143851382
uncurated
Precursor
C0033665
Precursor
sao2146594471
uncurated
Anaphase
0051322
Anaphase
C0002788
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).
sao21946128
Nuclear Pore
0005643
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).
C0028587
Nuclear Pore
sao220861693
uncurated
Tumor Necrosis Factor Alpha
C0041368
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).
TNF-alpha
Tumor Necrosis Factor Alpha
sao220868685
uncurated
Vesicle
0031982
Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology).
C0042219
Vesicle
sao221389602
uncurated
Synaptic Connectivity
Implies that a morphologically identified synapse exists between two cell components where release of transmitter from cell influences cell B.
Synaptic Connectivity
sao223845603
uncurated
Molecular Motor
C0600594
Molecular Motor
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).
sao225178797
uncurated
Eye Photoreceptor Cell
CL:0000287
Eye Photoreceptor Cell
sao226523927
uncurated
GABA
Abbreviation for gamma amino butyric acid, the major inhibitory neurotransmitter in the mammalian central nervous system.
C0016904
GABA
sao229636300
uncurated
SERCA1
C0916182
SERCA1
sao229773618
uncurated
Intracellular Membrane Formation
C0021868
Intracellular Membrane Formation
Specializations associated with intracellular membrane systems, e.g. lamellar bodies. Membranes of subcellular structures. (MSH)
sao237754030
uncurated
G Coupled Receptor
G Coupled Receptor
sao238175764
uncurated
Nuclear Inclusion
Cellular inclusion found in the nucleus.
Nuclear Inclusion
sao238602892
uncurated
Synaptic Cleft
0043083
C0682685
Synaptic Cleft
The narrow gap that separates the presynaptic and postsynaptic membranes, into which a neurotransmitter is released (Gene Ontology).
sao243541954
uncurated
Neurotubule
Neurotubule
Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings.
sao248349196
uncurated
Axolemma
0030673
Axolemma
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).
sao250772229
uncurated
G-actin
C0016890
G-actin
sao251535222
uncurated
Schmidtt-Lanterman Cleft
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.
Schmidtt-Lanterman Cleft
sao254777664
uncurated
Initial Segment
0043194
Initial Segment
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).
sao256000789
uncurated
Puncta Adhaerentia
A small version of the zonula adharens type junction, characterized by a symmetrical adherent point between two cells.
Puncta Adhaerentia
sao257629430
uncurated
AMPA Receptor
AMPA Receptor
C0072899
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).
sao265434492
uncurated
NG2 Cell
NG2 Cell
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
sao265591209
true
uncurated
Protein
Protein
sao26622963
uncurated
Branched Spine
Branched Spine
Characterized by two or more heads (Harris et. al 1992) that emerge from the same origin (Sorra KE and Harris KM, 2000).
sao268063700
uncurated
GTPases
C0018296
Enzymes that hydrolyze GTP to GDP. EC 3.6.1.- (MSH).
GTPases
sao271459227
uncurated
Orientation
Orientation
Refers to the "entities of reference" (FMA). Location may be defined by qualitative coodrinates or absolute coordinates.
sao271899308
uncurated
Apical Dendrite
Apical Dendrite
BF_C000112
sao273773228
uncurated
Measurement
false
Measurement
sao279801585
uncurated
Regional Part Of Axon
Regional Part Of Axon
sao280355188
uncurated
Terminal Specialization
Terminal Specialization
sao28175134
uncurated
Dopamine Transporter Type 1
C0114838
Dopamine Transporter Type 1
Sodium dependent transport protein, located on presynaptic terminals, involved in the uptake of dopamine; site at which cocaine exerts rewarding/ reinforcing effects (CSP).
sao285839036
uncurated
Chemical Synapse
Chemical Synapse
sao289211478
uncurated
Tyrosine Hydroxylase
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).
C0041491
Tyrosine Hydroxylase
sao289587392
uncurated
Myelin Associated Protein
Myelin Associated Protein
sao293240763
uncurated
Dendriole
Dendriole
sao295057932
uncurated
Bundled
Bundled
When several members of a class occur tightly apposed to one another or attached to one another in identifiable bundles.
sao296309608
uncurated
Lobulated Nucleus
Lobulated Nucleus
Nucleus with heavily indented nuclear membrane, giving the appearance of one or more lobes.
sao301169922
uncurated
Cell Body Referent Polarity
Cell Body Referent Polarity
sao311075036
uncurated
Glial Cell
(Reichenbach and Wolburg)
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.
C0027836
CL:0000125
Cell Type Ontology
Glial Cell
neuroglial cell
sao313023570
uncurated
Retrograde Transport
C0598953
Retrograde Transport
Transport in the direction towards the cell soma.
sao31662418
Stacked
Stacked
sao3169628
uncurated
Stubby Dendritic Spine
Stubby Dendritic Spine
sao317384566
uncurated
Cristae
0030061
Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology)
C0230844
Cristae
sao333328131
uncurated
Glial Fibrillary Acidic Protein
C0017626
GFAP
Glial Fibrillary Acidic Protein
The major component of glia-specific intermediate filament primarily found in astrocytes and Bergmann glia.
sao333741607
uncurated
Alpha Tubulin
Alpha Tubulin
C0002318
One of two globular polypeptides forming microtubules.
sao335197072
uncurated
Regional Part Of Cell
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).
Regional Part Of Cell
sao340271629
uncurated
Nucleus Type
Maryann Martone
Nucleus Type
The shape of the nucleus, e.g., round, lobulated, indented
sao343486489
uncurated
Polarity
Need to define property with "reference point"
Polarity
sao349337269
uncurated
Substantia Nigra Dopaminergic Cell
false
projection neuron
Substantia nigra pars compacta
multipolar
1
Substantia Nigra Dopaminergic Cell
sao34994437
true
uncurated
Orthodox
Morphological state characterized by an expanded matrix space and contracted intracristal space; observed experimentally when ADP is added (Mannella et al., 2001).
Orthodox
sao358853874
uncurated
Ependymoglial Cell
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)
Ependymoglial Cell
sao3593465546
true
Myelin Subcompartment
Myelin Subcompartment
sao359916506
uncurated
Neural Cell Adhesion Molecule
C0282587
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)
NCAM
Neural Cell Adhesion Molecule
sao365780568
uncurated
ANT-2
ANT-2
sao369353782
uncurated
Voltage Gated Potassium Channel
0008076
C0814023
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).
Voltage Gated Potassium Channel
sao371494298
uncurated
Protoplasmic Astrocyte
Astrocyte characterized by spongy appearance and many vellous processes; often found in gray matter.
C0228089
GluT Astrocyte
Passive Astrocyte
Protoplasmic Astrocyte
sao374942934
true
uncurated
Connexin 32
C0163743
Connexin 32
sao376700953
uncurated
Hippocampal CA3 Pyramidal Neuron
Hippocampal CA3 Pyramidal Neuron
sao383526650
true
uncurated
IP3R Type 1
IP3R Type 1
sao383990749
uncurated
Pre-synaptic Component
Pre-synaptic Component
sao386529203
Endfoot
Endfoot
Terminal process of astrocyte abutting non-neuronal surfaces in the brain.
graph position temporary
sao388182739
uncurated
Sub-ependymal Astrocyte
Large astrocyte that forms a layer that lies beneath the ependymal layer.
Sub-ependymal Astrocyte
sao399295448
true
uncurated
Somatic Portion
Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991).
Somatic Portion
sao401910342
uncurated
Docked Vesicle
Docked Vesicle
Synaptic vesicle docked at the pre-synaptic active zone.
sao403156667
uncurated
Schwann Cell
PNS
C0036387
CL:0000218
Neuroglial cells of the peripheral nervous system which form the insulating myelin sheaths of peripheral axons (MSH).
Note that the cell type ontology does not consider Schwann Cells to be macroglia
Schwann Cell
sao408819766
true
uncurated
Peri Cellular Basket
Peri Cellular Basket
Ramification of basket cell axon surrounding cell bodies, forming the characteristic peri-cellular baskets from which the cell class derives its name.
sao413722576
uncurated
Membrane Bound Organelle
0043227
Membrane Bound Organelle
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).
sao414196390
uncurated
Regional Part Of Dendrite
Regional Part Of Dendrite
sao420754792
uncurated
Septate Junction
0005918
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
Septate Junction
graph position temporary
sao427941916
Cochlear Inner Hair Cell
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)
C0018497
CL:0000589
Cochlear Inner Hair Cell
UMLS
sao429277527
true
uncurated
Longitudinal
Longitudinal
Oriented parallel to the long axis.
sao430240391
uncurated
Cortical Bipolar Cell
Cortical Bipolar Cell
Type of VIP containing neuron found in the visiual cortex.
sao436474611
true
uncurated
Epithelial Cell
C0014597
CL:0000066
Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH).
Epithelial Cell
sao441624014
uncurated
Connexon
0005922
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.
C0230609
Connexon
Wikipedia
hemichannel, connexon complex
sao445019788
uncurated
Extended Chromatin
0000791
A dispersed and relatively uncompacted form of chromatin (Gene Ontology).
Extended Chromatin
euchromatin
sao445485807
uncurated
Contact Site
Contact Site
Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000).
sao447856407
uncurated
Golgi Apparatus
0005794
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)
C0018042
Golgi Apparatus
golgi cisternae
sao451912436
uncurated
Membrane Receptor
C0230664
Membrane Receptor
sao452970150
uncurated
DNA
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).
C0012854
DNA
sao454034570
uncurated
Neurofilament 68kd
68 kd
Neurofilament 68kd
Neurofilament protein with molecular weight approximately 68 kd.
sao460214456
uncurated
Precursor Cell
Precursor Cell
progenitor cell
sao467424240
uncurated
PDZ Containing Protein
C0872241
PDZ Containing Protein
sao468574704
uncurated
Purkinje Cell
1
1
2
projection neuron
cerebellar cortex
true
C0034143
CL:0000121
Large branching neurons of the middle layer of cerebellar cortex, characterized by vast arrays of dendrites; involved in controlling complex movements (CSP).
Purkinje Cell
Purkinje neuron
sao471801888
true
uncurated
Granular Vesicle
Granular Vesicle
Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells.
sao478230652
uncurated
Smooth Nucleus
Nucleus with smooth membrane and no large folds or lobules.
Smooth Nucleus
sao47950958
uncurated
KIF3A
C0255106
KIF3A
sao483834130
uncurated
Activated Oligodendrocyte Precursor Cell
Activated Oligodendrocyte Precursor Cell
oligodendrocyte progenitor cell
sao484101752
uncurated
Calyx
Calyx
sao488120195
uncurated
Active Zone Dense Projection
Active Zone Dense Projection
Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004).
sao494258938
uncurated
Branched
Branched
sao497641585
uncurated
Peroxisome
0005777
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).
C0752063
Peroxisome
Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies.
sao499555322
uncurated
Molecule
Molecule
Want to organize this more carefully in the next version of the SAo
sao500241072
uncurated
Pre-synaptic Subcomponent
Pre-synaptic Subcomponent
sao503947499
uncurated
Nuclear Body
0016604
C0230595
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology).
Nuclear Body
sao505137457
uncurated
Laminated Body
Laminated Body
sao506721981
uncurated
Supra Cellular Structure
A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles.
Supra Cellular Structure
sao508165343
uncurated
Intracristal Space
Intracristal Space
The space bounded by the cristae membrane
sao508958414
true
uncurated
Type III IV Oligodendrocyte
Type III/IV Oligodendrocyte
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.
Type III IV Oligodendrocyte
definition incomplete
sao515196263
true
Endocytic Zone
Endocytic Zone
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).
sao517367952
Muscle Cell
C0596981
CL:0000187
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).
Muscle Cell
myocyte
sao519252327
uncurated
Clathrin
C0008905
Clathrin
Major protein of the polyhedral coat of coated pits and vesicles (EMBL-EBI).
sao5277619
uncurated
Non Myelinating Schwann Cell
Non Myelinating Schwann Cell
Schwann cell that forms a simple ensheathment around axons.
sao528084208
uncurated
Mitochondrial DNA
C0012929
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial genome is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins (MSH).
Mitochondrial DNA
sao529397229
uncurated
Spectrin
0008091
0008091
C0037799
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).
Spectrin
sao536287099
uncurated
Globular Bushy Cell
anterior ventral cochlear nucleus
Globular Bushy Cell
sao538050329
true
uncurated
Adjacency
Adjacency
C0923871
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).
sao542191739
uncurated
Fusiform
Elongated shape that tapers at both ends
Fusiform
Spindle
curation complete
sao542875575
Non Myelinating Oligodendrocyte
Non Myelinating Oligodendrocyte
sao546569295
uncurated
Single
Indicates that the feature exists in isolation, e.g., single filaments as opposed to bundled filaments.
Single
sao548826380
uncurated
Spine Related Site
Spine Related Site
sao553711217
Spinule
Spinule
sao553737851
uncurated
Regional Part Of Dendritic Tree
Regional Part Of Dendritic Tree
sao553876173
uncurated
Golgi Lamellae
Golgi Lamellae
sao561419532
uncurated
Node Of Ranvier
C0034667
Node Of Ranvier
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).
sao571652273
uncurated
Vesicle Other
Category for vesicles observed in electron micrographs with unknown function.
Vesicle Other
sao577473346
uncurated
Condensed Chromatin
0000792
A compact and highly condensed form of chromatin (Gene Ontology).
Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope.
Condensed Chromatin
heterochromatin
sao581845896
uncurated
Lysosome
0005764
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).
C0024369
Lysosome
sao585356902
uncurated
Neurotransmitter Receptor
C0034828
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).
Neurotransmitter Receptor
sao587592318
uncurated
Glomerulus
Glomerulus
Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets.
sao587858733
uncurated
Platelet Derived Growth Factor
C0032200
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).
PDGF
Platelet Derived Growth Factor
sao603947546
uncurated
ANT-1
ANT-1
sao607850352
uncurated
Carbohydrate
C0007004
Carbohydrate
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).
sao607978678
uncurated
Simple
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).
Simple
sao614188547
uncurated
Cristae Membrane
Cristae Membrane
sao614641003
uncurated
Respiratory Chain Complex
Respiratory Chain Complex
sao615619190
uncurated
RSlo
RSlo
sao618069210
uncurated
Radial Glia
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).
C0815005
CL:0000681
Radial Glia
radial glial cell
sao621772985
true
uncurated
Golgi Subcomponent
Golgi Subcomponent
sao624292949
uncurated
Radial Astrocyte
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)
Radial Astrocyte
graph position temporary
sao6261208102
true
Cell Secretion
Cell Secretion
sao627060194
Axon Hillock
0043203
Axon Hillock
C0228079
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).
sao627227260
uncurated
Post-synaptic Subcomponent
Post-synaptic Subcomponent
sao627589531
uncurated
Cellular Subcomponent
Cellular Subcomponent
sao628508602
uncurated
Cytoskeletal Associated Protein
Cytoskeletal Associated Protein
sao630204337
uncurated
Cochlear Hair Cell
Cochlear Hair Cell
sao630986029
true
uncurated
Cis Face
Cis Face
sao632188024
uncurated
Radius
Radius
sao632949619
uncurated
Spiny
Characterized by a high density of dendritic spines.
Spiny
sao638749545
uncurated
PSD95
PSD95
sao642625418
uncurated
Beta Tanycyte
Beta Tanycyte
sao647178911
true
uncurated
Actin Based Motility
Actin Based Motility
Mobility that is mediated by the actin cytoskeleton.
sao656094176
Cardiac Muscle Cell
C0225828
CL:0000746
Cardiac Muscle Cell
Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH).
cardiac myocyte
sao658938043
uncurated
Nucleoplasm
0005654
C0682537
Nucleoplasm
That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology).
sao661522542
uncurated
Potassium Channel
C0032824
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).
Potassium Channel
sao666200564
uncurated
Mitochondrial Subcomponent
Mitochondrial Subcomponent
sao666410040
uncurated
Cerebellar Basket Cell
multipolar
CNS
local circuit neuron
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.
Cerebellar Basket Cell
sao666951243
true
uncurated
Post-synaptic Subcompartment
Post-synaptic Subcompartment
sao671299150
Microvilli
Microvilli
sao671419673
uncurated
Membranous Inclusion
Membranous Inclusion
sao673040867
uncurated
Minus To Plus
Minus To Plus
sao675186109
uncurated
Smooth Muscle Cell
C1135918
CL:0000192
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).
Smooth Muscle Cell
UMLS
non-striated muscle cell
sao676858164
uncurated
Transverse
Oriented orthogonal to the long axis.
Transverse
sao679027665
uncurated
Tubulin
A heterodimer of tubulins alpha and beta that constitutes the protomer for microtubule assembly (Gene Ontology).
C1166787
Tubulin
sao680848918
uncurated
Tissue Plasminogen Activator
C0032143
Extracellular tissue protease that degrades a wide spectrum of extracellular matrix proteins.
Tissue Plasminogen Activator
sao681020632
tPA
uncurated
Medium Spiny Cell
CNS
projection neuron
neostriatum
multipolar
true
BF_C000100
Medium Spiny Cell
Medium Spiny Neuron
sao68203136
true
uncurated
Regional Part Of Astrocyte
Regional Part Of Astrocyte
sao685712019
uncurated
Neurotrophin-4
C0166894
Neurotrophin-4
sao692404013
uncurated
Granule
Granule
sao6934064108
small numerous cell
uncurated
Coated Tip
Coated Tip
Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002).
sao694815499
uncurated
EAAT4
EAAT4
sao696157048
uncurated
ERp57
C0528009
ERp57
sao698543279
uncurated
Gap Junction Plaque
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.
Gap Junction Plaque
Need to determine what is the proper relationships between an electrotonic synapse and a gap junction
sao700839054
Degradative Enzyme
Degradative Enzyme
sao701966895
uncurated
Axon Microtubule Fascicle
Axon Microtubule Fascicle
Refers to the bundled configuration of microtubules in the axon hillock and initial segment.
sao707332678
uncurated
Vestibular Hair Cell
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.
C0206511
CL:0000609
UMLS
Vestibular Hair Cell
sao709770772
true
uncurated
Smooth Endoplasmic Reticulum
0005790
C0230789
Smooth Endoplasmic Reticulum
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).
sao710427438
uncurated
Serotonin
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).
C0036751
Serotonin
sao711465902
uncurated
Choline Acetyltransferase
A synthetic enzyme that catalyzes the formation of acetylcholine from acetyl-CoA and choline. EC 2.3.1.6 (MSH).
C0008407
Choline Acetyltransferase
sao722953401
uncurated
Spatial Relationship
Spatial Relationship
These relationships are modeled after the spatial relationships contained in the FMA.
sao723896903
uncurated
Spine Apparatus
A specialization of the endomembrane system found in some classes of spines consisting of two or more closely apposed lamellae with interspersed dense material.
C0230810
Spine Apparatus
sao725931194
uncurated
Interphase
0051325
C0021798
Interphase
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).
sao727427771
Dense Body
An electron dense body, some of which contain granules (Peters, Palay and Webster (1991)
Dense Body
Not clear if this should be described as an organelle or an inclusion.
graph position temporary
sao730872736
Pinceau
Pinceau
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.
sao732341560
uncurated
Anatomical Pattern
Anatomical Pattern
sao732945962
uncurated
Primary Culture
Primary Culture
sao73984422
Kinase
Kinase
sao743185455
uncurated
Pathological
Cellular inclusions associated with pathological conditions.
Pathological
sao74391158
uncurated
Tufted
Characterized by a terminal tuft.
Tufted
sao754373097
uncurated
Juxtaparanode
Juxtaparanode
Region of nodal complex adjacent to the paranode
sao758620702
Cortical Smooth Stellate Cell
false
A non-pyramidal neuron class found primarily in layer IV of mammalian neocortex characterized by relatively smooth dendrites (While and Rock, 1980).
Cortical Smooth Stellate Cell
sao770302354
true
uncurated
Dense Core Vesicle
40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991).
C0887944
Dense Core Vesicle
sao772007592
uncurated
Myelin Basic Protein
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)
C0014063
Myelin Basic Protein
sao775011514
uncurated
Olfactory Granule Cell
Olfactory Granule Cell
sao776599268
true
uncurated
Pial Cell
Pial Cell
sao783352775
uncurated
Distal End
Distal End
Ending of a process furthest from the cell soma.
sao783483540
uncurated
Voltage Gated Sodium Channel
0001518
A sodium channel in a cell membrane whose opening is governed by the membrane potential (Gene Ontology).
C1153465
Voltage Gated Sodium Channel
sao785001660
uncurated
Betz Cell
motor cortex
primate
Betz Cell
C0228073
Giant pyramidal neuron found in primate motor cortex.
sao786552500
true
uncurated
Cilium
0005929
C0008778
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).
Cilium
sao787716553
uncurated
Microglia
CNS
multipolar
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.
C0206116
CL:0000129
Cell Ontology
Microglia
microglial cell
sao789292116
uncurated
Transporter
Transporter
sao791350993
uncurated
Pre-synaptic Active Zone
0048786
A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology).
Pre-synaptic Active Zone
sao792027222
uncurated
Satellite Cell
Satellite Cell
Schwann cell that apposes or encapsulates neuronal perikarya (Peters, Palay and Webster, 1991).
sao792373294
true
uncurated
Nissl Body
Nissl Body
Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes.
sao793088923
uncurated
NMDA Receptor
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).
C0080093
NMDA Receptor
sao794753833
uncurated
Vesicle Lumen
0031983
The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology).
Vesicle Lumen
sao797538226
uncurated
En Passant
En Passant
sao809320003
uncurated
Actin Associated Protein
Actin Associated Protein
sao811908115
uncurated
Proximal End
Ending of a process closest to the cell soma.
Proximal End
sao812067870
uncurated
Layer 2 3 Pyramidal Neuron
Layer 2 3 Pyramidal Neuron
sao816233655
true
uncurated
Component Part Of
Component Part Of
definition incomplete
sao818838791
Acute Slice
Acute Slice
sao819188787
Golgi-associated Vesicle
0005798
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).
C0230767
Golgi-associated Vesicle
sao819927218
uncurated
Striated Muscle Cell
CL:0000737
Striated Muscle Cell
sao82362520
uncurated
Cross Section Diameter Major
Cross Section Diameter Major
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.
sao824839913
uncurated
Internode Axon
Internode Axon
sao830092290
uncurated
Hippocampal CA1 Pyramidal Neuron
1
hippocampal area CA1
Hippocampal CA1 Pyramidal Neuron
sao830368389
true
uncurated
Intracellular Membrane
Intracellular Membrane
sao830981606
uncurated
Regional Part Of Oligodendrocyte
Regional Part Of Oligodendrocyte
sao831502550
uncurated
Slice Preparation
Slice Preparation
sao832793084
SERCA2a
SERCA2a
sao833348185
uncurated
Nucleic Acid
C0028606
High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages (MSH).
Nucleic Acid
sao83745184
uncurated
Layer 5 Pyramidal Neuron
Layer 5 Pyramidal Neuron
Pyramidal neuron whose cell soma resides in layer 5 or whose connectivity patterns resemble layer 5 neurons.
sao840814183
true
uncurated
Myelinating Oligodendrocyte
C0129447
Myelinating Oligodendrocyte
Oligodendrocyte that forms compact myelin sheath.
sao841915587
uncurated
Oligodendrocyte
CNS
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).
C0028944
CL:0000128
Oligodendrocyte
oligodendroglia
sao844118448
true
uncurated
Supracellular Object Part
Parts of a supracellular object, e.g., synapse.
Supracellular Object Part
We have not yet decided whether they are regional parts of some other sort. So for now, they are just parts.
sao85163621
Pleomorphic
Characterized by many shapes in glutaraldehyde fixed tissue.
Pleomorphic
sao854959971
uncurated
Ventricular Epithelial Cell
Epithelial cell lining the ventricles.
Ventricular Epithelial Cell
sao855466308
uncurated
F-actin
F-actin
sao856608566
uncurated
Protocadherin
Protocadherin
sao862229532
uncurated
Pyramidal Cell
multipolar
C0206441
CL:0000598
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).
Pyramidal Cell
UMLS
sao862606388
true
uncurated
Regional Part Of Neuron
Regional Part Of Neuron
neuron compartment
sao864921383
uncurated
Regional Part Of Spine
Regional Part Of Spine
sao866168499
uncurated
Regional Part Of Tanycyte
Regional Part Of Tanycyte
sao877341397
uncurated
Endosomal Subcompartment
Endosomal Subcompartment
sao879381135
uncurated
Clathrin Coat
0030118
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).
C1166728
Clathrin Coat
sao879919129
uncurated
Dendritic Branch
Dendritic Branch
Refers to dendrites arising from another dendrite.
sao884265541
uncurated
SAP97
C0295347
SAP97
sao885184181
uncurated
Transport Vesicle
0030133
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).
C0887882
Transport Vesicle
sao885490876
secretory vesicle
uncurated
Width
Width
sao888175480
uncurated
Metaphase
0051323
C0025564
Metaphase
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).
sao888950834
Regional Part Of Glia
Regional Part Of Glia
sao895885284
uncurated
In Vivo
In Vivo
Indicates that a feature was described in intact tissue.
sao897115057
Mitral Cell
mitral cell
projection neuron
olfactory bulb
Definition was modified from that in Wikipedia by MM
Mitral Cell
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.
Wikipedia
sao900005350
true
uncurated
Neck Portion
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).
Neck Portion
sao901230115
uncurated
uncurated
Regional Part Of Mitochondria
Regional Part Of Mitochondria
sao903454364
uncurated
Transcription Factor
C0040648
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).
Transcription Factor
sao906421617
uncurated
Rho GTPase
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).
C0174045
Rho GTPase
sao908816138
uncurated
Double Bouquet Cell
cerebral cortex
local circuit neuron
CNS
Double Bouquet Cell
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).
sao910084726
true
uncurated
Synapse
0045202
Synapse
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).
sao914572699
uncurated
L1
Cell adhesion molecule expressed at neuronal surface.
L1
sao915541959
uncurated
Terminal Loop
Portion of myelin-forming Schwann cell consisting of terminal cytoplasmic extensions adhered to the axon at the beginning and end of the myelin sheath.
Terminal Loop
sao924713546
uncurated
Actin
Actin
C0001271
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).
sao925531236
uncurated
Stellate
Generally star shaped multipoloar cell shpae with spherically extending processes
Stellate
sao9271919883
uncurated
SER Lumen
0048238
SER Lumen
The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology).
sao927884761
smooth endoplasmic reticulum lumen
uncurated
Paranode Axon
Paranode Axon
sao936144858
uncurated
Synaptic Vesicle Associated Protein
Synaptic Vesicle Associated Protein
sao936599761
uncurated
Spiny Bracelet Of Nageotte
Paranodal terminations of Schwann cells that do not directly contact the paranodal axon membane. Usually found in thicker myelin. (Sosinsky et al., 2005)
Spiny Bracelet Of Nageotte
sao937871668
uncurated
Neural Stem Cell
C1113654
Embryonic cell that develops into a neuron (CSP).
Nerve stem cell
Neural Stem Cell
sao938060309
uncurated
Cell Line
Cell Line
sao938874695
Ion Channel
C0022009
Ion Channel
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).
sao940366596
uncurated
Part Of Synapse
Part Of Synapse
sao941107815
uncurated
Sessile
Also refers to a stubby spine.
Sessile
sao941226261
uncurated
Lipofuscin
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).
C0023789
Lipofuscin
sao941755985
uncurated
Trans Golgi Network
0005802
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).
C0887838
Trans Golgi Network
sao9456487
uncurated
Interleukin-1
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).
C0021755
IL-1
Interleukin-1
sao950082944
uncurated
Centriole
0005814
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).
C0007708
Centriole
sao95019936
uncurated
Intermediate Filament
0005882
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).
C0021770
Intermediate Filament
sao952483289
uncurated
Spine Head
Spine Head
sao952643730
uncurated
Enzyme
A protein that speeds up chemical reactions in the body (PDQ).
C0014442
Enzyme
sao956358115
uncurated
Spherical
Generally round shape where minimum diameter and maximum diameter are roughly the same
Spherical
curation complete
sao957949983
Ryanodine Receptor
C0054493
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)
Ryanodine Receptor
sao960745141
uncurated
Round Clear
Round Clear
sao967304317
uncurated
Fibrillary Inclusion
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)
Fibrillary Inclusion
sao967812059
uncurated
Glycine
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).
C0017890
Glycine
sao968946794
uncurated
Continuity
C0934150
Continuity
sao969067581
uncurated
Alpha Tanycyte
Alpha Tanycyte
sao971374186
true
uncurated
Lumen Cargo
Lumen Cargo
Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin.
sao976831666
Endosomal Membrane
Endosomal Membrane
sao978443756
uncurated
Cell Component Aggregate Object
Cell Component Aggregate Object
sao991156472
Water Channel
C0599635
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).
Water Channel
sao992093782
uncurated
Anterograde Transport
Anterograde Transport
C0598952
Transport in the direction away from the cell soma.
sao992129328
Alpha 3 Acetylcholine Receptor
Alpha 3 Acetylcholine Receptor
sao99825125
uncurated
entity
continuant
Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
Synonyms: endurant
dependent_continuant
Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities.
Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart to pump blood
Synonyms: property, trope, mode
disposition
Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity.
fiat_object_part
Definition: An independent continuant [snap:IndependentContinuant] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso
Synonyms: fiat substance part
function
Definition: A realizable entity [span:RealizableEntity] the manifestation of which is an essentialy end-directed activity of a continuant [span:Continuant] entity in virtue of that continuant [span:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
Examples: the function of a birth canal to enable transport, the function of the heart in the body to pump blood, the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law
independent_continuant
Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
Synonyms: substantial entity
object
Definition: A independent continuant [span:IndependentContinuant] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities.
Examples: an organism, a heart, a chair, a lung, an apple
Synonyms: substance
object_aggregate
Definition: An independent continuant [snap:IndependentContinuant] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
Synonyms: substance aggregate
object_boundary
Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
Definition: An independent continuant [span:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [span:Object] entities that exist at exactly the point where the object [span:Object] is separated off from the rest of the existing entities in the world.
Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
Synonyms: substance boundary
one_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with one dimension.
Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space
quality
Definition: A dependent continuant [span:DependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
realizable_entity
Definition: A dependent continuant [span:DependentContinuant] that inheres in continuant [span:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity
role
Definition: A realizable entity [span:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [span:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [span:Continuant] in some kinds of natural, social or institutional contexts.
Examples: the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of a tree in maintaining stability in an ecosystem, the role of ingested matter in digestion
site
Comment: Site [snap:Site] entities should not be confused with spatial region [snap:SpatialRegion] entities. Site [snap:Site] entities characteristically have a filling or medium and are capable of altering their spatial location (moving from one spatial region [snap:SpatialRegion] to another) without altering their identity.
Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [span:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [span:Site] entities are entities that can be occupied by other continuant [span:Continuant] entities.
Examples: a city, a nasal cavity, a blood vein, an environment, sinuses, canals, ventricles, the lumen of the gastrointestinal tract, the location of the battle of Austerlitz, the interior of the aorta, the room in which one is located, the top of one's desk including the things that are on it and the atmosphere surrounding them.
spatial_region
Comment: Spatial region [span:spatialRegion] entities should not be confused with sites. Spatial region [span:spatialRegion] entities exist as parts of pure or absolute space, have a dimensionality and a shape but require no filling in order to exist and are also immobile.
Definition: An independent continuant [snap:IndependentContinuant] that is neither bearer of quality [span:Quality] entities nor inheres in any other entities.
Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe
three_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with three dimensions.
Examples: a cube-shaped part of space, a sphere-shaped part of space
two_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with two dimensions.
Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space
zero_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with no dimensions.
Examples: a point
connected_spatiotemporal_region
Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].
Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus
connected_temporal_region
Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis
fiat_process_part
Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life
occurrent
Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
Synonyms: perdurant
process
Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
Examples: the life of an organism, the process of sleeping, the process of cell-division
process_aggregate
Definition: A processual entity [span:ProcessualEntity] that is a meriological sum of process [span:Process] entities and possesses non-connected boundaries.
Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together
process_boundary
Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery
processual_context
Comment: setting
Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
Examples: a surgical operation as processual context for a nosocomical infection, a routine check-up as processual context for the finding of a tumor, a clinical trial as processual context for the discovery of a new treatment or drug
processual_entity
Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird
scattered_spatiotemporal_region
Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair
scattered_temporal_region
Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair
spatiotemporal_instant
Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process
spatiotemporal_interval
Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
Examples: the spatiotemporal region occupied by a process or by a fiat processual part
spatiotemporal_region
Comment: This is the time and space within which occurrent [span:Occurrent] entities exist. Occurrent [span:Occurrent] entities exist in space and time in a different way from that in which continuant [span:Continuant] entities do and thus the space and time in which they exist is itself different. The importance of spatiotemporal region [span:SpatiotemporalRegion] is primarily theoretical and it will not be used often in most domain ontology applications.
Definition: An occurrent [span:occurrent] at or in which processual entities can be located.
Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis
temporal_instant
Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death
temporal_interval
Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
Examples: any continuous temporal duration during which a process occurs
temporal_region
Comment: This is the time that is common to both SNAP and SPAN entities. The time of temporal region [span:TemporalRegion] and its sub-classes will normally be the time that should be referred to when sub-classing universals having to do with time in an ontology.
Definition: An occurrent [span:Occurrent] that is part of time.
Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death