Alan Ruttenberg Andrew Spear Pierre Grenon Holger Stenzhorn Maryann Martone, Lisa Fong, Stephen D. Larson, Lily Chen, and Amarnath Gupta July 06, 2007 application/rdf+xml http://www.ifomis.org/bfo/1.0 en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://creativecommons.org/licenses/by/3.0 Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Barry Smith: "Against Fantology" Barry Smith: "Basic Tools of Formal Ontology" Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Ontology for the subcellular anatomy of the nervous system Basic Formal Ontology (BFO) Subcellular Anatomy Ontology (SAO) uncurated Release Notes: 1.1 - 05/28/2007 Added definitions Modified Non-neuronal cell types, especially glial types Simplified properties Did a lot of work cleaning up restrictions 1.2 - 07/06/2007 Restructured cell class hierarchy for glia and epithelial cells Converted SAO class names into SAO ids Made SAO OWL-DL compliant Checked and corrected consistency and satisfiability issues 1.0 Version 1.2 sao1239937685 is Regional Part Of is Regional Part Of sao1356746816 Used to describe a physical relationship between two or more cellular components associated Cell Component associated Cell Component sao138767806 is Component Of is Component Of sao1434436507 has Regional Part has Regional Part sao1454173298 continuous With Centrifugal continuous With Centrifugal sao1490541696 Neurotransmitter associated with neuronal class has Neurotransmitter has Neurotransmitter sao152994059 has Molecular Constituent has Molecular Constituent sao158083006 continuous With Centripetal continuous With Centripetal sao1597912566 Location of a cell in a specific coordinate system Anatomical location: atlas anatomical Location Atlas anatomical Location Atlas sao1623809261 Cellular components found in typical cells. has Component has Component sao180517057 Cellular element derived from another cell associated with a compartment, e.g., myelin associated Cellular Element associated Cellular Element sao1844377738 Refers to a structure that defines the boundary of a given structure has Boundary has Boundary Physical continuity between structures sao1896217670 graph position temporary This idea was adopted from FMA but possibly needs reconsideration. continuous With continuous With sao1896476612 Need to determine whether this property is useful in conjunction with intercellular junctions, i.e., in order for two things to be attached, there must be a junction of some sort Indicates an intimate contact between two anatomical entities, each with their own real boundaries attached To attached To sao1939689633 is Molecular Constituent Of is Molecular Constituent Of sao2047323768 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 associated With sao2103390115 refers to a set of property classes that reflect unique aspects of a given structure, e.g., orientation, stability has Property has Property sao2422696582 is Aggregate Part of is Aggregate Part of sao333215121 Refers to the cellular component with which a feature is associated, e.g., ion receptor is associated with the plasma membrane location Component location Component sao3610809721 is Morphological Type Of is Morphological Type Of sao3762365186 has Vesicle Component has Vesicle Component sao3931558608 has Morphological Type has Morphological Type sao4245285112 located in located in sao45720944 is Intercellular Junction Compartment Of is Intercellular Junction Compartment Of sao548011359 Refers to the specific location of an instance of a cell anatomical Location Specific anatomical Location Specific sao554204175 contains Site contains Site sao5598458770 has Part has Part sao7122682114 anatomical Location anatomical Location sao7291254923 inverse of has Component 6 inverse of has Component 6 sao733319732 participates in one or more types of intercellular junctions intercellular Junction Compartment intercellular Junction Compartment sao872346836 Measurement associated with compartment morphometrics morphometrics sao8839644583 has Aggregate Part has Aggregate Part sao923422536 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 boundary Of sao924725934 is Neurotransmitter Of is Neurotransmitter Of sao9371595441 has Location Of has Location Of sao9906015852 is Part Of is Part Of asymmetric macular perforated symmetric sao1056822429 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 psd Morphology psd Morphology sao1065676773 graph position temporary 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 anatomical Location General false true sao1077517916 has Mass has Mass CNS PNS sao1130665397 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 location CNS PNS sao1185641609 Indicates the species of organism from which an observation derives species species sao1220772118 molecular Weight molecular weight molecular Weight false true sao1254683799 has Inherent 3D Shape has Inherent 3D Shape sao1267375031 isoform isoform sao1384659949 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 number Of Axons number Of Axons No Yes sao1428515021 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 population Object sao1429489883 Indicates under what conditions the observation was made observation Conditions observation Conditions excitatory inhibitory modulatory sao1608074544 functional categorization of cell, e.g., motor, sensory, secretory, myelinating functional Type functional Type sao1620782974 Standard error (+/-) standard Error standard Error concave convex cylindrical elliptical flat round spherical spindle-shaped sao166035570 Used to describe generic shape of a component or compartment shape shape distal proximal sao1669593695 Indicates the point at which a described measurement was taken point Of Measurement point Of Measurement sao1746944408 number Of Branches number Of Branches false true sao1798215493 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 is Continuant sao1804901442 Coordinate along the medial-lateral axis Atlas Coordinate M-L atlas Coordinate M-L atlas Coordinate M-L sao1863785805 Denotes whether a neuron or dendrite is characterized by at least one spine. is Spiny is spiny is Spiny sao1936650489 Refers to the maximum number of primary dendrites generally seen in a particulary neuronal class number Primary Dendrites Max number Primary Dendrites Max sao1945565347 Reference point of the coordinate system used, e.g., bregma Atlas reference point atlas Reference Point atlas Reference Point local circuit neuron projection neuron sao1967171150 circuit Type circuit Type Asserted abstract concrete sao1981606713 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. Cell ID parent Cell Identity parent Cell Identity sao2048509857 Coordiante along the anteior-posterior axis Atlas Coordinate A-P atlas Coordinate A-P atlas Coordinate A-P sao2110623092 Element with reference to which orientation is defined orientation Reference To orientation Reference To sao2134236783 Indicates the age of the animal in which the observation was made Age of Animal age Of Animal age Of Animal not found 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. sao2372462654 graph position temporary This property should be updated when we switch to OBR relations to the "lacks" relationship presence presence sao244654816 Name and edition of atlas used to derive coordinates Atlas Reference atlas Reference atlas Reference sao267012610 number number absolute average direct estimate greater than greater than or equal to less than less than or equal to range sao375065056 Describes whether the reported values are averages, estimates, ranges, or absolute values value Type value Type sao382106499 density density Female Male Unspecified sao392224970 Indicates the sex of the animal in which the observation was made. sex Of Animal sex Of Animal sao395752640 maximum value in a range maximum maximum angstroms cubic microns microns microns squared spines per micron sao40919963 unit of measurement unit unit sao431495567 Reference to which polarity is defined polarity Reference To polarity Reference To sao528500906 Cumulative length of all dendrites in the dendritic tree total Dendritic Length total Dendritic Length sao643761283 Minimum value in a range minimum minimum sao655061336 measurement value value value Unique identifier of an instance found in the CCDB. sao796296921 ccdb ID ccdb ID sao833783433 Coordinate along the dorsal ventral axis Atlas Coordinate D-V atlas Coordinate D-V atlas Coordinate D-V bipolar multipolar unipolar sao841626191 Describes the general morphology of a class of neurons with respect to the number of processes extending from the cell soma process Number process Number sao925977276 Refers to the maximum branch order of the dendritic tree maximum Branch Order maximum Branch Order sao950829914 Refers to the minimum number of primary dendrites arising from the cell soma Number of Primary Dendrites number Primary Dendrites Min number Primary Dendrites Min 2 3 >2 >3 sao996727841 A property of branching structures such as axons and dendrites branch Order branch Order asymmetrical symmetrical sao99760531 Classification of synaptic type according to Gray, except using the symmetrical (Gray's Type 2) and asymmetrical (Gray's Type 1) designations synapse Type synapse Type 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) 0030175 sao-1046371754 sao-1046371754 uncurated Filopodium Filopodium 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 sao-1067215520 sao-1067215520 uncurated Schwann Cell Paranodal Termination Schwann Cell Paranodal Termination 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 sao-1123256993 uncurated Schwann Cell Compact Myelin Schwann Cell Compact Myelin 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. sao-1126011106 sao-1126011106 Soma Type Soma Type Eric Bushong Glial cell type unique to primates which extend long processes throughout cortical lamina forming pallisades. sao-1220620412 sao-1220620412 true We need to create an object property that allows us to assign taxonomy information to classes that are only seen in certain taxa Interlaminar Astrocyte Interlaminar Astrocyte sao-1348591767 sao-1348591767 uncurated Branch Point Of Dendrite Branch Point Of Dendrite sao-1367457321 sao-1367457321 Mitochondrial Site Mitochondrial Site Generally triangular-shaped soma with a dendrite emerging from the apical pole and basilar dendrites emerging from two or more basal poles sao-1465673360 sao-1465673360 curation complete Pyramidal Pyramidal Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster). sao-1488888179 sao-1488888179 Pre-synaptic Ribbon Pre-synaptic Ribbon sao-1686050947 sao-1686050947 uncurated Regional Part Of Mitochondrial Membrane Regional Part Of Mitochondrial Membrane Maryann Martone Junctional complex consisting of two connexons that come together to form a communicating pore between two cells sao-1778046445 sao-1778046445 Intercellular Gap Junction Channel Intercellular Gap Junction Channel sao-1819020575 sao-1819020575 uncurated Regional Part Of Cell Component Regional Part Of Cell Component sao-1828894864 sao-1828894864 uncurated Cell Process Cell Process sao-1863852493 sao-1863852493 uncurated Glial Filament Glial Filament 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 sao-1865064409 sao-1865064409 true graph position temporary There is some discussion about whether all marginal glia are astrocytes. Marginal Astrocyte Marginal Astrocyte 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 sao-188049490 uncurated Node Of Ranvier Axon Node Of Ranvier Axon 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. 0031980 sao-1899375636 Inner Mitochondrial Compartment (from Peters, Palay, and Webster) sao-1899375636 true uncurated Mitochondrial Lumen Mitochondrial Lumen Part of nodal complex located underneath the compact myelin in between nodes of Ranvier sao-206157942 sao-206157942 Internode Internode Region of nodal complex adjacent to the nodal region sao-234066064 sao-234066064 Paranode Paranode 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. sao-243744138 sao-243744138 true graph position temporary Need to associate this with avians Pectin Glial Cell Pecten_Glial_Cell Pectin Glial Cell sao-250931889 sao-250931889 uncurated Neuron Protrusion Neuron Protrusion sao-282380853 sao-282380853 uncurated Basal Basal sao-301233507 sao-301233507 Junction Complex Junction Complex Interfascicular oligodendrocyte which can support myelin volumes of approximately 500 cubic microns and is associated with small diameter axons sao-32901633 sao-32901633 true definition incomplete Type I II Oligodendrocyte Type I/II Oligodendrocyte Type I II Oligodendrocyte Spaces defined by the inner and outer mitochondrial membranes sao-343550527 sao-343550527 true Mitochondrial Space Mitochondrial Space NG2 cell characterized by a differentiated, stellate appearance that lack expression of most differentiated glial cell-type specific markers. sao-408886955 sao-408886955 true graph position temporary 2007-01-13 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). 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. Synantocyte Synantocyte sao-420949334 sao-420949334 uncurated Regional Part Of Neuron Process Regional Part Of Neuron Process Located in the sub-retinal space, these cells form the sub-retinal blood-brain barrier and contain light-absorbing melanin pigment granules sao-423426544 sao-423426544 true There is a visual pigment cell in the cell type ontology but we are not sure if this is the same cell Pigment Epithelial Cell Pigment Epithelial Cell 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). sao-593830697 sao-593830697 uncurated Schwann Cell Myelin Sheath Schwann Cell Myelin Sheath Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode sao-596411490 sao-596411490 Node Related Site Node Related Site sao-699412220 sao-699412220 uncurated Regional Part Of SER Regional Part Of SER sao-750951932 sao-750951932 uncurated Regional Part Of Neuron Protrusion Regional Part Of Neuron Protrusion sao-820130069 sao-820130069 uncurated Pyramidal Neuronal Cell Body Pyramidal Neuronal Cell Body sao-82111036 sao-82111036 uncurated Cell Protrusion Cell Protrusion Anatomical location which specifies the relationship between one or more physical anatomical entities in terms of... sao-843826795 sao-843826795 FMA FMA uncurated Anatomical Coordinate Anatomical Coordinate sao-867568886 sao-867568886 Neuron Process Neuron Process sao-876577163 sao-876577163 uncurated Mushroom Dendritic Spine Mushroom Dendritic Spine sao-943768255 sao-943768255 Obsolete class Obsolete class sao-946766835 sao-946766835 Synaptic Site Synaptic Site sao-961694769 sao-961694769 uncurated Excrescence Excrescence sao-965204139 sao-965204139 uncurated Branched Dendritic Spine Branched Dendritic Spine CL:0000645 sao1004082033 C0229545 sao1004082033 true uncurated Pituicyte Pituicyte sao1004601938 sao1004601938 uncurated Dense Material Dense Material Cardiac muscle cell comprising the ventricles sao1011026882 ventricular myocyte sao1011026882 uncurated Ventricular Cardiac Muscle Cell Ventricular Cardiac Muscle Cell sao1016012060 C0916183 sao1016012060 uncurated SERCA2 SERCA2 The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS). 0005829 sao101633890 C0010854 sao101633890 uncurated Cytosol Cytosol sao1022370595 C0654870 sao1022370595 uncurated S100 beta S100 beta 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. sao1028571114 sao1028571114 uncurated Sorting Endosome Sorting Endosome 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). 0005783 sao1036339110 C0014239 sao1036339110 uncurated Endoplasmic Reticulum Endoplasmic Reticulum Refers to integral membrane proteins carried via the vesicle membrane. sao1037637579 sao1037637579 Membrane Cargo Membrane Cargo 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). sao1038025871 C0032592 sao1038025871 uncurated Polyribosome Polyribosome Refers to dendrites emanating from the cell soma. sao1039042901 sao1039042901 uncurated Dendritic Segment Dendritic Segment The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology). 0005802 sao1039242387 sao1039242387 uncurated Trans Face Trans Face Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA). sao1044911821 soma C0599444 sao1044911821 uncurated Neuronal Cell Body Neuronal Cell Body sao1045389829 sao1045389829 uncurated Mitochondrial Membrane Mitochondrial Membrane A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH). sao1048004962 C0206364 sao1048004962 uncurated Tyrosine Kinase Receptor Tyrosine Kinase Receptor sao1048879260 sao1048879260 uncurated Cell Adhesion Molecule Cell Adhesion Molecule 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). 0035061 sao1049471211 C0230547 sao1049471211 uncurated Interchromatin Granule Interchromatin Granule sao1049717962 sao1049717962 uncurated Regional Part Of Neuronal Cell Body Regional Part Of Neuronal Cell Body sao1057800815 sao1057800815 uncurated Morphological Type Morphological Type Synaptic arrangement where the axon courses orthogonal to and forms a synapse with a portion of dendrite. sao1062287912 sao1062287912 uncurated Axocruciform Axocruciform sao1070274187 sao1070274187 uncurated "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 Biological Occurrent 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). 0008021 sao1071221672 C0039065 sao1071221672 uncurated Synaptic Vesicle Synaptic Vesicle Microtubules are characterized by a + and a - end and may be oriented with respect to the soma (origin) in either + to - or - to +. sao107236050 sao107236050 uncurated Microtubule Polarity Microtubule Polarity sao1074198261 sao1074198261 Post-synaptic Site Post-synaptic Site 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). sao1077731745 C0085401 sao1077731745 uncurated Tau Tau sao1078172392 sao1078172392 uncurated Trunk Trunk sao1079900774 Basal Dendrite sao1079900774 uncurated Basilar Dendrite Basilar Dendrite 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). 0042587 sao1081228141 C0017911 sao1081228141 uncurated Glycogen Granule Glycogen Granule 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). sao1089608116 C0110613 sao1089608116 uncurated Connexin 43 Connexin 43 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). sao1090974305 sao1090974305 uncurated Boundary Boundary sao1091808058 sao1091808058 uncurated SERCA2b SERCA2b sao1091882528 sao1091882528 uncurated Membrane Pump Membrane Pump sao1093009192 sao1093009192 uncurated Neurofilament Protein Neurofilament Protein Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment. sao109906988 sao109906988 uncurated Pinceau Fiber Pinceau Fiber CL:0000573 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) sao1103104164 Cone cell C0206428 sao1103104164 true uncurated UMLS Retinal Cone Cell Retinal Cone Cell sao110773650 sao110773650 uncurated Dendritic Microtubule Dendritic Microtubule 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). sao1111202255 ribbon sao1111202255 Pre-synaptic Dense Body Pre-synaptic Dense Body sao1120063482 sao1120063482 definition incomplete Regional Part Of Regional Part Of Shaw-like family of voltage gated potassium channels. sao1120423785 sao1120423785 uncurated Kv3 Kv3 sao1121590138 sao1121590138 uncurated Sidekick Sidekick Pyramidal neuron whose cell soma resides in layer 3 of neocortex. sao1123695773 sao1123695773 true uncurated Layer 3 Pyramidal Neuron Layer 3 Pyramidal Neuron 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). 0031594 sao1124888485 sao1124888485 uncurated Neuromuscular Junction Neuromuscular Junction sao1127560844 C0916181 sao1127560844 uncurated SERCA3 SERCA3 sao113580911 sao113580911 uncurated Regional Part Of Nucleolus Regional Part Of Nucleolus sao1139385046 sao1139385046 uncurated Free Ribosome Free Ribosome A lysosome before it has fused with a vesicle or vacuole (Gene Ontology). 0005766 sao1140587416 C0230814 sao1140587416 uncurated Primary Lysosome Primary Lysosome 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. sao1141340175 sao1141340175 uncurated Filopodial Filopodial No particular orientation. sao1143221302 sao1143221302 uncurated Random Random sao1145756102 sao1145756102 uncurated Do spines only have a post synaptic density With the restrictions we are trying to say that if you are a spine, you may have one or more of the following parts, a head, a neck or a spinule. If you have one of these parts then you are likely a spine. Spine Spine CNS 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. sao1149261773 Stretch cells C0926518 sao1149261773 true uncurated Tanycyte Tanycyte Morphological state characterized by a contracted matrix and expanded intracristal space; observed experimentally when added ADP is used up (Mannella et al., 2001). sao1152497626 sao1152497626 uncurated Condensed Condensed 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). sao1152983960 sao1152983960 uncurated Intercalated Disk Intercalated Disk The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology). 0012506 sao1153182838 C1167317 sao1153182838 uncurated Vesicle Membrane Vesicle Membrane 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. sao1154704263 lower motor neuron sao1154704263 true uncurated Wikipedia Alpha Motor Neuron Alpha Motor Neuron 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). sao1164727693 C0061465 sao1164727693 uncurated Glutamate Receptor Glutamate Receptor 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 C0035696 sao116515730 uncurated MRNA MRNA Integral membrane proteins that transport molecules or ions into or out of the cell or compartment. sao1165516281 sao1165516281 uncurated Transporter Protein Transporter Protein sao1172124127 sao1172124127 uncurated Neurexin Neurexin Proteins found in the microtubules (MSH). sao1174532162 C0026042 sao1174532162 uncurated Microtubule Associated Protein Microtubule Associated Protein Refers to any specialized coating present on a vesicle membrane, e.g., clathrin. 0030120 sao1177708494 C1166749 sao1177708494 Vesicle Coat Vesicle Coat sao1179195262 C0923872 sao1179195262 uncurated Attachment Attachment sao1180716477 sao1180716477 Subcellular Fraction Subcellular Fraction Conceptual anatomical entity which describes the structural and transformation relationships between physical anatomical entities. Example: class subsumption relationship, structural relationship, anatomical tranformation relationship (FMA). FMAID:54723 sao1184653804 sao1184653804 FMA FMA uncurated Anatomical Relationship Anatomical Relationship 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). 0005921 sao118541872 C0206117 sao118541872 uncurated Gap Junction Gap Junction A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology). 0000262 sao1186327184 C1166687 sao1186327184 uncurated Mitochondrial Chromosome Mitochondrial Chromosome 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). 0043218 sao1186642361 sao1186642361 uncurated Oligodendrocyte Compact Myelin Oligodendrocyte Compact Myelin Portion of a cell soma closest to the point where the basilar dendrite emerges. sao1186862860 sao1186862860 uncurated Basal Pole Of Neuron Basal Pole Of Neuron Refers to the fine, veil-like terminal processes of protoplasmic astrocytes. sao1189060993 sao1189060993 graph position temporary uncurated is this the same as what is now termed the peripheral astrocyte process? Vellous Process Vellous Process The region between the inner and outer lipid bilayers of the mitochondrial envelope. (Gene Ontology). 0005758 sao118944228 C1166886 sao118944228 true graph position temporary 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 Mitochondrial Intermembrane Space Refers to the morphology of a bouton. sao1189513296 sao1189513296 uncurated Bouton Type Bouton Type Region of axon immediately adjacent to the paranode. sao1191319089 sao1191319089 uncurated Juxta Paranode Axon Juxta Paranode Axon BF_C000103 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). 0014069 sao1196688972 sao1196688972 Post-synaptic Density Post-synaptic Density 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). 0005932 sao11978067 C0230744 sao11978067 uncurated Basal Body Basal Body 200 kd Neurofilament protein with molecular weight 200 kd. sao1200165704 sao1200165704 uncurated Neurofilament 200kd Neurofilament 200kd One of two globular polypeptides forming microtubules. sao1202564066 C0005290 sao1202564066 uncurated Beta Tubulin Beta Tubulin 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) sao1202737159 C0031686 sao1202737159 uncurated Phosphatase Phosphatase Cellular inclusion found in the cytoplasm. sao120573470 sao120573470 uncurated Cellular Inclusion Cellular Inclusion sao120818728 sao120818728 uncurated Lumenal Surface Lumenal Surface Schwann cell that forms compact myelin sheath around axons. sao1209655615 sao1209655615 uncurated Myelinating Schwann Cell Myelinating Schwann Cell Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974). sao1210952635 sao1210952635 uncurated Nucleolus-associated Heterochromatin Nucleolus-associated Heterochromatin A branching protoplasmic process of a neuron that receive and integrate signals coming from axons of other neurons, and convey the resulting signal to the body of the cell (Gene Ontology). One of several similar processes that issue from the perikaryon of a neuron, generally specialized for receiving synaptic input from other neurons or transduction of signals from the environment. 0030425 sao1211023249 C0011305 sao1211023249 uncurated Dendrite Dendrite sao1211239798 C0925206 sao1211239798 uncurated Connectivity Connectivity sao1213292244 sao1213292244 uncurated OPC Oligodendrocyte Precursor Cell Oligodendrocyte Precursor Cell sao1217691568 sao1217691568 uncurated Length Length 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). sao1217793903 C0230580 sao1217793903 uncurated Pars Granulosa Pars Granulosa CL:0000710 sao1224657022 Neuroepithelial cell sao1224657022 uncurated Nerve Cell Nerve Cell sao1231384859 sao1231384859 uncurated Pigment Pigment sao1232021729 C0213974 sao1232021729 uncurated SAP90 SAP90 sao1232858786 sao1232858786 uncurated Thin Dendritic Spine Thin Dendritic Spine CL:0000210 A cell specialized to detect and transduce light (MESH). sao1233810115 sao1233810115 true uncurated Photoreceptor Cell Photoreceptor Cell true BF_T0000036 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). sao1236796660 sao1236796660 true uncurated Cortical Spiny Stellate Cell Cortical Spiny Stellate Cell 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) sao1239389 sao1239389 true graph position temporary Perivascular Astrocyte Perivascular Astrocyte Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating. sao1241866791 sao1241866791 uncurated Large Vesicle Large Vesicle A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). 0045334 sao1243595998 sao1243595998 uncurated Clathrin Coated Endocytic Vesicle Clathrin Coated Endocytic Vesicle 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 sao124393998 uncurated Endoplasmic Reticulum Exit Site Endoplasmic Reticulum Exit Site sao1245187339 sao1245187339 uncurated Perivascular Macrophage Perivascular Macrophage Measure of turnover. sao124571525 sao124571525 uncurated Half Life Half Life sao1246280606 C0597548 sao1246280606 uncurated Synthetic Enzyme Synthetic Enzyme sao1253297813 sao1253297813 uncurated Glial Subcompartment Glial Subcompartment cerebral cortex false 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 sao1267578530 true uncurated Chandelier Cell Chandelier Cell Nucleus with one or more indentations in the nuclear membrane. sao1277586470 sao1277586470 uncurated Indented Nucleus Indented Nucleus sao1278200674 sao1278200674 Cell Morphological Type Cell Morphological Type 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). 0043209 sao1279474730 C0026973 sao1279474730 uncurated Oligodendrocyte Myelin Sheath Oligodendrocyte Myelin Sheath sao1280179455 sao1280179455 uncurated Scaffolding Protein Scaffolding Protein Synaptic vesicle that is fused to the pre-synaptic membrane, forming the characteristic omega profile. sao128105491 Omega profile sao128105491 uncurated Fused Vesicle Fused Vesicle sao1281431356 sao1281431356 uncurated Actin Bundling Protein Actin Bundling Protein 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). sao128470897 sao128470897 uncurated Sub-surface Cisternae Sub-surface Cisternae A dendrite characterized by few or no recognizable dendritic spines. sao128827344 sao128827344 uncurated Aspiny Aspiny Characterized by a low density of dendritic spines. sao1288413465 sao1288413465 uncurated Sparsely Spiny Sparsely Spiny false Anatomical space occurring within a cell, usually formed by intracellular membranes. sao1289190043 sao1289190043 uncurated Cellular Space Cellular Space sao1289583168 sao1289583168 uncurated Arrangement of pre- and post-synaptic components. Synaptic Configuration Synaptic Configuration The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology). 0005741 sao1289741256 C0230839 sao1289741256 uncurated Mitochondrial Membrane Outer Mitochondrial Membrane Outer sao1290101869 sao1290101869 Cell Cyle Phase Cell Cyle Phase A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it. sao1291545653 sao1291545653 uncurated Membrane Bound Ribosome Membrane Bound Ribosome CNS CL:0000644 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. sao1299495391 radial epithelial cell C0228088 sao1299495391 true graph position temporary Wikipedia 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 Bergmann Glia Bergmann Glia Maryann Martone Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle sao1299635018 sao1299635018 uncurated 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 Cell Cell Contact Zone Cell Cell Contact Zone Refers to the transport of a structure via microtubules and microtubule-associated motors. sao1301290450 sao1301290450 Microtubule Mediated Motility Microtubule Mediated Motility A protoplasmic astrocyte with extremely thin veil-like (vellous) processes. sao1309473597 C0926509 sao1309473597 true uncurated Velate Astrocyte Velate Astrocyte 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 Electrical Synapse sao1311109124 uncurated Electrotonic Synapse Electrotonic Synapse sao131261273 sao131261273 true uncurated Hippocampal Pyramidal Neuron Hippocampal Pyramidal Neuron 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). 0005883 sao1316272517 C0027834 sao1316272517 uncurated Neurofilament Neurofilament sao1319795695 sao1319795695 uncurated Synapse Associated Protein Synapse Associated Protein sao1322219701 sao1322219701 uncurated GluR1 GluR1 sao1329750433 sao1329750433 uncurated Membrane Surface Membrane Surface Refers to the ability of structures to move about the cell. sao1330317521 sao1330317521 Motility Motility Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA). 0005575 sao1337158144 sao1337158144 uncurated 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). Cellular Component Cellular Component Refers to the terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance. sao1340260079 sao1340260079 uncurated Tuft Tuft sao1352451787 sao1352451787 uncurated Quiescent Oligodendrocyte Precursor Cell Quiescent Oligodendrocyte Precursor Cell Oligodendrocyte found in gray matter in close association with neurons (Peters, Palay and Webster, 1991). sao1353298471 C0949376 sao1353298471 true graph position temporary It is unclear to us whether perineuronal oligodendrocytes should be considered a separate class. Perineuronal Oligodendrocyte Perineuronal Oligodendrocyte 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 sao1354781919 Paranodal loop sao1354781919 uncurated Oligodendrocyte Paranodal Termination Oligodendrocyte Paranodal Termination bipolar CL:0000184 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). sao1355908696 Mural Cell Rouget Cell C0598800 sao1355908696 uncurated Pericyte Pericyte A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). 0030139 sao1362520468 C0887883 sao1362520468 uncurated Endocytic Vesicle Endocytic Vesicle ciliary ganglion projection neuron unipolar 0 sao1366775348 C0229060 sao1366775348 true uncurated Ciliary Ganglion Neuron Ciliary Ganglion Neuron Minimum diameter of a cross section through structure. sao136816674 sao136816674 uncurated Cross Section Diameter Minor Cross Section Diameter Minor 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). 0005743 sao1371347282 C0230840 sao1371347282 uncurated Mitochondrial Membrane Inner Mitochondrial Membrane Inner Indicates that two entities share a continuous space but that the continuity is formed through a specialized junctional component, e.g., gap junction. sao1374293695 sao1374293695 uncurated Junctional Continuity Junctional Continuity Refers to the process of the Schwann cell that surrounds an unmyelinated axon or cell soma. sao1376748732 sao1376748732 uncurated Ensheathing Process Ensheathing Process sao1379576571 sao1379576571 "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 Organismal Occurrent 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). 0042599 sao1379604862 sao1379604862 uncurated Lamellar Body Lamellar Body sao138219748 sao138219748 uncurated Vesicular Component Vesicular Component A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack) (Gene Ontology). 0030143 sao1382918459 sao1382918459 uncurated Inter-Golgi Transport Vesicle Inter-Golgi Transport Vesicle 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) sao138430598 sao138430598 uncurated Nematosome Nematosome sao138926812 sao138926812 uncurated Alpha 7 Acetylcholine Receptor Alpha 7 Acetylcholine Receptor sao1390810994 C0536483 sao1390810994 uncurated GluR2 GluR2 sao1392266325 sao1392266325 uncurated Junctional Connectivity Junctional Connectivity CNS CL:0000127 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). sao1394521419 C0004112 sao1394521419 true uncurated Astrocyte Astrocyte sao1395777368 sao1395777368 Intercellular Junction Intercellular Junction A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology). 0005605 sao1397492660 C0242195 sao1397492660 uncurated Basal Lamina Basal Lamina sao1399894198 C0061467 sao1399894198 uncurated Glutamate Transporter Glutamate Transporter Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991). sao1400623473 fascia adhaerens sao1400623473 uncurated Zonula Adhaerens Zonula Adhaerens cerebellar cortex local circuit neuron 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 sao1415726815 true uncurated Cerebellar Golgi Cell Cerebellar Golgi Cell Family of transmembrane heparan sulfate proteoglycans (CSP - Bonfire). sao1417256224 C0075691 sao1417256224 uncurated Syndecan Syndecan CL:0000540 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 C0027882 sao1417703748 true uncurated Neuron Neuron sao1423758634 sao1423758634 uncurated Junctional Part Junctional Part That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid (Gene Ontology). 0005616 sao1425028079 sao1425028079 uncurated Extracellular Space Extracellular Space Spatial association relationship which describes the containment, adjacency, and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate (FMA). sao1426984192 sao1426984192 uncurated Anatomical Location Anatomical Location 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). 0005840 sao1429207766 C0035553 sao1429207766 uncurated Ribosome Ribosome sao1430127373 sao1430127373 Monoamines Monoamines Refers to the morphological type of a spine. sao1436578787 sao1436578787 uncurated Spine Type Spine Type CL:0000717 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). sao1438006234 fusimotor neuron C0026610 sao1438006234 true uncurated Gamma Motor Neuron Gamma Motor Neuron sao1440704204 sao1440704204 uncurated Neurotransmitter Associated Protein Neurotransmitter Associated 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 C0079323 sao1442185587 uncurated Extracellular Matrix Protein Extracellular Matrix Protein sao1447478620 sao1447478620 uncurated Pial Endfoot Pial Endfoot sao1448451779 sao1448451779 uncurated Reactive Microglia Reactive Microglia sao1455064842 sao1455064842 Vesicle Subcomponent Vesicle Subcomponent 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). 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). 0005652 sao1455996588 C1136039 sao1455996588 uncurated Nuclear Lamina Nuclear Lamina Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes (Gene Ontology). 0043228 sao1456184038 sao1456184038 uncurated Non Membrane Bound Organelle Non Membrane Bound Organelle 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. sao1458938856 rod cell C0206427 sao1458938856 true uncurated Retinal Rod Cell retinal rod cell Retinal Rod Cell CL:0000100 Neurons which activate muscle cells (MSH). sao1460710779 C0026609 sao1460710779 true uncurated UMLS Motor Neuron Motor Neuron 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). sao1463925374 C0006631 sao1463925374 uncurated Cadherin Cadherin Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004). sao1470121605 sao1470121605 uncurated Active Zone Cytomatrix Active Zone Cytomatrix Smaller branches of an axon that emanate from the main axon cylinder. sao1470140754 sao1470140754 uncurated Axon Collateral Axon Collateral 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). sao1473913158 C0132298 sao1473913158 uncurated Neurotrophin Neurotrophin sao1475145503 sao1475145503 uncurated Clustered Clustered sao1482557638 C0906849 sao1482557638 uncurated Kv3.2 Kv3.2 anterior ventral cochlear nucleus sao1482618768 sao1482618768 true uncurated Spherical Bushy Cell Spherical Bushy Cell A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes (Gene Ontolgoy). 0030136 sao148845161 C0887885 sao148845161 uncurated Clathrin Coated Vesicle Clathrin Coated Vesicle Refers to the contents contained in the vesicle. sao1490223249 sao1490223249 Need to determine whether this should be a part of a vesicle; I think it shouldn't be Vesicle Cargo Vesicle Cargo A type of NG2 positive cell that resemble oligodendrocyte precursors sao1492258085 sao1492258085 true Ligon et al PNAS 2006, PMID: 16682644 Bipolar Progenitor Cell Bipolar Progenitor Cell Potassium channels whose activation is dependent on intracellular calcium concentrations (MSH). sao1494484467 C0949653 sao1494484467 uncurated Calcium Activated Potassium Channel Calcium Activated Potassium Channel sao149790201 sao149790201 uncurated Beta Neurexin Beta Neurexin sao1499850686 sao1499850686 uncurated Nuclear Subcomponent Nuclear Subcomponent sao1501064039 C0536486 sao1501064039 uncurated GlurR3 GlurR3 sao1504920769 fibroglycan C0174307 sao1504920769 uncurated Syndecan-2 Syndecan-2 Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991). Synaptic contact characterized by both electrical and chemical synaptic junctions. sao1506103497 sao1506103497 uncurated Mixed Synapse Mixed Synapse sao1507566336 sao1507566336 Post-synaptic Component Post-synaptic Component 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). sao1508721375 C0006787 sao1508721375 uncurated Calsequestrin Calsequestrin sao1510923311 sao1510923311 uncurated Density Density 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 C0002520 sao1511566913 uncurated Amino Acid Amino Acid sao1514682949 sao1514682949 uncurated Cytoplasmic Surface Cytoplasmic Surface Subcompartmentalization of cellular structures such as organelles. sao1515819812 sao1515819812 uncurated General Cell Subcompartment General Cell Subcompartment sao1517449491 C0056257 sao1517449491 uncurated Contactin Contactin sao1524397168 sao1524397168 Junctional Site Junctional Site 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 sao1531915298 uncurated Amorphous Vesicle Amorphous Vesicle PDZ containing proteins with F-actin binding protein activity. sao1535366556 sao1535366556 uncurated NeurabinI NeurabinI sao1536532595 sao1536532595 uncurated Sessile Dendritic Spine Sessile Dendritic Spine Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane (Gene Ontology). 0043226 sao1539965131 C0029219 sao1539965131 uncurated Organelle Organelle sao1540081501 sao1540081501 uncurated Capillary Endothelial Cell Capillary Endothelial Cell Cuboidal shaped epithelial cell forming one of the components of the choroid plexus (Peters, Palay and Webster, 1991). sao1541570510 sao1541570510 true uncurated Choroid Epithelial Cell Choroid Epithelial Cell sao1543450574 sao1543450574 uncurated This cell class is not contained in the Cell Type Ontology Vascular Endothelial Cell Vascular Endothelial Cell sao1546288504 sao1546288504 uncurated Regional Part Of Golgi Regional Part Of Golgi The volume enclosed by the membranes of an endosome (Gene Ontology). 0031904 sao1547508851 endosome lumen sao1547508851 uncurated Endosomal Lumen Endosomal Lumen AQP4 sao1548226791 C0292777 sao1548226791 uncurated Aquaporin 4 Aquaporin 4 Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology). 0005767 sao1549842807 C0230815 sao1549842807 uncurated Secondary Lysosome Secondary Lysosome Indicates that the feature was observed in tissue prepared by chemical fixation. sao1554187262 sao1554187262 Chemical Fixation Chemical Fixation Refers to the morphology of mitochondria. sao1562245920 sao1562245920 uncurated Mitochondrial Type Mitochondrial Type 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). sao1565708461 C0058836 sao1565708461 uncurated Dynamin Dynamin 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. sao1570660411 sao1570660411 uncurated Tubular Endosome Tubular Endosome sao1571698684 sao1571698684 uncurated Barr Body Barr Body Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain. sao1573004591 sao1573004591 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. graph position temporary It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet This comes from derouiche et al. J. Physol. Paris 2002 96:177 PubMedID:12445894 Peripheral Astrocyte Process Peripheral Astrocyte Process sao1579007712 sao1579007712 uncurated Cell Interior Cell Interior CL:0000601 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 C0206513 sao1582628662 true uncurated Cochlear Outer Hair Cell Cochlear Outer Hair Cell 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. sao1583093969 sao1583093969 curation complete Gray's Type 2 see example at: http://synapse-web.org/anatomy/chemical/symh.htm Symmetrical Symmetrical sao1585306176 sao1585306176 uncurated EAAT2 EAAT2 Terminal pre-synaptic ending of an axon or axon collateral. sao1586851177 sao1586851177 uncurated Regional Part Of Basket Cell Axon Regional Part Of Basket Cell Axon 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). 0005884 sao1588493326 C0025979 sao1588493326 uncurated Actin Filament Actin Filament sao1590928667 sao1590928667 uncurated Regional Part Of Spiny Dendrite Regional Part Of Spiny Dendrite 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 C0010852 sao1593305396 uncurated Cytoskeletal Protein Cytoskeletal Protein sao1594955670 sao1594955670 uncurated Dendritic Growth Cone Dendritic Growth Cone Generally rounded shape, where the minimum and maximum dimensions produce a roughly egg-shape. sao1595237779 sao1595237779 definition incomplete Oval Oval The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology). 0030868 sao1596955044 sao1596955044 uncurated SER Membrane SER Membrane sao1596955138 sao1596955138 Organotypic Slice Organotypic Slice Used to refer to the main axonal trunk, as opposed to the collaterals. sao1596975044 sao1596975044 uncurated Main Axon Main Axon sao1607047124 Post-synaptic compartment sao1607047124 uncurated 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. Post-synaptic Part Post-synaptic Part 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 C0079189 sao1611333173 uncurated Cytokine Cytokine The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology). 0005637 sao1612527463 sao1612527463 uncurated Nuclear Inner Membrane Nuclear Inner Membrane CL:0000636 Specialized glial cell of the retina that extends from the inner limiting membrane to the outer limiting membrane sao1615912903 sao1615912903 true graph position temporary 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 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. Muller Cell Muller Cell The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology). 0000785 sao1615953555 C0008546 sao1615953555 uncurated Chromatin Chromatin 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). 0005640 sao1617136075 sao1617136075 uncurated Nuclear Outer Membrane Nuclear Outer Membrane sao1619512288 sao1619512288 uncurated SER Subcompartment SER Subcompartment sao1624466407 sao1624466407 uncurated Vesicle Binding Protein Vesicle Binding Protein Calcium pump found in the membrane of the smooth endoplasmic reticulum. sao163038736 sao163038736 uncurated SERCA SERCA Refers to processes of astrocytes extending from the cell soma that wrap around neurons and conform to cellular components in the neuropil. sao1630537580 sao1630537580 uncurated Astrocyte Process Astrocyte Process 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 sao1634374950 uncurated Hypolemmal Cisternae Hypolemmal Cisternae sao1635329413 sao1635329413 uncurated Cytoskeletal Element Cytoskeletal Element Axon collateral that ramifies in the area of the soma of the cell of origin. sao1642494436 sao1642494436 uncurated Recurrent Collateral Recurrent Collateral sao1642908940 neck pedicle sao1642908940 uncurated Spine Neck Spine Neck 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). sao1643644091 sao1643644091 uncurated Thin Thin cerebral cortex local circuit neuron CL:0000122 sao164665273 sao164665273 true uncurated Cortical Stellate Cell Cortical Stellate Cell Indicates that the feature was observed in cells in culture or in isolated subcellular fractions. sao1649728317 sao1649728317 In Vitro In Vitro Cytoskeletal protein present in Z lines of muscle fibrils and at sites of non-muscle cell contact with a substrate (CSP). sao1659393491 C0917705 sao1659393491 uncurated Alpha Actinin Alpha Actinin The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology). 0005886 sao1663586795 cell membrane sao1663586795 C0007603 uncurated Plasma Membrane Plasma Membrane Signal molecules that are involved in the control of cell growth and differentiation (MSH). sao1671627152 C0018284 sao1671627152 uncurated Growth Factor Growth Factor sao1682692988 sao1682692988 uncurated Regional Part Of Spine Apparatus Regional Part Of Spine Apparatus sao1683772610 sao1683772610 uncurated Endosomal Subcomponent Endosomal Subcomponent sao1684283879 sao1684283879 uncurated Calyx Of Held Calyx Of Held Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology). 0031965 sao1687101204 C0028584 sao1687101204 uncurated Nuclear Membrane Nuclear Membrane Indicates that feature was described in tissue prepared by fast freezing followed by freeze substitution. sao1693353776 sao1693353776 Fast Frozen Freeze Substituted Fast Frozen Freeze Substituted Indicates that the feature was observed in the living animal. sao1694199019 sao1694199019 Living Animal Living Animal 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 C0034792 sao1700719022 uncurated Acetylcholine Receptor Acetylcholine Receptor sao1701066619 C0912988 sao1701066619 uncurated Olig2 Olig2 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). 0005634 sao1702920020 C0007610 sao1702920020 uncurated Nucleus Nucleus sao1703115805 sao1703115805 uncurated Apical Apical Characterized by numerous swellings or varicosities along their length. sao1706854098 sao1706854098 uncurated Varicose Dendrite Varicose Dendrite sao1707694834 C0024773 sao1707694834 uncurated MAP2 MAP2 CL:0000065 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). sao1714094301 C0228092 sao1714094301 true graph position temporary We are not sure whether ependymal cells should be considered a type of ependymoglial cell Ependymal Cell Ependymal Cell A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO). 0005768 sao1720343330 C0034850 sao1720343330 uncurated Endosome Endosome BF_C000102 The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. sao172297168 sao172297168 uncurated Dendritic Tree Dendritic Tree sao172764364 sao172764364 uncurated Resting Microglia Resting Microglia sao1728785226 sao1728785226 uncurated Intracellular Calcium Channel Intracellular Calcium Channel 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). sao1730664005 sao1730664005 uncurated Pre-synaptic Grid Pre-synaptic Grid cerebellar cortex 1 BF_C000108 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 sao1736323572 true uncurated Cerebellar Granule Cell Cerebellar Granule Cell CL:0000188 sao1741889714 sao1741889714 uncurated Skeletal Muscle Cell Skeletal Muscle Cell sao1744435799 C0220839 sao1744435799 uncurated Glutamate Glutamate sao1746643703 sao1746643703 definition incomplete Chemical Synapse Type Chemical Synapse Type sao1746802704 sao1746802704 Varicose Axon Varicose Axon Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins. sao1747012216 square array sao1747012216 uncurated Orthogonal Array Orthogonal Array 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). sao1749953771 sao1749953771 uncurated Tail Portion Tail Portion sao1757774791 sao1757774791 uncurated Terminal Bouton Terminal Bouton 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). sao1767745398 C0034830 sao1767745398 uncurated Nicotinic Acetylcholine Receptor Nicotinic Acetylcholine Receptor 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). 0030424 sao1770195789 C0004461 sao1770195789 uncurated Axon Axon Distance, usually in linear microns, from soma where a feature is observed. sao1779606731 sao1779606731 uncurated Distance From Soma Distance From Soma sao1784069613 sao1784069613 Synaptic Component Synaptic Component sao1785015039 sao1785015039 uncurated Nuclear DNA Nuclear DNA 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 C0001239 sao1785445428 uncurated Actin Binding Protein Actin Binding Protein Characterized by a flattened shape in glutaraldehyde fixed tissue. sao1785495506 sao1785495506 uncurated Flattened Flattened multipolar sao1785599611 anterior horn cell sao1785599611 uncurated Spinal Motor Neuron Spinal Motor Neuron Characterized by the diameter of the neck being similar to that of the head (Harris et. al 1992). sao1786354232 sao1786354232 uncurated Stubby Stubby A real boundary corresponds to its surface and designates a discontinuity between constitutional parts of anatomical entities (FMA: Mejino and Cornelius, ???) sao1786656680 sao1786656680 uncurated Real Boundary Real Boundary sao1788621392 sao1788621392 uncurated Surface Area Surface Area sao1791490892 sao1791490892 uncurated Regional Part Of Myelinated Axon Regional Part Of Myelinated Axon sao1794895660 sao1794895660 uncurated ATP Synthase ATP Synthase Cell membrane glycoproteins selective for sodium ions. Fast sodium current is associated with the action potential in neural membranes (MSH). sao1797800540 C0037492 sao1797800540 uncurated Sodium Channel Sodium Channel sao1798128207 C0171438 sao1798128207 uncurated RIM1 RIM1 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). 0043197 sao1799103720 C0872341 sao1799103720 uncurated Dendritic Spine Dendritic Spine Differentiates among different functional states of a cell or cell component, e.g., activated microglia, interphase nucleus, orthodox mitochondria. sao1802798922 sao1802798922 Functional State Functional State 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). 0005759 sao1804523077 C0230843 sao1804523077 uncurated Mitochondrial Matrix Mitochondrial Matrix A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology). 0031410 sao180601769 sao180601769 uncurated Cytoplasmic Vesicle Cytoplasmic Vesicle 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). sao1810043179 C0027096 sao1810043179 uncurated Myosin Myosin CL:0000000 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). 0005623 sao1813327414 sao1813327414 uncurated Cell Cell Process of astrocyte that extends to the surface of the central nervous system. Together, they form the glial limiting membrane or glial limitans. sao181458425 sao181458425 uncurated Glial Limiting Endfoot Glial Limiting Endfoot The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology). 0048237 sao1819509473 rough endoplasmic reticulum lumen sao1819509473 uncurated RER Lumen RER Lumen 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). 0005730 sao1820400233 C0007609 sao1820400233 uncurated Nucleolus Nucleolus Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991). sao18239917 sao18239917 uncurated Axonal Spine Axonal Spine 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). sao1825296048 sao1825296048 uncurated Virtual Boundary Virtual Boundary Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003). sao1825845900 sao1825845900 uncurated Crista Junction Crista Junction Subcompartment of a compartment. sao183270081 sao183270081 uncurated Subregional Part Of Neuron Process Subregional Part Of Neuron Process Indicates that the feature was observed in fixed tissue. sao1833377695 sao1833377695 Fixed Tissue Fixed Tissue Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974). sao1841764412 C0230581 sao1841764412 uncurated Pars Fibrosa Pars Fibrosa sao1842028314 sao1842028314 uncurated SER Subcomponent SER Subcomponent 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) sao1842089031 C0001044 sao1842089031 uncurated Acetylcholinesterase Acetylcholinesterase Refers to the morphology of mitochondrial cristae. sao1843037539 sao1843037539 uncurated Cristae Type Cristae Type 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) sao1843715402 C0035668 sao1843715402 uncurated RNA RNA sao1843719868 sao1843719868 uncurated Non Neural Cell Compartment Non Neural Cell Compartment Characterized by a nuclear membrane with no indentations. sao1845602529 sao1845602529 uncurated Smooth Membrane Smooth Membrane 150 kd Neurofilmanet protein with molecular weight 150 kd. sao1845865352 sao1845865352 uncurated Neurofilament 150kd Neurofilament 150kd Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane sao18461326 sao18461326 uncurated Inner Bounding Mitochondrial Membrane Inner Bounding Mitochondrial Membrane sao1846292151 C0021701 sao1846292151 uncurated Integrin Integrin 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). 0005874 sao1846835077 C0026046 sao1846835077 uncurated Microtubule Microtubule 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 C0006685 sao1846985919 uncurated Calcium Channel Calcium Channel Cell that comprises the meninges sao1847837612 sao1847837612 uncurated This needs to be extensively investigated Meninges Cell Meninges Cell 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). sao185580330 C0001041 sao185580330 uncurated Acetylcholine Acetylcholine 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). 0051324 sao1856556831 C0033464 sao1856556831 Prophase Prophase CL:0000235 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). sao185843373 sao185843373 uncurated Macrophage Macrophage 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 sao1858501007 uncurated Bridge Contact Site Bridge Contact Site 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). 0005739 sao1860313010 C0026237 sao1860313010 uncurated Mitochondrion Mitochondrion sao1863115908 sao1863115908 uncurated "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 Organismal Continuant Refers to the morphology of a vesicle. sao1863391630 sao1863391630 uncurated Vesicle Type Vesicle Type false Large cholinergic interneuron in the caudate nucleus, putamen and nucleus accumbens. sao1866881837 sao1866881837 true uncurated Cholinergic Striatal Neuron Cholinergic Striatal Neuron sao18717211 sao18717211 uncurated Refers to a specialized arrangements of a cellular component or other structure that is characteristic of a given region, e.g., bundled microtubules. Configuration Configuration Refers to a bundle of closely apposed microtubules running parallel to each other. sao1872343973 sao1872343973 uncurated Microtubule Fascicle Microtubule Fascicle Terminal pre-synaptic ending of an axon or axon collateral. sao187426937 sao187426937 uncurated Synaptic Bouton Synaptic Bouton Portion of a cell soma closest to the point where the apical dendrite emerges. sao1877927224 sao1877927224 uncurated Apical Pole Of Neuron Apical Pole Of Neuron 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). 0005791 sao1881364067 Nissl substance C0230779 sao1881364067 uncurated Rough Endoplasmic Reticulum Rough Endoplasmic Reticulum 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 sao1884931180 uncurated Ribbon Synapse Ribbon Synapse 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 sao1890444066 uncurated Schwann Cell Microvillus Schwann Cell Microvillus sao189141251 C0068587 sao189141251 uncurated Neurofascin Neurofascin CL:0000126 sao1895605722 macroglial cell C0228087 sao1895605722 true uncurated SAO classifies Schwann cells as a type of macroglia; Cell Type Ontology includes only astrocytes and oligodendroglia Macroglia Macroglia The space between the inner and outer nuclear membranes sao1908934319 sao1908934319 uncurated Intranuclear Membrane Space Intranuclear Membrane Space sao1911631652 sao1911631652 uncurated Pre-synaptic Active Zone Component Pre-synaptic Active Zone Component medial nucleus of the trapezoid body CNS multipolar 1 Properties derived from Gersdorff and Borst (2002). sao1918137235 sao1918137235 true uncurated Principal Cells Medial Nucleus Trapezoid Body Principal Cells Medial Nucleus Trapezoid Body Doral root ganglion unipolar 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 sao1919499702 true uncurated Dorsal Root Ganglion Cell Dorsal Root Ganglion Cell sao1920358312 sao1920358312 uncurated IP3R Type 2 IP3R Type 2 The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells. 0005911 sao1922892319 sao1922892319 definition incomplete 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. Intercellular Junction Site Intercellular Junction Site sao1925368674 sao1925368674 uncurated Pinocytic Vesicle Pinocytic Vesicle sao1928362432 sao1928362432 uncurated Brainstem Motor Neuron Brainstem Motor Neuron 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). sao1933817066 sao1933817066 uncurated Mitochondrial Adhaerens Complex Mitochondrial Adhaerens Complex 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 sao1938587839 sao1938587839 definition incomplete 2007-02-23 Subplasmalemmal Coating Subplasmalemmal Coating 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). 0005923 sao1939999134 tight junction sao1939999134 uncurated Zonula Occludens Zonula Occludens 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). sao1943947957 sao1943947957 uncurated Peg And Socket Contact Peg And Socket Contact sao1950472752 sao1950472752 uncurated "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 Biological Continuant Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum. sao1950673097 sao1950673097 uncurated Schaffer Collateral Schaffer Collateral sao1951490568 C0059259 sao1951490568 uncurated Endoplasmin Endoplasmin sao195217619 sao195217619 uncurated Regional Part Of Schwann Cell Regional Part Of Schwann Cell White matter oligodendrocytes that may be aligned in rows (Peters, Palay and Webster, 1991). sao1952867392 C0205867 sao1952867392 true uncurated Interfascicular Oligodendrocyte Interfascicular Oligodendrocyte sao1956231674 sao1956231674 uncurated Golgi Lumen Golgi Lumen sao1956738165 sao1956738165 uncurated Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction Macular Adhaerentia Macular Adhaerentia Characterization based on high or low density of classical spines on dendrites. sao1959705051 sao1959705051 uncurated Dendrite Type Dendrite Type Indicates the experimental conditions under which a feature was observed. sao1960697157 sao1960697157 uncurated All experimental entities will be ported into a separate ontology based on OBI Experimental Condition Experimental Condition sao1968590282 sao1968590282 uncurated 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. Anatomical Part Anatomical Part Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003). sao1969557946 C0009143 sao1969557946 uncurated Coated Pit Coated Pit sao196989303 sao196989303 uncurated Volume Volume sao196990275 C0017911 sao196990275 uncurated Glycogen Glycogen sao1970895398 sao1970895398 Cell Regional Part Aggregate Object Cell Regional Part Aggregate Object Cells that line the inner and outer surfaces of the body (MSH). sao197110912 C0225336 sao197110912 uncurated Vascular Cell Vascular Cell sao1974433376 C0932419 sao1974433376 uncurated Regional Part Of Epithelial Cell Regional Part Of Epithelial Cell Characterized by the diameter of the head being much greater than that of the neck (Harris et. al 1992). sao1983595164 sao1983595164 uncurated Mushroom Mushroom 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). 0030135 sao1985096626 C0242915 sao1985096626 uncurated Coated Vesicle Coated Vesicle Refers to cristae with a flattened, extended appearance. sao1995010823 sao1995010823 uncurated Lamellar Lamellar sao1996310556 C0068608 sao1996310556 uncurated Neuromelanin Neuromelanin sao2003006393 sao2003006393 uncurated IP3R Type 3 IP3R Type 3 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) sao2006047981 C0025979 sao2006047981 uncurated Microfilament Microfilament 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 sao2007137787 uncurated Axon Terminal Axon Terminal dentate gyrus CNS true local circuit neuron 1 sao2007319345 sao2007319345 true uncurated Dentate Gyrus Granule Cell Dentate Gyrus Granule Cell sao2016979058 sao2016979058 uncurated EAAT1 EAAT1 sao2017162875 sao2017162875 uncurated Age Associated Age Associated 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 sao2019617624 uncurated Regional Part Of RER Regional Part Of RER sao2022412481 sao2022412481 true uncurated Modified Astrocyte Modified Astrocyte sao2023460124 neurabinII sao2023460124 uncurated Spinophliln Spinophliln sao2023779072 sao2023779072 Cell Cell Contact Cell Cell Contact 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). sao2031592629 sao2031592629 uncurated Neurosecretory Vesicle Neurosecretory Vesicle BF_C000106 Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology). 0043198 sao2034472720 sao2034472720 uncurated Dendritic Shaft Dendritic Shaft Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004). sao2038461087 sao2038461087 uncurated Active Zone Plasma Membrane Active Zone Plasma Membrane sao203987954 sao203987954 uncurated Axonal Growth Cone Axonal Growth Cone sao2044996357 Pre-synaptic compartment sao2044996357 uncurated Pre-synaptic Part Pre-synaptic Part 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. sao2045795635 sao2045795635 graph position temporary May need to do more reading to determine whether this should be a parent of mushroom and thin. Pedunculated Pedunculated 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). 0005771 sao2045955158 C0230825 sao2045955158 uncurated Multivesicular Body Multivesicular Body CL:0000202 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 C0018496 sao2046464388 true uncurated Hair Cell hair cell Hair Cell CNS Multipolar neuron found in cerebellar molecular layer. sao2046525601 sao2046525601 true uncurated Cerebellar Stellate Cell Cerebellar Stellate Cell 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. sao2047438300 sao2047438300 curation complete Gray's Type 1 see example at: http://synapse-web.org/anatomy/chemical/asymh.htm Asymmetrical Asymmetrical Spine emanating from the cell soma. sao2048514053 sao2048514053 uncurated Somatic Spine Somatic Spine sao2048701763 sao2048701763 uncurated We are unclear why this is causing an inconsistency error. Perivascular Endfoot Perivascular Endfoot 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 C0013030 sao2050279787 uncurated Dopamine Dopamine sao2052625281 sao2052625281 graph position temporary Atlas Location Atlas Location 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). sao205380252 C0228081 sao205380252 uncurated Neuropil Neuropil 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). sao2056711309 C0110611 sao2056711309 uncurated Connexin Connexin 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). sao2060855807 C0054543 sao2060855807 uncurated Calreticulin Calreticulin 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). sao2062447305 C0034826 sao2062447305 uncurated Muscarinic Acetylcholine Receptor Muscarinic Acetylcholine Receptor sao2064469343 sao2064469343 uncurated Vascular Endfoot Vascular Endfoot Transports adenine nucleotides (AMP, ADP, and ATP) across membranes (Gene Ontology). 0000295 sao2077117136 C1153655 sao2077117136 uncurated Adenine Nucleotide Transporter Adenine Nucleotide Transporter sao2077793822 sao2077793822 uncurated Radial Radial Astrocytes characterized by high content of intermediate filaments and few vellous processes; often found in white matter. sao2078084673 C0228090 sao2078084673 true uncurated Fibrous Astrocyte Fibrous Astrocyte sao2081625415 sao2081625415 graph position temporary 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. Regional Part Of Cell Cell Contact Zone Regional Part Of Cell Cell Contact Zone Cellular inclusion containing filamentous structures. sao2081684219 sao2081684219 uncurated Filamentous Inclusion Filamentous Inclusion sao2082026326 sao2082026326 uncurated Rosette Rosette Refers to the morphology of an axon. sao2088691397 sao2088691397 uncurated Axon Type Axon Type Cellular inclusion found in the cytoplasm. sao2092254444 sao2092254444 uncurated Cytoplasmic Inclusion Cytoplasmic Inclusion sao2102170307 sao2102170307 uncurated Speed Speed Peptides released by neurons as intercellular messengers. Many neuropeptides are also hormones released by non-neuronal cells (MSH). sao2106486330 C0027895 sao2106486330 uncurated Neuropeptide Neuropeptide sao2108323256 sao2108323256 Pre-synaptic Site Pre-synaptic Site Refers to crisate with a roughly circular profile in cross section. sao2110170574 sao2110170574 uncurated Tubular Tubular 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) 0003735 sao2114723559 C0035701 sao2114723559 uncurated Ribosomal RNA Ribosomal RNA 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). sao2114874506 sao2114874506 uncurated Membrane Stack Membrane Stack sao2115096416 C0063592 sao2115096416 uncurated Inositol 1 4 5 Trisphosphate Receptor Inositol 1 4 5 Trisphosphate Receptor sao211804939 sao211804939 Supra-organismal Occurrent Supra-organismal Occurrent Refers to the average distance between features. sao2126482353 sao2126482353 uncurated Spacing Spacing 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 sao2127666702 uncurated Mesaxon Mesaxon multipolar sao2127763636 sao2127763636 created for testing purposes only Random Cell Random Cell Maryann Martone 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). sao2128156969 sao2128156969 2007-02-09 Spine Mat Spine Mat Pyramidal neuron from the cerebral cortex (not including hippocampus). sao2128417084 sao2128417084 true uncurated Cortical Pyramidal Neuron Cortical Pyramidal Neuron sao2135015805 sao2135015805 uncurated Extracellular Surface Extracellular Surface sao2138417829 sao2138417829 uncurated Calcium Binding Protein Calcium Binding Protein sao2139310701 sao2139310701 uncurated Plus To Minus Plus To Minus 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). sao2143851382 C0085252 sao2143851382 uncurated Synapsin Synapsin sao2146594471 C0033665 sao2146594471 uncurated Precursor Precursor 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). 0051322 sao21946128 C0002788 sao21946128 Anaphase Anaphase 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). 0005643 sao220861693 C0028587 sao220861693 uncurated Nuclear Pore Nuclear Pore TNF-alpha 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). sao220868685 C0041368 sao220868685 uncurated Tumor Necrosis Factor Alpha Tumor Necrosis Factor Alpha Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology). 0031982 sao221389602 C0042219 sao221389602 uncurated Vesicle Vesicle Implies that a morphologically identified synapse exists between two cell components where release of transmitter from cell influences cell B. sao223845603 sao223845603 uncurated Synaptic Connectivity Synaptic Connectivity 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 C0600594 sao225178797 uncurated Molecular Motor Molecular Motor CL:0000287 sao226523927 sao226523927 uncurated Eye Photoreceptor Cell Eye Photoreceptor Cell Abbreviation for gamma amino butyric acid, the major inhibitory neurotransmitter in the mammalian central nervous system. sao229636300 C0016904 sao229636300 uncurated GABA GABA sao229773618 C0916182 sao229773618 uncurated SERCA1 SERCA1 Specializations associated with intracellular membrane systems, e.g. lamellar bodies. Membranes of subcellular structures. (MSH) sao237754030 C0021868 sao237754030 uncurated Intracellular Membrane Formation Intracellular Membrane Formation sao238175764 sao238175764 uncurated G Coupled Receptor G Coupled Receptor Cellular inclusion found in the nucleus. sao238602892 sao238602892 uncurated Nuclear Inclusion Nuclear Inclusion The narrow gap that separates the presynaptic and postsynaptic membranes, into which a neurotransmitter is released (Gene Ontology). 0043083 sao243541954 C0682685 sao243541954 uncurated Synaptic Cleft Synaptic Cleft Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings. sao248349196 sao248349196 uncurated Neurotubule Neurotubule 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). 0030673 sao250772229 sao250772229 uncurated Axolemma Axolemma sao251535222 C0016890 sao251535222 uncurated G-actin G-actin 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. sao254777664 sao254777664 uncurated Schmidtt-Lanterman Cleft Schmidtt-Lanterman Cleft 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). 0043194 sao256000789 sao256000789 uncurated Initial Segment Initial Segment A small version of the zonula adharens type junction, characterized by a symmetrical adherent point between two cells. sao257629430 sao257629430 uncurated Puncta Adhaerentia Puncta Adhaerentia 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 C0072899 sao265434492 uncurated AMPA Receptor AMPA Receptor sao265591209 sao265591209 true uncurated 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 NG2 Cell NG2 Cell sao26622963 sao26622963 uncurated Protein Protein Characterized by two or more heads (Harris et. al 1992) that emerge from the same origin (Sorra KE and Harris KM, 2000). sao268063700 sao268063700 uncurated Branched Spine Branched Spine Enzymes that hydrolyze GTP to GDP. EC 3.6.1.- (MSH). sao271459227 C0018296 sao271459227 uncurated GTPases GTPases Refers to the "entities of reference" (FMA). Location may be defined by qualitative coodrinates or absolute coordinates. sao271899308 sao271899308 uncurated Orientation Orientation BF_C000112 sao273773228 sao273773228 uncurated Apical Dendrite Apical Dendrite false sao279801585 sao279801585 uncurated Measurement Measurement sao280355188 sao280355188 uncurated Regional Part Of Axon Regional Part Of Axon sao28175134 sao28175134 uncurated Terminal Specialization Terminal Specialization Sodium dependent transport protein, located on presynaptic terminals, involved in the uptake of dopamine; site at which cocaine exerts rewarding/ reinforcing effects (CSP). sao285839036 C0114838 sao285839036 uncurated Dopamine Transporter Type 1 Dopamine Transporter Type 1 sao289211478 sao289211478 uncurated Chemical Synapse Chemical Synapse 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). sao289587392 C0041491 sao289587392 uncurated Tyrosine Hydroxylase Tyrosine Hydroxylase sao293240763 sao293240763 uncurated Myelin Associated Protein Myelin Associated Protein sao295057932 sao295057932 uncurated Dendriole Dendriole When several members of a class occur tightly apposed to one another or attached to one another in identifiable bundles. sao296309608 sao296309608 uncurated Bundled Bundled Nucleus with heavily indented nuclear membrane, giving the appearance of one or more lobes. sao301169922 sao301169922 uncurated Lobulated Nucleus Lobulated Nucleus sao311075036 sao311075036 uncurated Cell Body Referent Polarity Cell Body Referent Polarity CL:0000125 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. sao313023570 neuroglial cell C0027836 sao313023570 uncurated Cell Type Ontology (Reichenbach and Wolburg) Glial Cell Glial Cell Transport in the direction towards the cell soma. sao31662418 C0598953 sao31662418 Retrograde Transport Retrograde Transport sao3169628 sao3169628 uncurated Stacked Stacked sao317384566 sao317384566 uncurated Stubby Dendritic Spine Stubby Dendritic Spine Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology) 0030061 sao333328131 C0230844 sao333328131 uncurated Cristae Cristae GFAP The major component of glia-specific intermediate filament primarily found in astrocytes and Bergmann glia. sao333741607 C0017626 sao333741607 uncurated Glial Fibrillary Acidic Protein Glial Fibrillary Acidic Protein One of two globular polypeptides forming microtubules. sao335197072 C0002318 sao335197072 uncurated Alpha Tubulin Alpha Tubulin sao340271629 sao340271629 uncurated 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 Regional Part Of Cell Maryann Martone The shape of the nucleus, e.g., round, lobulated, indented sao343486489 sao343486489 uncurated Nucleus Type Nucleus Type sao349337269 sao349337269 uncurated Need to define property with "reference point" Polarity Polarity Substantia nigra pars compacta false projection neuron multipolar 1 sao34994437 sao34994437 true uncurated Substantia Nigra Dopaminergic Cell Substantia Nigra Dopaminergic Cell Morphological state characterized by an expanded matrix space and contracted intracristal space; observed experimentally when ADP is added (Mannella et al., 2001). sao358853874 sao358853874 uncurated Orthodox Orthodox 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) sao3593465546 sao3593465546 true Ependymoglial Cell Ependymoglial Cell sao359916506 sao359916506 uncurated Myelin Subcompartment Myelin Subcompartment NCAM 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) sao365780568 C0282587 sao365780568 uncurated Neural Cell Adhesion Molecule Neural Cell Adhesion Molecule sao369353782 sao369353782 uncurated ANT-2 ANT-2 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). 0008076 sao371494298 C0814023 sao371494298 uncurated Voltage Gated Potassium Channel Voltage Gated Potassium Channel Astrocyte characterized by spongy appearance and many vellous processes; often found in gray matter. sao374942934 GluT Astrocyte Passive Astrocyte C0228089 sao374942934 true uncurated Protoplasmic Astrocyte Protoplasmic Astrocyte sao376700953 C0163743 sao376700953 uncurated Connexin 32 Connexin 32 sao383526650 sao383526650 true uncurated Hippocampal CA3 Pyramidal Neuron Hippocampal CA3 Pyramidal Neuron sao383990749 sao383990749 uncurated IP3R Type 1 IP3R Type 1 sao386529203 sao386529203 Pre-synaptic Component Pre-synaptic Component Terminal process of astrocyte abutting non-neuronal surfaces in the brain. sao388182739 sao388182739 graph position temporary uncurated Endfoot Endfoot Large astrocyte that forms a layer that lies beneath the ependymal layer. sao399295448 sao399295448 true uncurated Sub-ependymal Astrocyte Sub-ependymal Astrocyte Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991). sao401910342 sao401910342 uncurated Somatic Portion Somatic Portion Synaptic vesicle docked at the pre-synaptic active zone. sao403156667 sao403156667 uncurated Docked Vesicle Docked Vesicle PNS CL:0000218 Neuroglial cells of the peripheral nervous system which form the insulating myelin sheaths of peripheral axons (MSH). sao408819766 C0036387 sao408819766 true uncurated Note that the cell type ontology does not consider Schwann Cells to be macroglia Schwann Cell Schwann Cell Ramification of basket cell axon surrounding cell bodies, forming the characteristic peri-cellular baskets from which the cell class derives its name. sao413722576 sao413722576 uncurated Peri Cellular Basket Peri Cellular Basket 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). 0043227 sao414196390 sao414196390 uncurated Membrane Bound Organelle Membrane Bound Organelle sao420754792 sao420754792 uncurated Regional Part Of Dendrite Regional Part Of Dendrite 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 0005918 sao427941916 sao427941916 graph position temporary Septate Junction Septate Junction CL:0000589 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) sao429277527 C0018497 sao429277527 true uncurated UMLS Cochlear Inner Hair Cell Cochlear Inner Hair Cell Oriented parallel to the long axis. sao430240391 sao430240391 uncurated Longitudinal Longitudinal Type of VIP containing neuron found in the visiual cortex. sao436474611 sao436474611 true uncurated Cortical Bipolar Cell Cortical Bipolar Cell CL:0000066 Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH). sao441624014 C0014597 sao441624014 uncurated Epithelial Cell Epithelial Cell 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. 0005922 sao445019788 hemichannel, connexon complex C0230609 sao445019788 uncurated Wikipedia Connexon Connexon A dispersed and relatively uncompacted form of chromatin (Gene Ontology). 0000791 sao445485807 euchromatin sao445485807 uncurated Extended Chromatin Extended Chromatin Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000). sao447856407 sao447856407 uncurated Contact Site Contact Site 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) 0005794 sao451912436 golgi cisternae C0018042 sao451912436 uncurated Golgi Apparatus Golgi Apparatus sao452970150 C0230664 sao452970150 uncurated Membrane Receptor Membrane Receptor 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). sao454034570 C0012854 sao454034570 uncurated DNA DNA 68 kd Neurofilament protein with molecular weight approximately 68 kd. sao460214456 sao460214456 uncurated Neurofilament 68kd Neurofilament 68kd sao467424240 sao467424240 uncurated progenitor cell Precursor Cell Precursor Cell sao468574704 C0872241 sao468574704 uncurated PDZ Containing Protein PDZ Containing Protein 1 2 cerebellar cortex true projection neuron 1 CL:0000121 Large branching neurons of the middle layer of cerebellar cortex, characterized by vast arrays of dendrites; involved in controlling complex movements (CSP). sao471801888 Purkinje neuron C0034143 sao471801888 true uncurated Purkinje Cell Purkinje Cell Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells. sao478230652 sao478230652 uncurated Granular Vesicle Granular Vesicle Nucleus with smooth membrane and no large folds or lobules. sao47950958 sao47950958 uncurated Smooth Nucleus Smooth Nucleus sao483834130 C0255106 sao483834130 uncurated KIF3A KIF3A sao484101752 sao484101752 uncurated oligodendrocyte progenitor cell Activated Oligodendrocyte Precursor Cell Activated Oligodendrocyte Precursor Cell sao488120195 sao488120195 uncurated Calyx Calyx Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004). sao494258938 sao494258938 uncurated Active Zone Dense Projection Active Zone Dense Projection sao497641585 sao497641585 uncurated Branched Branched 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). Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies. 0005777 sao499555322 C0752063 sao499555322 uncurated Peroxisome Peroxisome sao500241072 sao500241072 uncurated Want to organize this more carefully in the next version of the SAo Molecule Molecule sao503947499 sao503947499 uncurated Pre-synaptic Subcomponent Pre-synaptic Subcomponent Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology). 0016604 sao505137457 C0230595 sao505137457 uncurated Nuclear Body Nuclear Body sao506721981 sao506721981 uncurated Laminated Body Laminated Body A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles. sao508165343 sao508165343 uncurated Supra Cellular Structure Supra Cellular Structure The space bounded by the cristae membrane sao508958414 sao508958414 true uncurated Intracristal Space Intracristal Space 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. sao515196263 sao515196263 true definition incomplete Type III IV Oligodendrocyte Type III/IV Oligodendrocyte Type III IV Oligodendrocyte 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 sao517367952 Endocytic Zone Endocytic Zone 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). sao519252327 myocyte C0596981 sao519252327 uncurated Muscle Cell Muscle Cell Major protein of the polyhedral coat of coated pits and vesicles (EMBL-EBI). sao5277619 C0008905 sao5277619 uncurated Clathrin Clathrin Schwann cell that forms a simple ensheathment around axons. sao528084208 sao528084208 uncurated Non Myelinating Schwann Cell Non Myelinating Schwann Cell Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial genome is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins (MSH). sao529397229 C0012929 sao529397229 uncurated Mitochondrial DNA Mitochondrial DNA 0008091 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). 0008091 sao536287099 C0037799 sao536287099 uncurated Spectrin Spectrin anterior ventral cochlear nucleus sao538050329 sao538050329 true uncurated Globular Bushy Cell Globular Bushy Cell 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 C0923871 sao542191739 uncurated Adjacency Adjacency Elongated shape that tapers at both ends sao542875575 Spindle sao542875575 curation complete Fusiform Fusiform sao546569295 sao546569295 uncurated Non Myelinating Oligodendrocyte Non Myelinating Oligodendrocyte Indicates that the feature exists in isolation, e.g., single filaments as opposed to bundled filaments. sao548826380 sao548826380 uncurated Single Single sao553711217 sao553711217 Spine Related Site Spine Related Site sao553737851 sao553737851 uncurated Spinule Spinule sao553876173 sao553876173 uncurated Regional Part Of Dendritic Tree Regional Part Of Dendritic Tree sao561419532 sao561419532 uncurated Golgi Lamellae Golgi Lamellae 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 C0034667 sao571652273 uncurated Node Of Ranvier Node Of Ranvier Category for vesicles observed in electron micrographs with unknown function. sao577473346 sao577473346 uncurated Vesicle Other Vesicle Other A compact and highly condensed form of chromatin (Gene Ontology). Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope. 0000792 sao581845896 heterochromatin sao581845896 uncurated Condensed Chromatin Condensed Chromatin 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). 0005764 sao585356902 C0024369 sao585356902 uncurated Lysosome Lysosome 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). sao587592318 C0034828 sao587592318 uncurated Neurotransmitter Receptor Neurotransmitter Receptor Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets. sao587858733 sao587858733 uncurated Glomerulus Glomerulus PDGF 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). sao603947546 C0032200 sao603947546 uncurated Platelet Derived Growth Factor Platelet Derived Growth Factor sao607850352 sao607850352 uncurated ANT-1 ANT-1 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 C0007004 sao607978678 uncurated Carbohydrate Carbohydrate 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). sao614188547 sao614188547 uncurated Simple Simple sao614641003 sao614641003 uncurated Cristae Membrane Cristae Membrane sao615619190 sao615619190 uncurated Respiratory Chain Complex Respiratory Chain Complex sao618069210 sao618069210 uncurated RSlo RSlo CL:0000681 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). sao621772985 radial glial cell C0815005 sao621772985 true uncurated Radial Glia Radial Glia sao624292949 sao624292949 uncurated Golgi Subcomponent Golgi Subcomponent 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) sao6261208102 sao6261208102 true graph position temporary Radial Astrocyte Radial Astrocyte sao627060194 sao627060194 Cell Secretion Cell Secretion 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). 0043203 sao627227260 C0228079 sao627227260 uncurated Axon Hillock Axon Hillock sao627589531 sao627589531 uncurated Post-synaptic Subcomponent Post-synaptic Subcomponent sao628508602 sao628508602 uncurated Cellular Subcomponent Cellular Subcomponent sao630204337 sao630204337 uncurated Cytoskeletal Associated Protein Cytoskeletal Associated Protein sao630986029 sao630986029 true uncurated Cochlear Hair Cell Cochlear Hair Cell sao632188024 sao632188024 uncurated Cis Face Cis Face sao632949619 sao632949619 uncurated Radius Radius Characterized by a high density of dendritic spines. sao638749545 sao638749545 uncurated Spiny Spiny sao642625418 sao642625418 uncurated PSD95 PSD95 sao647178911 sao647178911 true uncurated Beta Tanycyte Beta Tanycyte Mobility that is mediated by the actin cytoskeleton. sao656094176 sao656094176 Actin Based Motility Actin Based Motility CL:0000746 Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH). sao658938043 cardiac myocyte C0225828 sao658938043 uncurated Cardiac Muscle Cell Cardiac Muscle Cell That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology). 0005654 sao661522542 C0682537 sao661522542 uncurated Nucleoplasm Nucleoplasm 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). sao666200564 C0032824 sao666200564 uncurated Potassium Channel Potassium Channel sao666410040 sao666410040 uncurated Mitochondrial Subcomponent Mitochondrial Subcomponent CNS local circuit neuron multipolar 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. sao666951243 sao666951243 true uncurated Cerebellar Basket Cell Cerebellar Basket Cell sao671299150 sao671299150 Post-synaptic Subcompartment Post-synaptic Subcompartment sao671419673 sao671419673 uncurated Microvilli Microvilli sao673040867 sao673040867 uncurated Membranous Inclusion Membranous Inclusion sao675186109 sao675186109 uncurated Minus To Plus Minus To Plus 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). sao676858164 non-striated muscle cell C1135918 sao676858164 uncurated UMLS Smooth Muscle Cell Smooth Muscle Cell Oriented orthogonal to the long axis. sao679027665 sao679027665 uncurated Transverse Transverse A heterodimer of tubulins alpha and beta that constitutes the protomer for microtubule assembly (Gene Ontology). sao680848918 C1166787 sao680848918 uncurated Tubulin Tubulin tPA Extracellular tissue protease that degrades a wide spectrum of extracellular matrix proteins. sao681020632 C0032143 sao681020632 uncurated Tissue Plasminogen Activator Tissue Plasminogen Activator neostriatum CNS true projection neuron multipolar BF_C000100 sao68203136 Medium Spiny Neuron sao68203136 true uncurated Medium Spiny Cell Medium Spiny Cell sao685712019 sao685712019 uncurated Regional Part Of Astrocyte Regional Part Of Astrocyte sao692404013 C0166894 sao692404013 uncurated Neurotrophin-4 Neurotrophin-4 sao6934064108 sao6934064108 uncurated small numerous cell Granule Granule Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002). sao694815499 sao694815499 uncurated Coated Tip Coated Tip sao696157048 sao696157048 uncurated EAAT4 EAAT4 sao698543279 C0528009 sao698543279 uncurated ERp57 ERp57 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. sao700839054 sao700839054 Need to determine what is the proper relationships between an electrotonic synapse and a gap junction Gap Junction Plaque Gap Junction Plaque sao701966895 sao701966895 uncurated Degradative Enzyme Degradative Enzyme Refers to the bundled configuration of microtubules in the axon hillock and initial segment. sao707332678 sao707332678 uncurated Axon Microtubule Fascicle Axon Microtubule Fascicle CL:0000609 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. sao709770772 C0206511 sao709770772 true uncurated UMLS Vestibular Hair Cell Vestibular Hair Cell 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). 0005790 sao710427438 C0230789 sao710427438 uncurated Smooth Endoplasmic Reticulum Smooth Endoplasmic Reticulum 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). sao711465902 C0036751 sao711465902 uncurated Serotonin Serotonin A synthetic enzyme that catalyzes the formation of acetylcholine from acetyl-CoA and choline. EC 2.3.1.6 (MSH). sao722953401 C0008407 sao722953401 uncurated Choline Acetyltransferase Choline Acetyltransferase These relationships are modeled after the spatial relationships contained in the FMA. sao723896903 sao723896903 uncurated Spatial Relationship Spatial Relationship A specialization of the endomembrane system found in some classes of spines consisting of two or more closely apposed lamellae with interspersed dense material. sao725931194 C0230810 sao725931194 uncurated Spine Apparatus Spine Apparatus 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). 0051325 sao727427771 C0021798 sao727427771 Interphase Interphase An electron dense body, some of which contain granules (Peters, Palay and Webster (1991) sao730872736 sao730872736 graph position temporary Not clear if this should be described as an organelle or an inclusion. Dense Body Dense Body 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 sao732341560 uncurated Pinceau Pinceau sao732945962 sao732945962 uncurated Anatomical Pattern Anatomical Pattern sao73984422 sao73984422 Primary Culture Primary Culture sao743185455 sao743185455 uncurated Kinase Kinase Cellular inclusions associated with pathological conditions. sao74391158 sao74391158 uncurated Pathological Pathological Characterized by a terminal tuft. sao754373097 sao754373097 uncurated Tufted Tufted Region of nodal complex adjacent to the paranode sao758620702 sao758620702 Juxtaparanode Juxtaparanode false A non-pyramidal neuron class found primarily in layer IV of mammalian neocortex characterized by relatively smooth dendrites (While and Rock, 1980). sao770302354 sao770302354 true uncurated Cortical Smooth Stellate Cell Cortical Smooth Stellate Cell 40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991). sao772007592 C0887944 sao772007592 uncurated Dense Core Vesicle Dense Core Vesicle 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) sao775011514 C0014063 sao775011514 uncurated Myelin Basic Protein Myelin Basic Protein sao776599268 sao776599268 true uncurated Olfactory Granule Cell Olfactory Granule Cell sao783352775 sao783352775 uncurated Pial Cell Pial Cell Ending of a process furthest from the cell soma. sao783483540 sao783483540 uncurated Distal End Distal End A sodium channel in a cell membrane whose opening is governed by the membrane potential (Gene Ontology). 0001518 sao785001660 C1153465 sao785001660 uncurated Voltage Gated Sodium Channel Voltage Gated Sodium Channel motor cortex primate Giant pyramidal neuron found in primate motor cortex. sao786552500 C0228073 sao786552500 true uncurated Betz Cell Betz Cell 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). 0005929 sao787716553 C0008778 sao787716553 uncurated Cilium Cilium CNS multipolar CL:0000129 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. sao789292116 microglial cell C0206116 sao789292116 uncurated Cell Ontology Microglia Microglia sao791350993 sao791350993 uncurated Transporter Transporter A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology). 0048786 sao792027222 sao792027222 uncurated Pre-synaptic Active Zone Pre-synaptic Active Zone Schwann cell that apposes or encapsulates neuronal perikarya (Peters, Palay and Webster, 1991). sao792373294 sao792373294 true uncurated Satellite Cell Satellite Cell Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes. sao793088923 sao793088923 uncurated Nissl Body Nissl Body 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). sao794753833 C0080093 sao794753833 uncurated NMDA Receptor NMDA Receptor The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology). 0031983 sao797538226 sao797538226 uncurated Vesicle Lumen Vesicle Lumen sao809320003 sao809320003 uncurated En Passant En Passant sao811908115 sao811908115 uncurated Actin Associated Protein Actin Associated Protein Ending of a process closest to the cell soma. sao812067870 sao812067870 uncurated Proximal End Proximal End sao816233655 sao816233655 true uncurated Layer 2 3 Pyramidal Neuron Layer 2 3 Pyramidal Neuron sao818838791 sao818838791 definition incomplete Component Part Of Component Part Of sao819188787 sao819188787 Acute Slice Acute Slice 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). 0005798 sao819927218 C0230767 sao819927218 uncurated Golgi-associated Vesicle Golgi-associated Vesicle CL:0000737 sao82362520 sao82362520 uncurated Striated Muscle Cell Striated Muscle Cell 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 sao824839913 uncurated Cross Section Diameter Major Cross Section Diameter Major sao830092290 sao830092290 uncurated Internode Axon Internode Axon hippocampal area CA1 1 sao830368389 sao830368389 true uncurated Hippocampal CA1 Pyramidal Neuron Hippocampal CA1 Pyramidal Neuron sao830981606 sao830981606 uncurated Intracellular Membrane Intracellular Membrane sao831502550 sao831502550 uncurated Regional Part Of Oligodendrocyte Regional Part Of Oligodendrocyte sao832793084 sao832793084 Slice Preparation Slice Preparation sao833348185 sao833348185 uncurated SERCA2a SERCA2a High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages (MSH). sao83745184 C0028606 sao83745184 uncurated Nucleic Acid Nucleic Acid Pyramidal neuron whose cell soma resides in layer 5 or whose connectivity patterns resemble layer 5 neurons. sao840814183 sao840814183 true uncurated Layer 5 Pyramidal Neuron Layer 5 Pyramidal Neuron Oligodendrocyte that forms compact myelin sheath. sao841915587 C0129447 sao841915587 uncurated Myelinating Oligodendrocyte Myelinating Oligodendrocyte CNS CL:0000128 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). sao844118448 oligodendroglia C0028944 sao844118448 true uncurated Oligodendrocyte Oligodendrocyte Parts of a supracellular object, e.g., synapse. sao85163621 sao85163621 We have not yet decided whether they are regional parts of some other sort. So for now, they are just parts. Supracellular Object Part Supracellular Object Part Characterized by many shapes in glutaraldehyde fixed tissue. sao854959971 sao854959971 uncurated Pleomorphic Pleomorphic Epithelial cell lining the ventricles. sao855466308 sao855466308 uncurated Ventricular Epithelial Cell Ventricular Epithelial Cell sao856608566 sao856608566 uncurated F-actin F-actin sao862229532 sao862229532 uncurated Protocadherin Protocadherin multipolar 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). sao862606388 C0206441 sao862606388 true uncurated UMLS Pyramidal Cell Pyramidal Cell sao864921383 neuron compartment sao864921383 uncurated Regional Part Of Neuron Regional Part Of Neuron sao866168499 sao866168499 uncurated Regional Part Of Spine Regional Part Of Spine sao877341397 sao877341397 uncurated Regional Part Of Tanycyte Regional Part Of Tanycyte sao879381135 sao879381135 uncurated Endosomal Subcompartment Endosomal Subcompartment 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). 0030118 sao879919129 C1166728 sao879919129 uncurated Clathrin Coat Clathrin Coat Refers to dendrites arising from another dendrite. sao884265541 sao884265541 uncurated Dendritic Branch Dendritic Branch sao885184181 C0295347 sao885184181 uncurated SAP97 SAP97 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). 0030133 sao885490876 secretory vesicle C0887882 sao885490876 uncurated Transport Vesicle Transport Vesicle sao888175480 sao888175480 uncurated Width Width 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). 0051323 sao888950834 C0025564 sao888950834 Metaphase Metaphase sao895885284 sao895885284 uncurated Regional Part Of Glia Regional Part Of Glia Indicates that a feature was described in intact tissue. sao897115057 sao897115057 In Vivo In Vivo olfactory bulb projection neuron 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. Definition was modified from that in Wikipedia by MM sao900005350 sao900005350 true uncurated Wikipedia Mitral Cell mitral cell Mitral Cell 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). sao901230115 sao901230115 uncurated Neck Portion uncurated Neck Portion sao903454364 sao903454364 uncurated Regional Part Of Mitochondria Regional Part Of Mitochondria 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). sao906421617 C0040648 sao906421617 uncurated Transcription Factor Transcription Factor 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). sao908816138 C0174045 sao908816138 uncurated Rho GTPase Rho GTPase cerebral cortex CNS local circuit neuron 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 sao910084726 true uncurated Double Bouquet Cell Double Bouquet Cell 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). 0045202 sao914572699 sao914572699 uncurated Synapse Synapse Cell adhesion molecule expressed at neuronal surface. sao915541959 sao915541959 uncurated L1 L1 Portion of myelin-forming Schwann cell consisting of terminal cytoplasmic extensions adhered to the axon at the beginning and end of the myelin sheath. sao924713546 sao924713546 uncurated Terminal Loop Terminal Loop 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 C0001271 sao925531236 uncurated Actin Actin Generally star shaped multipoloar cell shpae with spherically extending processes sao9271919883 sao9271919883 uncurated Stellate Stellate The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology). 0048238 sao927884761 smooth endoplasmic reticulum lumen sao927884761 uncurated SER Lumen SER Lumen sao936144858 sao936144858 uncurated Paranode Axon Paranode Axon sao936599761 sao936599761 uncurated Synaptic Vesicle Associated Protein Synaptic Vesicle Associated Protein Paranodal terminations of Schwann cells that do not directly contact the paranodal axon membane. Usually found in thicker myelin. (Sosinsky et al., 2005) sao937871668 sao937871668 uncurated Spiny Bracelet Of Nageotte Spiny Bracelet Of Nageotte Embryonic cell that develops into a neuron (CSP). sao938060309 Nerve stem cell C1113654 sao938060309 uncurated Neural Stem Cell Neural Stem Cell sao938874695 sao938874695 Cell Line Cell Line 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 C0022009 sao940366596 uncurated Ion Channel Ion Channel sao941107815 sao941107815 uncurated Part Of Synapse Part Of Synapse Also refers to a stubby spine. sao941226261 sao941226261 uncurated Sessile Sessile 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). sao941755985 C0023789 sao941755985 uncurated Lipofuscin Lipofuscin 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). 0005802 sao9456487 C0887838 sao9456487 uncurated Trans Golgi Network Trans Golgi Network IL-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). sao950082944 C0021755 sao950082944 uncurated Interleukin-1 Interleukin-1 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). 0005814 sao95019936 C0007708 sao95019936 uncurated Centriole Centriole 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). 0005882 sao952483289 C0021770 sao952483289 uncurated Intermediate Filament Intermediate Filament sao952643730 sao952643730 uncurated Spine Head Spine Head A protein that speeds up chemical reactions in the body (PDQ). sao956358115 C0014442 sao956358115 uncurated Enzyme Enzyme Generally round shape where minimum diameter and maximum diameter are roughly the same sao957949983 sao957949983 curation complete Spherical Spherical 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) sao960745141 C0054493 sao960745141 uncurated Ryanodine Receptor Ryanodine Receptor sao967304317 sao967304317 uncurated Round Clear Round Clear 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) sao967812059 sao967812059 uncurated Fibrillary Inclusion Fibrillary Inclusion 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). sao968946794 C0017890 sao968946794 uncurated Glycine Glycine sao969067581 C0934150 sao969067581 uncurated Continuity Continuity sao971374186 sao971374186 true uncurated Alpha Tanycyte Alpha Tanycyte Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin. sao976831666 sao976831666 Lumen Cargo Lumen Cargo sao978443756 sao978443756 uncurated Endosomal Membrane Endosomal Membrane sao991156472 sao991156472 Cell Component Aggregate Object Cell Component Aggregate Object 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). sao992093782 C0599635 sao992093782 uncurated Water Channel Water Channel Transport in the direction away from the cell soma. sao992129328 C0598952 sao992129328 Anterograde Transport Anterograde Transport sao99825125 sao99825125 uncurated Alpha 3 Acetylcholine Receptor Alpha 3 Acetylcholine Receptor bfo:Entity entity snap: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 continuant snap:DependentContinuant 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 dependent_continuant snap: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. disposition snap:FiatObjectPart 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 fiat_object_part snap: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 function snap:IndependentContinuant 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 independent_continuant snap: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 snap:ObjectAggregate 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_aggregate snap:ObjectBoundary 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 object_boundary snap:OneDimensionalRegion 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 one_dimensional_region snap: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 quality snap:RealizableEntity 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 realizable_entity snap: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 role snap: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. site snap:SpatialRegion 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 spatial_region snap:ThreeDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with three dimensions. Examples: a cube-shaped part of space, a sphere-shaped part of space three_dimensional_region snap:TwoDimensionalRegion 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 two_dimensional_region snap:ZeroDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with no dimensions. Examples: a point zero_dimensional_region span:ConnectedSpatiotemporalRegion 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_spatiotemporal_region span:ConnectedTemporalRegion 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 connected_temporal_region span:FiatProcessPart 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 fiat_process_part span: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 occurrent span: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 span:ProcessAggregate 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_aggregate span:ProcessBoundary 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 process_boundary span:ProcessualContext 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_context span:ProcessualEntity 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 processual_entity span:ScatteredSpatiotemporalRegion 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_spatiotemporal_region span:ScatteredTemporalRegion 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 scattered_temporal_region span:SpatiotemporalInstant 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_instant span:SpatiotemporalInterval 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_interval span:SpatiotemporalRegion 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 spatiotemporal_region span:TemporalInstant 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_instant span:TemporalInterval 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_interval span:TemporalRegion 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 temporal_region owl:Thing Version 1.2 Maryann Martone, Lisa Fong, Stephen D. Larson, Lily Chen, and Amarnath Gupta July 06, 2007 Ontology for the subcellular anatomy of the nervous system Subcellular Anatomy Ontology (SAO) uncurated Release Notes: 1.1 - 05/28/2007 Added definitions Modified Non-neuronal cell types, especially glial types Simplified properties Did a lot of work cleaning up restrictions 1.2 - 07/06/2007 Restructured cell class hierarchy for glia and epithelial cells Converted SAO class names into SAO ids Made SAO OWL-DL compliant Checked and corrected consistency and satisfiability issues Version 1.2 Alan Ruttenberg Andrew Spear Pierre Grenon Holger Stenzhorn application/rdf+xml http://www.ifomis.org/bfo/1.0 en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://creativecommons.org/licenses/by/3.0 Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Barry Smith: "Against Fantology" Barry Smith: "Basic Tools of Formal Ontology" Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Basic Formal Ontology (BFO) 1.0