Subcellular Anatomy Ontology (SAO)
type: Ontology
comment: 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
creator: Maryann Martone, Lisa Fong, Stephen D. Larson, Lily Chen, and Amarnath Gupta
subject: Ontology for the subcellular anatomy of the nervous system
date: July 06, 2007
version info: Version 1.2
imports: http://www.ifomis.org/bfo/1.0
curation status: uncurated

Vesicle Binding Protein
type: Class
subclass of: Synaptic Vesicle Associated Protein
curation status: uncurated
sao ID: sao1624466407

Synaptic Vesicle Associated Protein
type: Class
disjoint with: Clathrin
disjoint with: Enzyme
subclass of: Protein
disjoint with: Membrane Receptor
curation status: uncurated
disjoint with: Transporter Protein
disjoint with: Extracellular Matrix Protein
disjoint with: Respiratory Chain Complex
disjoint with: Membrane Pump
disjoint with: PDZ Containing Protein
disjoint with: Myelin Associated Protein
sao ID: sao936599761

Obsolete class
type: Class
sao ID: sao-943768255

Modified Astrocyte
type: Class
subclass of: Obsolete class
disjoint with: Astrocyte
disjoint with: Oligodendrocyte
disjoint with: Pectin Glial Cell
disjoint with: Schwann Cell
sao ID: sao2022412481
curation status: uncurated
subclasses disjoint: true

Astrocyte
type: Class
subclass of: Macroglia
disjoint with: Schwann Cell
subclass of: Restriction
  on property: has Regional Part
  some values from: Regional Part Of Astrocyte
curation status: uncurated
disjoint with: Oligodendrocyte
disjoint with: Ependymoglial Cell
subclass of: Restriction
  on property: location CNS PNS
  has value: CNS
sao ID: sao1394521419
umls ID: C0004112
subclasses disjoint: true
cell ontology ID: CL:0000127
definition: 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).

Oligodendrocyte
type: Class
disjoint with: Ependymoglial Cell
subclass of: Restriction
  on property: location CNS PNS
  has value: CNS
subclasses disjoint: true
subclass of: Restriction
  all values from: Regional Part Of Oligodendrocyte
  on property: has Regional Part
umls ID: C0028944
definition: 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).
cell ontology ID: CL:0000128
disjoint with: Schwann Cell
subclass of: Macroglia
curation status: uncurated
sao ID: sao844118448
synonym: oligodendroglia

Pectin Glial Cell
type: Class
disjoint with: Pigment Epithelial Cell
disjoint with: Oligodendrocyte
subclasses disjoint: true
comment: Need to associate this with avians
disjoint with: Ependymoglial Cell
disjoint with: Choroid Epithelial Cell
disjoint with: Astrocyte
disjoint with: Ependymal Cell
curation status: graph position temporary
sao ID: sao-243744138
disjoint with: Schwann Cell
alternative label: Pecten_Glial_Cell
definition: 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.
subclass of: Macroglia

Schwann Cell
type: Class
comment: Note that the cell type ontology does not consider Schwann Cells to be macroglia
sao ID: sao408819766
umls ID: C0036387
curation status: uncurated
subclass of: Restriction
  has value: PNS
  on property: location CNS PNS
subclass of: Glial Cell
definition: Neuroglial cells of the peripheral nervous system which form the insulating myelin sheaths of peripheral axons (MSH).
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of Schwann Cell
cell ontology ID: CL:0000218
subclasses disjoint: true

Neuromuscular Junction
type: Class
subclass of: Chemical Synapse
definition: 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).
gene ontology ID: 0031594
curation status: uncurated
sao ID: sao1124888485

Chemical Synapse
type: Class
curation status: uncurated
sao ID: sao289211478
subclass of: Synapse
subclass of: Restriction
  some values from: Post-synaptic Part
  on property: has Aggregate Part
subclass of: Restriction
  some values from: Pre-synaptic Part
  on property: has Aggregate Part
subclass of: Restriction
  on property: has Aggregate Part
  some values from: Synaptic Cleft

Molecular Motor
type: Class
disjoint with: Ion Channel
definition: 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).
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Growth Factor
umls ID: C0600594
disjoint with: Transporter Protein
disjoint with: Myelin Associated Protein
sao ID: sao225178797
disjoint with: Cell Adhesion Molecule
disjoint with: Cytokine
disjoint with: Cytoskeletal Associated Protein
subclass of: Protein
disjoint with: Synapse Associated Protein
disjoint with: Membrane Pump
disjoint with: Clathrin
disjoint with: Membrane Receptor
disjoint with: PDZ Containing Protein
disjoint with: Connexin
disjoint with: Enzyme
disjoint with: Transcription Factor
disjoint with: Extracellular Matrix Protein
disjoint with: Calcium Binding Protein
curation status: uncurated
disjoint with: Respiratory Chain Complex

Ion Channel
type: Class
curation status: uncurated
disjoint with: Transporter Protein
disjoint with: Extracellular Matrix Protein
definition: 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).
disjoint with: Clathrin
umls ID: C0022009
disjoint with: Connexin
disjoint with: Enzyme
subclass of: Protein
disjoint with: PDZ Containing Protein
sao ID: sao940366596
disjoint with: Respiratory Chain Complex
disjoint with: Membrane Receptor
disjoint with: Cytokine
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Membrane Pump
disjoint with: Myelin Associated Protein

Growth Factor
type: Class
disjoint with: Ion Channel
disjoint with: Myelin Associated Protein
disjoint with: Synapse Associated Protein
umls ID: C0018284
disjoint with: Cell Adhesion Molecule
disjoint with: Membrane Pump
disjoint with: Transporter Protein
sao ID: sao1671627152
disjoint with: Connexin
disjoint with: Cytokine
curation status: uncurated
subclass of: Protein
disjoint with: Respiratory Chain Complex
disjoint with: PDZ Containing Protein
definition: Signal molecules that are involved in the control of cell growth and differentiation (MSH).
disjoint with: Clathrin
disjoint with: Membrane Receptor
disjoint with: Enzyme
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Extracellular Matrix Protein

Transporter Protein
type: Class
disjoint with: Extracellular Matrix Protein
curation status: uncurated
disjoint with: Clathrin
definition: Integral membrane proteins that transport molecules or ions into or out of the cell or compartment.
subclass of: Protein
disjoint with: Membrane Pump
disjoint with: Enzyme
disjoint with: PDZ Containing Protein
disjoint with: Membrane Receptor
sao ID: sao1165516281

Myelin Associated Protein
type: Class
disjoint with: Extracellular Matrix Protein
subclass of: Protein
curation status: uncurated
disjoint with: PDZ Containing Protein
sao ID: sao293240763
disjoint with: Transporter Protein
disjoint with: Clathrin
disjoint with: Enzyme
disjoint with: Membrane Pump
disjoint with: Membrane Receptor

Cell Adhesion Molecule
type: Class
disjoint with: Ion Channel
curation status: uncurated
disjoint with: Transporter Protein
disjoint with: Respiratory Chain Complex
disjoint with: Extracellular Matrix Protein
disjoint with: Myelin Associated Protein
disjoint with: Membrane Receptor
disjoint with: PDZ Containing Protein
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Cytokine
disjoint with: Clathrin
disjoint with: Connexin
subclass of: Protein
sao ID: sao1048879260
disjoint with: Membrane Pump
disjoint with: Enzyme

Cytokine
type: Class
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Myelin Associated Protein
disjoint with: Respiratory Chain Complex
subclass of: Protein
disjoint with: Transporter Protein
disjoint with: Clathrin
umls ID: C0079189
disjoint with: Membrane Pump
sao ID: sao1611333173
definition: 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).
disjoint with: Extracellular Matrix Protein
disjoint with: PDZ Containing Protein
disjoint with: Enzyme
disjoint with: Membrane Receptor
curation status: uncurated

Cytoskeletal Associated Protein
type: Class
disjoint with: Connexin
disjoint with: Respiratory Chain Complex
disjoint with: Cell Adhesion Molecule
disjoint with: Membrane Receptor
disjoint with: PDZ Containing Protein
disjoint with: Clathrin
subclass of: Protein
disjoint with: Cytokine
disjoint with: Myelin Associated Protein
disjoint with: Membrane Pump
curation status: uncurated
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Growth Factor
disjoint with: Extracellular Matrix Protein
disjoint with: Synapse Associated Protein
disjoint with: Transporter Protein
disjoint with: Enzyme
sao ID: sao630204337
disjoint with: Ion Channel

Protein
type: Class
subclass of: Molecule
disjoint with: Amino Acid
disjoint with: Monoamines
disjoint with: Carbohydrate
disjoint with: Neuropeptide
disjoint with: Nucleic Acid
curation status: uncurated
sao ID: sao26622963

Synapse Associated Protein
type: Class
disjoint with: Enzyme
disjoint with: Membrane Receptor
disjoint with: Respiratory Chain Complex
disjoint with: PDZ Containing Protein
disjoint with: Ion Channel
disjoint with: Connexin
disjoint with: Transporter Protein
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Clathrin
curation status: uncurated
sao ID: sao1319795695
disjoint with: Myelin Associated Protein
disjoint with: Cytokine
disjoint with: Extracellular Matrix Protein
disjoint with: Cell Adhesion Molecule
subclass of: Obsolete class
disjoint with: Membrane Pump

Membrane Pump
type: Class
sao ID: sao1091882528
disjoint with: Clathrin
disjoint with: Extracellular Matrix Protein
disjoint with: PDZ Containing Protein
disjoint with: Membrane Receptor
disjoint with: Enzyme
curation status: uncurated
subclass of: Protein

Clathrin
type: Class
umls ID: C0008905
sao ID: sao5277619
subclass of: Protein
curation status: uncurated
definition: Major protein of the polyhedral coat of coated pits and vesicles (EMBL-EBI).

Membrane Receptor
type: Class
umls ID: C0230664
disjoint with: Clathrin
sao ID: sao452970150
subclass of: Protein
curation status: uncurated

PDZ Containing Protein
type: Class
subclass of: Protein
disjoint with: Membrane Receptor
disjoint with: Extracellular Matrix Protein
disjoint with: Clathrin
disjoint with: Enzyme
umls ID: C0872241
curation status: uncurated
sao ID: sao468574704

Connexin
type: Class
disjoint with: Clathrin
disjoint with: Myelin Associated Protein
subclass of: Restriction
  on property: is Molecular Constituent Of
  some values from: Connexon
disjoint with: Transporter Protein
umls ID: C0110611
sao ID: sao2056711309
disjoint with: Membrane Receptor
curation status: uncurated
disjoint with: Respiratory Chain Complex
disjoint with: Enzyme
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: PDZ Containing Protein
subclass of: Protein
disjoint with: Membrane Pump
disjoint with: Extracellular Matrix Protein
definition: 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).
disjoint with: Cytokine

Enzyme
type: Class
disjoint with: Membrane Receptor
disjoint with: Extracellular Matrix Protein
disjoint with: Clathrin
curation status: uncurated
sao ID: sao956358115
umls ID: C0014442
definition: A protein that speeds up chemical reactions in the body (PDQ).
subclass of: Protein

Transcription Factor
type: Class
sao ID: sao906421617
disjoint with: Enzyme
disjoint with: Respiratory Chain Complex
disjoint with: Membrane Receptor
disjoint with: Cytokine
definition: 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).
disjoint with: Cytoskeletal Associated Protein
disjoint with: Clathrin
disjoint with: Extracellular Matrix Protein
subclass of: Protein
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: PDZ Containing Protein
disjoint with: Growth Factor
disjoint with: Membrane Pump
disjoint with: Synapse Associated Protein
umls ID: C0040648
disjoint with: Myelin Associated Protein
disjoint with: Connexin
disjoint with: Cell Adhesion Molecule
disjoint with: Transporter Protein
disjoint with: Ion Channel
curation status: uncurated

Extracellular Matrix Protein
type: Class
subclass of: Protein
disjoint with: Clathrin
disjoint with: Membrane Receptor
sao ID: sao1442185587
definition: 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)
curation status: uncurated
umls ID: C0079323

Calcium Binding Protein
type: Class
disjoint with: PDZ Containing Protein
disjoint with: Ion Channel
disjoint with: Membrane Receptor
disjoint with: Synapse Associated Protein
disjoint with: Extracellular Matrix Protein
disjoint with: Cytoskeletal Associated Protein
subclass of: Protein
curation status: uncurated
sao ID: sao2138417829
disjoint with: Clathrin
disjoint with: Growth Factor
disjoint with: Membrane Pump
disjoint with: Myelin Associated Protein
disjoint with: Respiratory Chain Complex
disjoint with: Transporter Protein
disjoint with: Enzyme
disjoint with: Cytokine
disjoint with: Cell Adhesion Molecule
disjoint with: Transcription Factor
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Connexin

Respiratory Chain Complex
type: Class
sao ID: sao615619190
disjoint with: PDZ Containing Protein
disjoint with: Myelin Associated Protein
disjoint with: Membrane Pump
disjoint with: Enzyme
disjoint with: Membrane Receptor
disjoint with: Extracellular Matrix Protein
disjoint with: Clathrin
disjoint with: Transporter Protein
curation status: uncurated
subclass of: Protein

Endosomal Membrane
type: Class
curation status: uncurated
disjoint with: Vesicle Membrane
subclass of: Intracellular Membrane
sao ID: sao978443756

Vesicle Membrane
type: Class
curation status: uncurated
gene ontology ID: 0012506
subclass of: Intracellular Membrane
umls ID: C1167317
definition: The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology).
sao ID: sao1153182838

Intracellular Membrane
type: Class
curation status: uncurated
disjoint with: Intracellular Membrane Formation
sao ID: sao830981606
subclass of: Cellular Component

GlurR3
type: Class
subclass of: AMPA Receptor
sao ID: sao1501064039
curation status: uncurated
umls ID: C0536486

AMPA Receptor
type: Class
sao ID: sao265434492
umls ID: C0072899
definition: 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).
curation status: uncurated
subclass of: Glutamate Receptor

Spatial Relationship
type: Class
curation status: uncurated
sao ID: sao723896903
definition: These relationships are modeled after the spatial relationships contained in the FMA.
subclass of: Anatomical Relationship

Anatomical Relationship
type: Class
curation status: uncurated
subclass of: Obsolete class
definition: Conceptual anatomical entity which describes the structural and transformation relationships between physical anatomical entities. Example: class subsumption relationship, structural relationship, anatomical tranformation relationship (FMA).
birnlex definition source: FMA
externally sourced definition: FMAID:54723
sao ID: sao1184653804
birnlex external source: FMA

Multivesicular Body
type: Class
subclass of: Membrane Bound Organelle
curation status: uncurated
gene ontology ID: 0005771
disjoint with: Peroxisome
sao ID: sao2045955158
definition: 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).
umls ID: C0230825

Membrane Bound Organelle
type: Class
curation status: uncurated
sao ID: sao414196390
gene ontology ID: 0043227
definition: 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).
subclass of: Organelle
disjoint with: Non Membrane Bound Organelle

Peroxisome
type: Class
umls ID: C0752063
sao ID: sao499555322
gene ontology ID: 0005777
curation status: uncurated
definition: Resembles lysosomes in appearance (Peters, Palay and Webster, 1991). According to the latter, peroxisome is synonymous with microbodies.
definition: 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).
subclass of: Membrane Bound Organelle

Plus To Minus
type: Class
sao ID: sao2139310701
disjoint with: Minus To Plus
curation status: uncurated
subclass of: Microtubule Polarity

Minus To Plus
type: Class
curation status: uncurated
subclass of: Microtubule Polarity
sao ID: sao675186109

Microtubule Polarity
type: Class
subclass of: Polarity
curation status: uncurated
sao ID: sao107236050
definition: Microtubules are characterized by a + and a - end and may be oriented with respect to the soma (origin) in either + to - or - to +.
disjoint with: Cell Body Referent Polarity

Volume
type: Class
sao ID: sao196989303
subclass of: Measurement
disjoint with: Half Life
disjoint with: Spacing
curation status: uncurated

Measurement
type: Class
sao ID: sao279801585
subclass of: Restriction
  has value: false
  on property: has Inherent 3D Shape
subclass of: Quality
curation status: uncurated

Half Life
type: Class
definition: Measure of turnover.
sao ID: sao124571525
subclass of: Measurement
curation status: uncurated

Spacing
type: Class
sao ID: sao2126482353
disjoint with: Half Life
definition: Refers to the average distance between features.
subclass of: Measurement
curation status: uncurated

Olig2
type: Class
sao ID: sao1701066619
subclass of: Transcription Factor
umls ID: C0912988
curation status: uncurated

Regional Part Of Dendrite
type: Class
curation status: uncurated
subclass of: Regional Part Of Neuron Process
disjoint with: Subregional Part Of Neuron Process
disjoint with: Regional Part Of Axon
sao ID: sao420754792

Regional Part Of Neuron Process
type: Class
disjoint with: Neuron Protrusion
disjoint with: Regional Part Of Neuron Protrusion
disjoint with: Neuron Process
sao ID: sao-420949334
curation status: uncurated
subclass of: Regional Part Of Neuron

Subregional Part Of Neuron Process
type: Class
sao ID: sao183270081
definition: Subcompartment of a compartment.
curation status: uncurated
subclass of: Regional Part Of Neuron Process

Regional Part Of Axon
type: Class
disjoint with: Subregional Part Of Neuron Process
curation status: uncurated
sao ID: sao280355188
subclass of: Regional Part Of Neuron Process

Prophase
type: Class
umls ID: C0033464
definition: 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).
sao ID: sao1856556831
gene ontology ID: 0051324
subclass of: Cell Cyle Phase

Cell Cyle Phase
type: Class
subclass of: Organismal Occurrent
sao ID: sao1290101869

Schmidtt-Lanterman Cleft
type: Class
disjoint with: Vesicle Lumen
disjoint with: RER Lumen
disjoint with: Mitochondrial Space
disjoint with: Endosomal Lumen
subclass of: Cellular Space
curation status: uncurated
sao ID: sao254777664
definition: 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.

Vesicle Lumen
type: Class
gene ontology ID: 0031983
subclass of: Cellular Space
curation status: uncurated
definition: The volume enclosed by the membrane or protein that forms a vesicle (Gene Ontology).
sao ID: sao797538226

RER Lumen
type: Class
synonym: rough endoplasmic reticulum lumen
definition: The volume enclosed by the membranes of the rough endoplasmic reticulum (Gene Ontology).
sao ID: sao1819509473
gene ontology ID: 0048237
subclass of: Cellular Space
curation status: uncurated
disjoint with: Vesicle Lumen

Mitochondrial Space
type: Class
sao ID: sao-343550527
disjoint with: Vesicle Lumen
disjoint with: RER Lumen
subclass of: Cellular Space
definition: Spaces defined by the inner and outer mitochondrial membranes
subclasses disjoint: true

Endosomal Lumen
type: Class
synonym: endosome lumen
gene ontology ID: 0031904
subclass of: Cellular Space
sao ID: sao1547508851
disjoint with: RER Lumen
disjoint with: Vesicle Lumen
curation status: uncurated
disjoint with: Mitochondrial Space
definition: The volume enclosed by the membranes of an endosome (Gene Ontology).

Cellular Space
type: Class
disjoint with: Cell Cell Contact Zone
disjoint with: Node Related Site
curation status: uncurated
disjoint with: Cell Interior
disjoint with: Apical Pole Of Neuron
subclass of: Restriction
  has value: false
  on property: has Inherent 3D Shape
sao ID: sao1289190043
definition: Anatomical space occurring within a cell, usually formed by intracellular membranes.
disjoint with: Basal Pole Of Neuron
subclass of: Site
disjoint with: Regional Part Of Neuronal Cell Body

Endosomal Subcompartment
type: Class
curation status: uncurated
sao ID: sao879381135
disjoint with: SER Subcompartment
subclass of: General Cell Subcompartment

SER Subcompartment
type: Class
curation status: uncurated
sao ID: sao1619512288
subclass of: General Cell Subcompartment

General Cell Subcompartment
type: Class
disjoint with: Regional Part Of Neuron
disjoint with: Cell Protrusion
disjoint with: Non Neural Cell Compartment
disjoint with: Cell Process
disjoint with: Regional Part Of Glia
subclass of: Regional Part Of Cell
definition: Subcompartmentalization of cellular structures such as organelles.
curation status: uncurated
sao ID: sao1515819812

Nerve Cell
type: Class
sao ID: sao1224657022
cell ontology ID: CL:0000710
curation status: uncurated
synonym: Neuroepithelial cell
disjoint with: Microglia
subclass of: Cell

Microglia
type: Class
synonym: microglial cell
umls ID: C0206116
cell ontology ID: CL:0000129
subclass of: Restriction
  has value: CNS
  on property: location CNS PNS
externally sourced definition: Cell Ontology
sao ID: sao789292116
subclass of: Cell
definition: 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.
curation status: uncurated
subclass of: Restriction
  has value: multipolar
  on property: process Number

Cell
type: Class
subclass of: Restriction
  on property: has Component
  some values from: Nucleus
gene ontology ID: 0005623
subclass of: Object
sao ID: sao1813327414
curation status: uncurated
subclass of: Restriction
  some values from: Cytosol
  on property: has Component
definition: 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).
cell ontology ID: CL:0000000
subclass of: Restriction
  on property: has Component
  some values from: Plasma Membrane

Microtubule
type: Class
curation status: uncurated
umls ID: C0026046
subclass of: Cytoskeletal Element
gene ontology ID: 0005874
sao ID: sao1846835077
definition: 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).

Cytoskeletal Element
type: Class
sao ID: sao1635329413
subclass of: Cellular Component
disjoint with: Vesicle
disjoint with: Intracellular Membrane Formation
disjoint with: Intracellular Membrane
curation status: uncurated

Spine Neck
type: Class
subclass of: Regional Part Of Spine
disjoint with: Spinule
synonym: pedicle
subclass of: Restriction
  on property: continuous With
  all values from: Class
    union of: Dendritic Shaft
    union of: Spine Head
sao ID: sao1642908940
curation status: uncurated
disjoint with: Spine Head
subclass of: Restriction
  on property: continuous With
  some values from: Dendritic Shaft
synonym: neck
subclass of: Restriction
  on property: continuous With
  some values from: Spine Head

Regional Part Of Spine
type: Class
sao ID: sao866168499
curation status: uncurated
subclass of: Regional Part Of Neuron
disjoint with: Neuron Process
disjoint with: Neuron Protrusion
disjoint with: Regional Part Of Neuron Protrusion
disjoint with: Regional Part Of Neuron Process

Spinule
type: Class
subclass of: Restriction
  some values from: Spine Head
  on property: continuous With
subclass of: Regional Part Of Spine
curation status: uncurated
sao ID: sao553737851

continuous With
type: ObjectProperty
sao ID: sao1896217670
curation status: graph position temporary
sub property of: associated With
comment: This idea was adopted from FMA but possibly needs reconsideration.
definition: Physical continuity between structures

Dendritic Shaft
type: Class
subclass of: Regional Part Of Spiny Dendrite
bonfire ID: BF_C000106
gene ontology ID: 0043198
curation status: uncurated
sao ID: sao2034472720
definition: Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines (Gene Ontology).

Spine Head
type: Class
subclass of: Regional Part Of Spine
subclass of: Restriction
  on property: continuous With
  some values from: Class
    union of: Spine Neck
    union of: Dendritic Shaft
curation status: uncurated
disjoint with: Spinule
sao ID: sao952643730

Hippocampal CA3 Pyramidal Neuron
type: Class
curation status: uncurated
subclass of: Hippocampal Pyramidal Neuron
subclass of: Restriction
  on property: has Regional Part
  some values from: Schaffer Collateral
sao ID: sao383526650
subclasses disjoint: true

Hippocampal Pyramidal Neuron
type: Class
subclasses disjoint: true
curation status: uncurated
subclass of: Pyramidal Cell
disjoint with: Cortical Pyramidal Neuron
sao ID: sao131261273

has Regional Part
type: TransitiveProperty
range: FiatObjectPart
sao ID: sao1434436507
inverse of: is Regional Part Of
sub property of: has Part
domain: IndependentContinuant
type: ObjectProperty

Schaffer Collateral
type: Class
definition: Axon collateral of CA3 pyramidal neurons that project to CA1 and synapse in the zona radiatum.
curation status: uncurated
sao ID: sao1950673097
subclass of: Axon Collateral

Ribbon Synapse
type: Class
definition: 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)
sao ID: sao1884931180
subclass of: Chemical Synapse
subclass of: Restriction
  some values from: Pre-synaptic Dense Body
  on property: has Aggregate Part
subclass of: Restriction
  on property: has Aggregate Part
  some values from: Pre-synaptic Ribbon
curation status: uncurated

Pre-synaptic Dense Body
type: Class
sao ID: sao1111202255
synonym: ribbon
subclass of: Pre-synaptic Component
definition: 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).

has Aggregate Part
type: ObjectProperty
domain: ObjectAggregate
inverse of: is Aggregate Part of
range: IndependentContinuant
sub property of: has Part
sao ID: sao8839644583

Pre-synaptic Ribbon
type: Class
subclass of: Pre-synaptic Component
sao ID: sao-1488888179
definition: Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster).

Clathrin Coated Vesicle
type: Class
umls ID: C0887885
curation status: uncurated
gene ontology ID: 0030136
sao ID: sao148845161
definition: A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes (Gene Ontolgoy).
subclass of: Coated Vesicle

Coated Vesicle
type: Class
disjoint with: Synaptic Vesicle
curation status: uncurated
disjoint with: Vesicle Other
disjoint with: Granular Vesicle
umls ID: C0242915
gene ontology ID: 0030135
definition: 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).
subclass of: Obsolete class
sao ID: sao1985096626
disjoint with: Transport Vesicle

Choline Acetyltransferase
type: Class
disjoint with: Tyrosine Hydroxylase
definition: A synthetic enzyme that catalyzes the formation of acetylcholine from acetyl-CoA and choline. EC 2.3.1.6 (MSH).
subclass of: Synthetic Enzyme
umls ID: C0008407
sao ID: sao722953401
curation status: uncurated

Tyrosine Hydroxylase
type: Class
sao ID: sao289587392
subclass of: Synthetic Enzyme
definition: 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).
umls ID: C0041491
curation status: uncurated

Synthetic Enzyme
type: Class
curation status: uncurated
umls ID: C0597548
subclass of: Neurotransmitter Associated Protein
sao ID: sao1246280606

Syndecan
type: Class
umls ID: C0075691
disjoint with: Neurofascin
subclass of: Cell Adhesion Molecule
definition: Family of transmembrane heparan sulfate proteoglycans (CSP - Bonfire).
sao ID: sao1417256224
curation status: uncurated

Neurofascin
type: Class
sao ID: sao189141251
umls ID: C0068587
subclass of: Cell Adhesion Molecule
curation status: uncurated

Pyramidal Cell
type: Class
cell ontology ID: CL:0000598
subclasses disjoint: true
subclass of: Restriction
  on property: has Neurotransmitter
  all values from: Glutamate
subclass of: Neuron
disjoint with: Double Bouquet Cell
subclass of: Restriction
  on property: process Number
  has value: multipolar
disjoint with: Spherical Bushy Cell
disjoint with: Cortical Stellate Cell
disjoint with: Random Cell
definition: 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).
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: Glutamate
definition source: UMLS
umls ID: C0206441
sao ID: sao862606388
curation status: uncurated
subclass of: Restriction
  on property: has Regional Part
  some values from: Neuronal Cell Body

Cortical Pyramidal Neuron
type: Class
subclass of: Pyramidal Cell
definition: Pyramidal neuron from the cerebral cortex (not including hippocampus).
sao ID: sao2128417084
curation status: uncurated
subclasses disjoint: true

Junctional Continuity
type: Class
subclass of: Continuity
definition: Indicates that two entities share a continuous space but that the continuity is formed through a specialized junctional component, e.g., gap junction.
curation status: uncurated
sao ID: sao1374293695

Continuity
type: Class
umls ID: C0934150
subclass of: Connectivity
curation status: uncurated
sao ID: sao969067581

Type III/IV Oligodendrocyte
type: Class
subclasses disjoint: true
subclass of: Interfascicular Oligodendrocyte
curation status: definition incomplete
sao ID: sao515196263
definition: 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.
label: Type III IV Oligodendrocyte

Interfascicular Oligodendrocyte
type: Class
umls ID: C0205867
curation status: uncurated
definition: White matter oligodendrocytes that may be aligned in rows (Peters, Palay and Webster, 1991).
subclasses disjoint: true
sao ID: sao1952867392
disjoint with: Perineuronal Oligodendrocyte
subclass of: Oligodendrocyte

Adjacency
type: Class
sao ID: sao542191739
definition: 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).
umls ID: C0923871
subclass of: Spatial Relationship
curation status: uncurated

Actin
type: Class
sao ID: sao925531236
subclass of: Cytoskeletal Protein
umls ID: C0001271
definition: 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).
disjoint with: Neurofilament Protein
disjoint with: Tubulin
curation status: uncurated

Cytoskeletal Protein
type: Class
curation status: uncurated
disjoint with: Extracellular Matrix Protein
sao ID: sao1593305396
disjoint with: GTPases
disjoint with: Cytokine
disjoint with: Calcium Binding Protein
disjoint with: Ion Channel
subclass of: Protein
disjoint with: Clathrin
disjoint with: Cell Adhesion Molecule
disjoint with: Transcription Factor
disjoint with: Molecular Motor
disjoint with: Myelin Associated Protein
disjoint with: Cytoskeletal Associated Protein
disjoint with: Connexin
disjoint with: Transporter Protein
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Enzyme
definition: 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).
disjoint with: Synapse Associated Protein
disjoint with: Membrane Receptor
disjoint with: Growth Factor
disjoint with: Respiratory Chain Complex
disjoint with: Membrane Pump
disjoint with: PDZ Containing Protein
umls ID: C0010852
disjoint with: Neurotransmitter Associated Protein

Neurofilament Protein
type: Class
sao ID: sao1093009192
subclass of: Cytoskeletal Protein
curation status: uncurated

Tubulin
type: Class
sao ID: sao680848918
umls ID: C1166787
definition: A heterodimer of tubulins alpha and beta that constitutes the protomer for microtubule assembly (Gene Ontology).
disjoint with: Neurofilament Protein
subclass of: Cytoskeletal Protein
curation status: uncurated

Nuclear Body
type: Class
umls ID: C0230595
disjoint with: Nucleolus
curation status: uncurated
definition: Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology).
disjoint with: Nuclear Lamina
gene ontology ID: 0016604
sao ID: sao505137457
subclass of: Nuclear Subcomponent
disjoint with: Interchromatin Granule

Nucleolus
type: Class
sao ID: sao1820400233
definition: 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).
umls ID: C0007609
gene ontology ID: 0005730
curation status: uncurated
subclass of: Nuclear Subcomponent
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of Nucleolus

Nuclear Lamina
type: Class
sao ID: sao1455996588
disjoint with: Nucleolus
disjoint with: Interchromatin Granule
subclass of: Nuclear Subcomponent
curation status: uncurated
definition: 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).
umls ID: C1136039
gene ontology ID: 0005652
definition: Meshwork of extremely fine filaments composed of polypeptides called lamins that run parallel with the inner surface of the nuclear envelope (Peters, Palay and Webster, 1991).

Nuclear Subcomponent
type: Class
subclass of: Cellular Subcomponent
sao ID: sao1499850686
curation status: uncurated

Interchromatin Granule
type: Class
curation status: uncurated
disjoint with: Nucleolus
umls ID: C0230547
sao ID: sao1049471211
definition: 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).
subclass of: Nuclear Subcomponent
gene ontology ID: 0035061

Pre-synaptic Component
type: Class
disjoint with: Post-synaptic Component
sao ID: sao386529203
subclass of: Synaptic Component

Junctional Site
type: Class
sao ID: sao1524397168
subclass of: Synaptic Site

Synaptic Site
type: Class
sao ID: sao-946766835
disjoint with: Zonula Occludens
disjoint with: Septate Junction
disjoint with: Zonula Adhaerens
disjoint with: Macular Adhaerentia
subclass of: Intercellular Junction Site

Terminal Specialization
type: Class
disjoint with: Trunk
subclass of: Regional Part Of Dendrite
sao ID: sao28175134
curation status: uncurated

Trunk
type: Class
subclass of: Regional Part Of Dendrite
sao ID: sao1078172392
curation status: uncurated

Configuration
type: Class
disjoint with: Orientation
comment: Refers to a specialized arrangements of a cellular component or other structure that is characteristic of a given region, e.g., bundled microtubules.
subclass of: Anatomical Pattern
curation status: uncurated
sao ID: sao18717211

Orientation
type: Class
curation status: uncurated
subclass of: Anatomical Pattern
sao ID: sao271899308
definition: Refers to the "entities of reference" (FMA). Location may be defined by qualitative coodrinates or absolute coordinates.

Anatomical Pattern
type: Class
subclass of: Quality
sao ID: sao732945962
disjoint with: Measurement
curation status: uncurated

Metaphase
type: Class
subclass of: Cell Cyle Phase
definition: 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).
gene ontology ID: 0051323
sao ID: sao888950834
umls ID: C0025564

location CNS PNS
type: FunctionalProperty
sao ID: sao1130665397
type: DatatypeProperty
range: DataRange
  one of: CNS
  one of: PNS
domain: Cell
comment: 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.

process Number
type: FunctionalProperty
range: DataRange
  one of: bipolar
  one of: unipolar
  one of: multipolar
domain: Class
  union of: Cell
  union of: Nerve Cell
  union of: Pericyte
comment: Describes the general morphology of a class of neurons with respect to the number of processes extending from the cell soma
sao ID: sao841626191
type: DatatypeProperty

Sidekick
type: Class
disjoint with: Cadherin
disjoint with: Neurofascin
disjoint with: Protocadherin
curation status: uncurated
subclass of: Cell Adhesion Molecule
disjoint with: Syndecan
sao ID: sao1121590138
disjoint with: Integrin
disjoint with: Contactin
disjoint with: Neurexin
disjoint with: L1
disjoint with: Neural Cell Adhesion Molecule

Cadherin
type: Class
curation status: uncurated
subclass of: Cell Adhesion Molecule
sao ID: sao1463925374
umls ID: C0006631
disjoint with: Neurofascin
disjoint with: Syndecan
disjoint with: Protocadherin
definition: 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).

Protocadherin
type: Class
subclass of: Cell Adhesion Molecule
sao ID: sao862229532
curation status: uncurated
disjoint with: Syndecan
disjoint with: Neurofascin

Integrin
type: Class
disjoint with: Neurofascin
disjoint with: Protocadherin
disjoint with: Syndecan
disjoint with: Cadherin
sao ID: sao1846292151
curation status: uncurated
subclass of: Cell Adhesion Molecule
umls ID: C0021701

Contactin
type: Class
disjoint with: Protocadherin
subclass of: Cell Adhesion Molecule
disjoint with: Neurofascin
disjoint with: Integrin
umls ID: C0056257
disjoint with: Syndecan
disjoint with: Cadherin
sao ID: sao1517449491
curation status: uncurated

Neurexin
type: Class
disjoint with: Syndecan
disjoint with: Protocadherin
sao ID: sao1172124127
disjoint with: Contactin
curation status: uncurated
disjoint with: Cadherin
disjoint with: Integrin
disjoint with: Neurofascin
subclass of: Cell Adhesion Molecule

L1
type: Class
disjoint with: Neural Cell Adhesion Molecule
disjoint with: Protocadherin
disjoint with: Integrin
disjoint with: Cadherin
disjoint with: Contactin
definition: Cell adhesion molecule expressed at neuronal surface.
subclass of: Cell Adhesion Molecule
sao ID: sao915541959
disjoint with: Neurexin
disjoint with: Neurofascin
curation status: uncurated
disjoint with: Syndecan

Neural Cell Adhesion Molecule
type: Class
definition: 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)
curation status: uncurated
subclass of: Cell Adhesion Molecule
disjoint with: Contactin
umls ID: C0282587
disjoint with: Neurofascin
abbreviation: NCAM
disjoint with: Protocadherin
disjoint with: Integrin
disjoint with: Cadherin
disjoint with: Syndecan
sao ID: sao365780568
disjoint with: Neurexin

Motility
type: Class
sao ID: sao1330317521
definition: Refers to the ability of structures to move about the cell.
subclass of: Organismal Occurrent

Organismal Occurrent
type: Class
subclass of: Biological Occurrent
comment: "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).
sao ID: sao1379576571

Intracellular Calcium Channel
type: Class
sao ID: sao1728785226
subclass of: Calcium Channel
subclass of: Restriction
  on property: location Component
  some values from: SER Membrane
curation status: uncurated

Calcium Channel
type: Class
sao ID: sao1846985919
umls ID: C0006685
disjoint with: Potassium Channel
curation status: uncurated
subclass of: Ion Channel
definition: 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).

location Component
type: ObjectProperty
range: Cellular Subcomponent
comment: Refers to the cellular component with which a feature is associated, e.g., ion receptor is associated with the plasma membrane
sao ID: sao333215121
domain: Class
  union of: Cellular Inclusion
  union of: Molecule
sub property of: anatomical Location

SER Membrane
type: Class
definition: The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology).
sao ID: sao1596955044
gene ontology ID: 0030868
curation status: uncurated
subclass of: SER Subcomponent
subclass of: Restriction
  some values from: SER Lumen
  on property: boundary Of

Calyx
type: Class
sao ID: sao488120195
subclass of: Axon Terminal
curation status: uncurated

Axon Terminal
type: Class
sao ID: sao2007137787
definition: 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).
curation status: uncurated
subclass of: Regional Part Of Axon
subclass of: Restriction
  on property: continuous With
  some values from: Axon

Cross Section Diameter Minor
type: Class
definition: Minimum diameter of a cross section through structure.
disjoint with: Spacing
disjoint with: Density
disjoint with: Half Life
subclass of: Measurement
disjoint with: Surface Area
curation status: uncurated
disjoint with: Speed
disjoint with: Volume
sao ID: sao136816674

Density
type: Class
disjoint with: Surface Area
disjoint with: Half Life
disjoint with: Volume
disjoint with: Spacing
curation status: uncurated
sao ID: sao1510923311
subclass of: Measurement

Surface Area
type: Class
sao ID: sao1788621392
curation status: uncurated
subclass of: Measurement
disjoint with: Half Life
disjoint with: Spacing
disjoint with: Volume

Speed
type: Class
subclass of: Measurement
curation status: uncurated
disjoint with: Surface Area
disjoint with: Spacing
disjoint with: Half Life
disjoint with: Density
disjoint with: Volume
sao ID: sao2102170307

Spine Type
type: Class
disjoint with: Cristae Type
disjoint with: Axon Type
disjoint with: Mitochondrial Type
disjoint with: Chemical Synapse Type
sao ID: sao1436578787
curation status: uncurated
definition: Refers to the morphological type of a spine.
subclass of: Morphological Type

Cristae Type
type: Class
subclass of: Morphological Type
disjoint with: Chemical Synapse Type
disjoint with: Mitochondrial Type
disjoint with: Axon Type
definition: Refers to the morphology of mitochondrial cristae.
sao ID: sao1843037539
curation status: uncurated

Axon Type
type: Class
curation status: uncurated
sao ID: sao2088691397
disjoint with: Mitochondrial Type
disjoint with: Chemical Synapse Type
subclass of: Morphological Type
definition: Refers to the morphology of an axon.

Mitochondrial Type
type: Class
curation status: uncurated
disjoint with: Chemical Synapse Type
subclass of: Morphological Type
sao ID: sao1562245920
definition: Refers to the morphology of mitochondria.

Chemical Synapse Type
type: Class
curation status: definition incomplete
sao ID: sao1746643703
subclass of: Morphological Type

Morphological Type
type: Class
sao ID: sao1057800815
subclass of: Quality
curation status: uncurated
disjoint with: Polarity
disjoint with: Measurement
disjoint with: Anatomical Pattern

SERCA
type: Class
curation status: uncurated
sao ID: sao163038736
definition: Calcium pump found in the membrane of the smooth endoplasmic reticulum.
subclass of: Membrane Pump

In Vivo
type: Class
sao ID: sao897115057
subclass of: Experimental Condition
definition: Indicates that a feature was described in intact tissue.

Experimental Condition
type: Class
subclass of: Obsolete class
pending action note: All experimental entities will be ported into a separate ontology based on OBI
curation status: uncurated
definition: Indicates the experimental conditions under which a feature was observed.
sao ID: sao1960697157

En Passant
type: Class
sao ID: sao809320003
curation status: uncurated
disjoint with: Terminal Bouton
subclass of: Bouton Type

Terminal Bouton
type: Class
curation status: uncurated
subclass of: Bouton Type
sao ID: sao1757774791

Bouton Type
type: Class
disjoint with: Axon Type
disjoint with: Mitochondrial Type
curation status: uncurated
disjoint with: Chemical Synapse Type
disjoint with: Vesicle Type
disjoint with: Spine Type
sao ID: sao1189513296
disjoint with: Nucleus Type
subclass of: Morphological Type
definition: Refers to the morphology of a bouton.
disjoint with: Cristae Type

Cortical Stellate Cell
type: Class
subclass of: Restriction
  on property: circuit Type
  has value: local circuit neuron
disjoint with: Double Bouquet Cell
subclass of: Neuron
disjoint with: Random Cell
curation status: uncurated
sao ID: sao164665273
disjoint with: Spherical Bushy Cell
subclass of: Restriction
  on property: anatomical Location General
  has value: cerebral cortex
cell ontology ID: CL:0000122
subclasses disjoint: true

circuit Type
type: FunctionalProperty
domain: Neuron
range: DataRange
  one of: projection neuron
  one of: local circuit neuron
sao ID: sao1967171150
type: DatatypeProperty

Double Bouquet Cell
type: Class
subclass of: Restriction
  on property: circuit Type
  has value: local circuit neuron
subclass of: Restriction
  has value: CNS
  on property: location CNS PNS
subclass of: Neuron
subclasses disjoint: true
curation status: uncurated
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: GABA
definition: 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).
sao ID: sao910084726
subclass of: Restriction
  has value: cerebral cortex
  on property: anatomical Location General

Neuron
type: Class
sao ID: sao1417703748
subclass of: Nerve Cell
umls ID: C0027882
disjoint with: Neural Stem Cell
definition: 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).
subclasses disjoint: true
disjoint with: Glial Cell
subclass of: Restriction
  some values from: Neuronal Cell Body
  on property: has Regional Part
cell ontology ID: CL:0000540
curation status: uncurated

Random Cell
type: Class
subclass of: Restriction
  on property: process Number
  has value: multipolar
subclass of: Restriction
  on property: has Regional Part
  some values from: Pyramidal Neuronal Cell Body
subclass of: Neuron
subclass of: Restriction
  some values from: Glutamate
  on property: has Neurotransmitter
sao ID: sao2127763636
disjoint with: Double Bouquet Cell
comment: created for testing purposes only

Spherical Bushy Cell
type: Class
sao ID: sao1482618768
curation status: uncurated
subclasses disjoint: true
disjoint with: Double Bouquet Cell
disjoint with: Random Cell
subclass of: Neuron
subclass of: Restriction
  on property: anatomical Location General
  has value: anterior ventral cochlear nucleus

anatomical Location General
type: DatatypeProperty
sao ID: sao1065676773
comment: 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.
comment: 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
curation status: graph position temporary
range: string

Mitochondrial Lumen
type: Class
curation status: uncurated
synonym: Inner Mitochondrial Compartment (from Peters, Palay, and Webster)
gene ontology ID: 0031980
subclasses disjoint: true
sao ID: sao-1899375636
definition: 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.
subclass of: Mitochondrial Space

Eye Photoreceptor Cell
type: Class
sao ID: sao226523927
cell ontology ID: CL:0000287
subclass of: Photoreceptor Cell
curation status: uncurated

Photoreceptor Cell
type: Class
curation status: uncurated
sao ID: sao1233810115
cell ontology ID: CL:0000210
definition: A cell specialized to detect and transduce light (MESH).
subclass of: Neuron
disjoint with: Double Bouquet Cell
disjoint with: Cortical Stellate Cell
disjoint with: Motor Neuron
disjoint with: Random Cell
disjoint with: Olfactory Granule Cell
subclasses disjoint: true
disjoint with: mitral cell
disjoint with: Spherical Bushy Cell
disjoint with: Pyramidal Cell

Axon Collateral
type: Class
subclass of: Regional Part Of Axon
definition: Smaller branches of an axon that emanate from the main axon cylinder.
sao ID: sao1470140754
curation status: uncurated
disjoint with: Axon Terminal
disjoint with: Axon Hillock
disjoint with: Regional Part Of Basket Cell Axon
disjoint with: Axonal Growth Cone

Axon Hillock
type: Class
definition: 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).
disjoint with: Axonal Growth Cone
subclass of: Regional Part Of Axon
subclass of: Restriction
  some values from: Axon
  on property: continuous With
sao ID: sao627227260
umls ID: C0228079
disjoint with: Axon Terminal
gene ontology ID: 0043203
curation status: uncurated
disjoint with: Regional Part Of Basket Cell Axon

Regional Part Of Basket Cell Axon
type: Class
subclass of: Regional Part Of Axon
curation status: uncurated
definition: Terminal pre-synaptic ending of an axon or axon collateral.
sao ID: sao1586851177
disjoint with: Axon Terminal
disjoint with: Axonal Growth Cone

Axonal Growth Cone
type: Class
subclass of: Regional Part Of Axon
curation status: uncurated
sao ID: sao203987954
disjoint with: Axon Terminal

Secondary Lysosome
type: Class
sao ID: sao1549842807
umls ID: C0230815
gene ontology ID: 0005767
definition: Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology).
subclass of: Lysosome
curation status: uncurated

Lysosome
type: Class
umls ID: C0024369
curation status: uncurated
subclass of: Membrane Bound Organelle
gene ontology ID: 0005764
disjoint with: Multivesicular Body
disjoint with: Peroxisome
sao ID: sao585356902
definition: 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).

Monoamines
type: Class
sao ID: sao1430127373
subclass of: Molecule

Molecule
type: Class
sao ID: sao500241072
curation status: uncurated
comment: Want to organize this more carefully in the next version of the SAo
subclass of: Object

Regional Part Of Neuronal Cell Body
type: Class
disjoint with: Basal Pole Of Neuron
disjoint with: Node Related Site
disjoint with: Cell Interior
disjoint with: Apical Pole Of Neuron
disjoint with: Cell Cell Contact Zone
sao ID: sao1049717962
curation status: uncurated
subclass of: Regional Part Of Neuron

Basal Pole Of Neuron
type: Class
subclass of: Site
curation status: uncurated
definition: Portion of a cell soma closest to the point where the basilar dendrite emerges.
sao ID: sao1186862860

Node Related Site
type: Class
sao ID: sao-596411490
subclass of: Site
disjoint with: Basal Pole Of Neuron
definition: Site defined with respect to the Node of Ranvier, e.g., node, paranode, juxtaparanode

Cell Interior
type: Class
sao ID: sao1579007712
disjoint with: Basal Pole Of Neuron
disjoint with: Node Related Site
curation status: uncurated
subclass of: Site

Apical Pole Of Neuron
type: Class
curation status: uncurated
subclass of: Site
sao ID: sao1877927224
definition: Portion of a cell soma closest to the point where the apical dendrite emerges.
disjoint with: Node Related Site
disjoint with: Basal Pole Of Neuron
disjoint with: Cell Interior

Cell Cell Contact Zone
type: Class
definition: Extended zone of intimate apposition between two cells containing one or more types of intercellular junctions, e.g., the intercalated disk of muscle
contributor: Maryann Martone
comment: 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
sao ID: sao1299635018
disjoint with: Node Related Site
disjoint with: Cell Interior
curation status: uncurated
disjoint with: Basal Pole Of Neuron
subclass of: Site
disjoint with: Apical Pole Of Neuron

Regional Part Of Neuron
type: Class
sao ID: sao864921383
subclass of: Regional Part Of Cell
synonym: neuron compartment
curation status: uncurated
disjoint with: Non Neural Cell Compartment
disjoint with: Regional Part Of Glia
disjoint with: Cell Protrusion

Nicotinic Acetylcholine Receptor
type: Class
umls ID: C0034830
sao ID: sao1767745398
definition: 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).
disjoint with: Muscarinic Acetylcholine Receptor
curation status: uncurated
subclass of: Acetylcholine Receptor

Muscarinic Acetylcholine Receptor
type: Class
sao ID: sao2062447305
subclass of: Acetylcholine Receptor
curation status: uncurated
definition: 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).
umls ID: C0034826

Acetylcholine Receptor
type: Class
curation status: uncurated
subclass of: Neurotransmitter Receptor
umls ID: C0034792
sao ID: sao1700719022
definition: 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).

Functional State
type: Class
subclass of: Organismal Occurrent
sao ID: sao1802798922
definition: Differentiates among different functional states of a cell or cell component, e.g., activated microglia, interphase nucleus, orthodox mitochondria.

Cytoplasmic Vesicle
type: Class
subclass of: Vesicle
sao ID: sao180601769
definition: A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology).
gene ontology ID: 0031410
curation status: uncurated

Vesicle
type: Class
disjoint with: Intracellular Membrane
definition: Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology).
gene ontology ID: 0031982
curation status: uncurated
subclass of: Cellular Component
subclass of: Restriction
  all values from: Pre-synaptic Part
  on property: located in
disjoint with: Intracellular Membrane Formation
subclass of: Restriction
  all values from: Vesicle Type
  on property: has Morphological Type
umls ID: C0042219
sao ID: sao221389602

Single
type: Class
curation status: uncurated
disjoint with: Bundled
subclass of: Configuration
disjoint with: Clustered
disjoint with: Rosette
disjoint with: Stacked
sao ID: sao548826380
disjoint with: Branched
disjoint with: Synaptic Configuration
definition: Indicates that the feature exists in isolation, e.g., single filaments as opposed to bundled filaments.

Bundled
type: Class
curation status: uncurated
sao ID: sao296309608
subclass of: Configuration
definition: When several members of a class occur tightly apposed to one another or attached to one another in identifiable bundles.
disjoint with: Stacked
disjoint with: Synaptic Configuration

Clustered
type: Class
subclass of: Configuration
sao ID: sao1475145503
disjoint with: Rosette
disjoint with: Synaptic Configuration
disjoint with: Stacked
disjoint with: Bundled
curation status: uncurated

Rosette
type: Class
subclass of: Configuration
sao ID: sao2082026326
disjoint with: Synaptic Configuration
disjoint with: Stacked
disjoint with: Bundled
curation status: uncurated

Stacked
type: Class
curation status: uncurated
subclass of: Configuration
disjoint with: Synaptic Configuration
sao ID: sao3169628

Branched
type: Class
subclass of: Configuration
sao ID: sao497641585
disjoint with: Rosette
disjoint with: Stacked
disjoint with: Bundled
disjoint with: Synaptic Configuration
disjoint with: Clustered
curation status: uncurated

Synaptic Configuration
type: Class
comment: Arrangement of pre- and post-synaptic components.
curation status: uncurated
subclass of: Configuration
sao ID: sao1289583168

Amino Acid
type: Class
disjoint with: Monoamines
sao ID: sao1511566913
curation status: uncurated
subclass of: Molecule
definition: 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).
umls ID: C0002520

Carbohydrate
type: Class
umls ID: C0007004
curation status: uncurated
disjoint with: Amino Acid
disjoint with: Monoamines
disjoint with: Nucleic Acid
subclass of: Molecule
sao ID: sao607978678
definition: 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).

Neuropeptide
type: Class
subclass of: Molecule
definition: Peptides released by neurons as intercellular messengers. Many neuropeptides are also hormones released by non-neuronal cells (MSH).
umls ID: C0027895
disjoint with: Nucleic Acid
sao ID: sao2106486330
disjoint with: Carbohydrate
disjoint with: Monoamines
disjoint with: Amino Acid
curation status: uncurated

Nucleic Acid
type: Class
subclass of: Molecule
definition: High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages (MSH).
disjoint with: Amino Acid
disjoint with: Monoamines
sao ID: sao83745184
curation status: uncurated
umls ID: C0028606

has Component
type: TransitiveProperty
sub property of: has Part
domain: Object
comment: Cellular components found in typical cells.
inverse of: is Component Of
sao ID: sao1623809261
type: ObjectProperty
range: Class
  union of: Object
  union of: FiatObjectPart

Nucleus
type: Class
disjoint with: Lysosome
subclass of: Membrane Bound Organelle
definition: 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).
disjoint with: Multivesicular Body
disjoint with: Peroxisome
curation status: uncurated
gene ontology ID: 0005634
sao ID: sao1702920020
disjoint with: Endoplasmic Reticulum
umls ID: C0007610
disjoint with: Golgi Apparatus
disjoint with: Endosome

Cytosol
type: Class
disjoint with: Intracellular Membrane
definition: The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS).
disjoint with: Cytoskeletal Element
disjoint with: Cellular Inclusion
disjoint with: Intracellular Membrane Formation
disjoint with: Vesicle
disjoint with: Cellular Subcomponent
disjoint with: Subplasmalemmal Coating
disjoint with: Coated Pit
disjoint with: Cilium
curation status: uncurated
disjoint with: Plasma Membrane
gene ontology ID: 0005829
sao ID: sao101633890
disjoint with: Glycogen Granule
umls ID: C0010854
subclass of: Cellular Component
disjoint with: Basal Lamina

Plasma Membrane
type: Class
disjoint with: Cellular Subcomponent
disjoint with: Cytoskeletal Element
synonym: cell membrane
disjoint with: Intracellular Membrane Formation
disjoint with: Cellular Inclusion
disjoint with: Intracellular Membrane
gene ontology ID: 0005886
sao ID: sao1663586795
disjoint with: Cilium
disjoint with: Vesicle
subclass of: Cellular Component
umls cui: C0007603
curation status: uncurated
definition: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology).

Spherical
type: Class
subclass of: Soma Type
definition: Generally round shape where minimum diameter and maximum diameter are roughly the same
sao ID: sao957949983
curation status: curation complete
disjoint with: Oval

Soma Type
type: Class
sao ID: sao-1126011106
disjoint with: Cristae Type
disjoint with: Chemical Synapse Type
disjoint with: Spine Type
disjoint with: Nucleus Type
disjoint with: Mitochondrial Type
disjoint with: Dendrite Type
disjoint with: Vesicle Type
disjoint with: Axon Type
definition: 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.
subclass of: Morphological Type
disjoint with: Bouton Type

Oval
type: Class
subclass of: Soma Type
sao ID: sao1595237779
curation status: definition incomplete
definition: Generally rounded shape, where the minimum and maximum dimensions produce a roughly egg-shape.

Glutamate
type: Class
curation status: uncurated
sao ID: sao1744435799
umls ID: C0220839
subclass of: Amino Acid
disjoint with: GABA
disjoint with: Glycine

GABA
type: Class
sao ID: sao229636300
subclass of: Amino Acid
disjoint with: Glycine
definition: Abbreviation for gamma amino butyric acid, the major inhibitory neurotransmitter in the mammalian central nervous system.
curation status: uncurated
umls ID: C0016904

Glycine
type: Class
umls ID: C0017890
subclass of: Amino Acid
definition: 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).
sao ID: sao968946794
curation status: uncurated

Axon
type: Class
subclass of: Neuron Process
sao ID: sao1770195789
subclass of: Restriction
  all values from: Axon Type
  on property: has Morphological Type
umls ID: C0004461
disjoint with: Dendrite
definition: 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).
curation status: uncurated
subclass of: Restriction
  all values from: Regional Part Of Axon
  on property: has Regional Part
definition: Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA)
gene ontology ID: 0030424
subclass of: Restriction
  on property: has Regional Part
  some values from: Regional Part Of Axon
subclass of: Restriction
  some values from: Axon Type
  on property: has Morphological Type

Neuron Process
type: Class
sao ID: sao-867568886
subclass of: Regional Part Of Neuron

has Morphological Type
type: ObjectProperty
sub property of: has Property
range: Morphological Type
domain: Class
  union of: Mitochondrion
  union of: Regional Part Of Cell
  union of: Intercellular Junction Site
  union of: Cellular Component
  union of: Cell
inverse of: is Morphological Type Of
sao ID: sao3931558608

Dendrite
type: Class
subclass of: Restriction
  all values from: Regional Part Of Dendrite
  on property: has Regional Part
definition: 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).
definition: 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.
subclass of: Restriction
  some values from: Regional Part Of Dendrite
  on property: has Regional Part
sao ID: sao1211023249
subclass of: Restriction
  on property: has Morphological Type
  some values from: Dendrite Type
subclass of: Restriction
  on property: has Morphological Type
  all values from: Dendrite Type
subclass of: Neuron Process
curation status: uncurated
subclass of: Restriction
  on property: continuous With
  some values from: Class
    union of: Dendritic Spine
    union of: Neuronal Cell Body
    union of: Spine Neck
    union of: Cellular Subcomponent
    union of: Subregional Part Of Neuron Process
    union of: Regional Part Of Neuron
    union of: Tuft
gene ontology ID: 0030425
umls ID: C0011305

Myelinating Schwann Cell
type: Class
definition: Schwann cell that forms compact myelin sheath around axons.
subclass of: Obsolete class
sao ID: sao1209655615
curation status: uncurated

G Coupled Receptor
type: Class
curation status: uncurated
subclass of: Membrane Receptor
sao ID: sao238175764

Golgi Apparatus
type: Class
curation status: uncurated
disjoint with: Peroxisome
definition: 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)
synonym: golgi cisternae
umls ID: C0018042
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of Golgi
gene ontology ID: 0005794
disjoint with: Lysosome
sao ID: sao451912436
disjoint with: Endoplasmic Reticulum
disjoint with: Multivesicular Body
subclass of: Membrane Bound Organelle
disjoint with: Endosome

Regional Part Of Golgi
type: Class
subclass of: Regional Part Of Cell Component
sao ID: sao1546288504
curation status: uncurated
disjoint with: Regional Part Of RER
disjoint with: Regional Part Of Mitochondria
disjoint with: Regional Part Of Mitochondrial Membrane

Endoplasmic Reticulum
type: Class
disjoint with: Lysosome
disjoint with: Peroxisome
curation status: uncurated
umls ID: C0014239
disjoint with: Multivesicular Body
gene ontology ID: 0005783
sao ID: sao1036339110
subclass of: Membrane Bound Organelle
definition: 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).

Endosome
type: Class
sao ID: sao1720343330
disjoint with: Lysosome
disjoint with: Multivesicular Body
curation status: uncurated
definition: A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation (GO).
disjoint with: Endoplasmic Reticulum
disjoint with: Peroxisome
gene ontology ID: 0005768
umls ID: C0034850
subclass of: Membrane Bound Organelle

Pial Endfoot
type: Class
subclass of: Regional Part Of Tanycyte
curation status: uncurated
sao ID: sao1447478620
disjoint with: Neck Portion
disjoint with: Tail Portion
disjoint with: Somatic Portion
disjoint with: Vascular Endfoot

Regional Part Of Tanycyte
type: Class
sao ID: sao877341397
curation status: uncurated
subclass of: Non Neural Cell Compartment

Neck Portion
type: Class
subclass of: Regional Part Of Tanycyte
disjoint with: Vascular Endfoot
sao ID: sao901230115
disjoint with: Tail Portion
definition: 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).
curation status: uncurated
subclass of: Restriction
  some values from: Somatic Portion
  on property: continuous With
disjoint with: Somatic Portion

Tail Portion
type: Class
subclass of: Regional Part Of Tanycyte
subclass of: Restriction
  some values from: Class
    union of: Somatic Portion
    union of: Vascular Endfoot
    union of: Pial Endfoot
  on property: continuous With
disjoint with: Vascular Endfoot
disjoint with: Somatic Portion
sao ID: sao1749953771
curation status: uncurated
definition: 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).

Somatic Portion
type: Class
curation status: uncurated
definition: Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991).
disjoint with: Vascular Endfoot
subclass of: Regional Part Of Tanycyte
subclass of: Restriction
  some values from: Class
    union of: Neck Portion
    union of: Tail Portion
  on property: continuous With
sao ID: sao401910342

Vascular Endfoot
type: Class
sao ID: sao2064469343
subclass of: Regional Part Of Tanycyte
subclass of: Restriction
  some values from: Tail Portion
  on property: continuous With
curation status: uncurated

Cortical Bipolar Cell
type: Class
disjoint with: Pyramidal Cell
curation status: uncurated
definition: Type of VIP containing neuron found in the visiual cortex.
disjoint with: Spherical Bushy Cell
disjoint with: Random Cell
disjoint with: mitral cell
disjoint with: Olfactory Granule Cell
subclasses disjoint: true
sao ID: sao436474611
disjoint with: Photoreceptor Cell
disjoint with: Cortical Stellate Cell
subclass of: Neuron
disjoint with: Motor Neuron
disjoint with: Double Bouquet Cell

mitral cell
type: Class
note: Definition was modified from that in Wikipedia by MM
subclass of: Neuron
subclasses disjoint: true
sao ID: sao900005350
disjoint with: Pyramidal Cell
disjoint with: Cortical Stellate Cell
curation status: uncurated
definition source: Wikipedia
subclass of: Restriction
  on property: anatomical Location General
  has value: olfactory bulb
disjoint with: Motor Neuron
disjoint with: Spherical Bushy Cell
subclass of: Restriction
  has value: projection neuron
  on property: circuit Type
disjoint with: Random Cell
definition: 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.
disjoint with: Double Bouquet Cell
label: Mitral Cell

Olfactory Granule Cell
type: Class
disjoint with: Motor Neuron
sao ID: sao776599268
disjoint with: Cortical Stellate Cell
subclass of: Neuron
subclasses disjoint: true
disjoint with: mitral cell
disjoint with: Double Bouquet Cell
curation status: uncurated
disjoint with: Spherical Bushy Cell
disjoint with: Random Cell
disjoint with: Pyramidal Cell

Motor Neuron
type: Class
sao ID: sao1460710779
subclass of: Neuron
disjoint with: Pyramidal Cell
curation status: uncurated
disjoint with: Double Bouquet Cell
subclass of: Restriction
  some values from: Acetylcholine
  on property: has Neurotransmitter
umls ID: C0026609
disjoint with: Spherical Bushy Cell
cell ontology ID: CL:0000100
definition: Neurons which activate muscle cells (MSH).
subclasses disjoint: true
disjoint with: Random Cell
definition source: UMLS
disjoint with: Cortical Stellate Cell

Amorphous Vesicle
type: Class
definition: 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.
curation status: uncurated
subclass of: Vesicle Other
sao ID: sao1531915298

Vesicle Other
type: Class
subclass of: Cytoplasmic Vesicle
definition: Category for vesicles observed in electron micrographs with unknown function.
curation status: uncurated
disjoint with: Granular Vesicle
disjoint with: Transport Vesicle
sao ID: sao577473346

Organelle
type: Class
disjoint with: Cilium
umls ID: C0029219
disjoint with: Synaptic Component
sao ID: sao1539965131
disjoint with: Vesicle
disjoint with: Plasma Membrane
disjoint with: Cytoskeletal Element
disjoint with: Coated Pit
curation status: uncurated
disjoint with: Pigment
disjoint with: Intracellular Membrane Formation
disjoint with: Cellular Inclusion
disjoint with: Dense Body
subclass of: Cellular Component
disjoint with: Cytosol
disjoint with: Basal Lamina
disjoint with: Intracellular Membrane
disjoint with: Glycogen Granule
gene ontology ID: 0043226
disjoint with: Basal Body
definition: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane (Gene Ontology).
disjoint with: Subplasmalemmal Coating
disjoint with: Cellular Subcomponent

Non Membrane Bound Organelle
type: Class
definition: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes (Gene Ontology).
subclass of: Organelle
sao ID: sao1456184038
gene ontology ID: 0043228
curation status: uncurated

Smooth Muscle Cell
type: Class
subclass of: Muscle Cell
curation status: uncurated
definition: 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).
sao ID: sao676858164
definition source: UMLS
disjoint with: Striated Muscle Cell
synonym: non-striated muscle cell
cell ontology ID: CL:0000192
umls ID: C1135918

Muscle Cell
type: Class
disjoint with: Epithelial Cell
umls ID: C0596981
disjoint with: Nerve Cell
sao ID: sao519252327
curation status: uncurated
synonym: myocyte
disjoint with: Macrophage
disjoint with: Microglia
cell ontology ID: CL:0000187
definition: 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).
subclass of: Cell
disjoint with: Vascular Cell

Striated Muscle Cell
type: Class
sao ID: sao82362520
curation status: uncurated
cell ontology ID: CL:0000737
subclass of: Muscle Cell

Lumen Cargo
type: Class
sao ID: sao976831666
definition: Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin.
subclass of: Vesicle Cargo
disjoint with: Membrane Cargo

Vesicle Cargo
type: Class
comment: Need to determine whether this should be a part of a vesicle; I think it shouldn't be
sao ID: sao1490223249
subclass of: Vesicle Subcomponent
definition: Refers to the contents contained in the vesicle.

Membrane Cargo
type: Class
definition: Refers to integral membrane proteins carried via the vesicle membrane.
subclass of: Vesicle Cargo
sao ID: sao1037637579

Transport Vesicle
type: Class
definition: 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).
synonym: secretory vesicle
curation status: uncurated
sao ID: sao885490876
gene ontology ID: 0030133
subclass of: Cytoplasmic Vesicle
umls ID: C0887882

Granular Vesicle
type: Class
disjoint with: Transport Vesicle
curation status: uncurated
definition: Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells.
subclass of: Cytoplasmic Vesicle
sao ID: sao478230652

Bergmann Glia
type: Class
sao ID: sao1299495391
definition source: Wikipedia
subclass of: Radial Astrocyte
umls ID: C0228088
subclass of: Restriction
  on property: location CNS PNS
  has value: CNS
comment: 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
curation status: graph position temporary
cell ontology ID: CL:0000644
synonym: radial epithelial cell
subclasses disjoint: true
definition: 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.

Radial Astrocyte
type: Class
subclass of: Astrocyte
definition: 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)
subclasses disjoint: true
disjoint with: Protoplasmic Astrocyte
curation status: graph position temporary
sao ID: sao6261208102

Basal Body
type: Class
umls ID: C0230744
disjoint with: Vesicle
disjoint with: Subplasmalemmal Coating
disjoint with: Intracellular Membrane Formation
subclass of: Cellular Component
disjoint with: Pigment
disjoint with: Cilium
disjoint with: Cellular Subcomponent
disjoint with: Synaptic Component
disjoint with: Cellular Inclusion
disjoint with: Coated Pit
disjoint with: Glycogen Granule
disjoint with: Cytoskeletal Element
disjoint with: Plasma Membrane
disjoint with: Basal Lamina
curation status: uncurated
sao ID: sao11978067
disjoint with: Dense Body
gene ontology ID: 0005932
disjoint with: Cytosol
definition: 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).
disjoint with: Intracellular Membrane

Subplasmalemmal Coating
type: Class
sao ID: sao1938587839
definition: 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
disjoint with: Glycogen Granule
disjoint with: Cellular Subcomponent
disjoint with: Coated Pit
disjoint with: Intracellular Membrane
subclass of: Cellular Component
disjoint with: Plasma Membrane
disjoint with: Cilium
modified date: 2007-02-23
disjoint with: Cellular Inclusion
disjoint with: Basal Lamina
disjoint with: Intracellular Membrane Formation
disjoint with: Vesicle
disjoint with: Cytoskeletal Element
curation status: definition incomplete

Intracellular Membrane Formation
type: Class
subclass of: Obsolete class
definition: Specializations associated with intracellular membrane systems, e.g. lamellar bodies. Membranes of subcellular structures. (MSH)
sao ID: sao237754030
curation status: uncurated
umls ID: C0021868

Cellular Component
type: Class
definition: Cell part which has a definable shape, bounded predominantly by bonafide boundaries and is countable (FMA).
curation status: uncurated
gene ontology ID: 0005575
sao ID: sao1337158144
comment: 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).
subclass of: Object

Pigment
type: Class
disjoint with: Basal Lamina
disjoint with: Cellular Inclusion
disjoint with: Intracellular Membrane Formation
disjoint with: Cytosol
sao ID: sao1231384859
disjoint with: Cilium
disjoint with: Glycogen Granule
curation status: uncurated
disjoint with: Vesicle
disjoint with: Cellular Subcomponent
subclass of: Cellular Component
disjoint with: Intracellular Membrane
disjoint with: Cytoskeletal Element
disjoint with: Plasma Membrane
disjoint with: Subplasmalemmal Coating
disjoint with: Coated Pit
disjoint with: Synaptic Component

Cilium
type: Class
disjoint with: Cytoskeletal Element
disjoint with: Cellular Subcomponent
curation status: uncurated
gene ontology ID: 0005929
disjoint with: Intracellular Membrane Formation
definition: 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).
subclass of: Cellular Component
disjoint with: Intracellular Membrane
umls ID: C0008778
sao ID: sao787716553
disjoint with: Vesicle
disjoint with: Cellular Inclusion

Cellular Subcomponent
type: Class
curation status: uncurated
sao ID: sao628508602
disjoint with: Cytoskeletal Element
disjoint with: Intracellular Membrane
disjoint with: Intracellular Membrane Formation
disjoint with: Vesicle
subclass of: Cellular Component

Synaptic Component
type: Class
disjoint with: Cilium
disjoint with: Cellular Subcomponent
disjoint with: Subplasmalemmal Coating
subclass of: Cellular Component
disjoint with: Coated Pit
disjoint with: Plasma Membrane
disjoint with: Basal Lamina
disjoint with: Glycogen Granule
sao ID: sao1784069613
disjoint with: Vesicle
disjoint with: Intracellular Membrane
disjoint with: Cytoskeletal Element
disjoint with: Cytosol
disjoint with: Intracellular Membrane Formation
disjoint with: Cellular Inclusion

Cellular Inclusion
type: Class
definition: Cellular inclusion found in the cytoplasm.
disjoint with: Intracellular Membrane
subclass of: Cellular Component
curation status: uncurated
disjoint with: Cytoskeletal Element
sao ID: sao120573470
disjoint with: Vesicle
disjoint with: Cellular Subcomponent
disjoint with: Intracellular Membrane Formation

Coated Pit
type: Class
subclass of: Cellular Component
disjoint with: Vesicle
curation status: uncurated
disjoint with: Intracellular Membrane
umls ID: C0009143
disjoint with: Cytoskeletal Element
disjoint with: Cellular Subcomponent
sao ID: sao1969557946
disjoint with: Cilium
disjoint with: Intracellular Membrane Formation
disjoint with: Cellular Inclusion
disjoint with: Basal Lamina
disjoint with: Plasma Membrane
definition: Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003).

Glycogen Granule
type: Class
disjoint with: Cellular Subcomponent
disjoint with: Cellular Inclusion
definition: 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).
disjoint with: Vesicle
disjoint with: Basal Lamina
sao ID: sao1081228141
subclass of: Cellular Component
umls ID: C0017911
disjoint with: Plasma Membrane
curation status: uncurated
disjoint with: Intracellular Membrane Formation
gene ontology ID: 0042587
disjoint with: Cilium
subclass of: Restriction
  some values from: Glycogen
  on property: has Molecular Constituent
disjoint with: Intracellular Membrane
disjoint with: Coated Pit
disjoint with: Cytoskeletal Element

Basal Lamina
type: Class
disjoint with: Vesicle
subclass of: Cellular Component
umls ID: C0242195
curation status: uncurated
disjoint with: Cellular Inclusion
disjoint with: Cellular Subcomponent
disjoint with: Plasma Membrane
definition: A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix (Gene Ontology).
disjoint with: Cytoskeletal Element
disjoint with: Intracellular Membrane Formation
disjoint with: Cilium
gene ontology ID: 0005605
sao ID: sao1397492660
disjoint with: Intracellular Membrane

Dense Body
type: Class
disjoint with: Vesicle
disjoint with: Plasma Membrane
sao ID: sao730872736
disjoint with: Subplasmalemmal Coating
definition: An electron dense body, some of which contain granules (Peters, Palay and Webster (1991)
disjoint with: Cytosol
disjoint with: Glycogen Granule
comment: Not clear if this should be described as an organelle or an inclusion.
disjoint with: Pigment
subclass of: Cellular Component
disjoint with: Intracellular Membrane
disjoint with: Cellular Subcomponent
disjoint with: Intracellular Membrane Formation
disjoint with: Coated Pit
disjoint with: Cilium
disjoint with: Cytoskeletal Element
curation status: graph position temporary
disjoint with: Synaptic Component
disjoint with: Basal Lamina
disjoint with: Cellular Inclusion

Active Zone Plasma Membrane
type: Class
sao ID: sao2038461087
curation status: uncurated
subclass of: Pre-synaptic Active Zone Component
subclass of: Restriction
  on property: has Molecular Constituent
  some values from: Calcium Channel
disjoint with: Pre-synaptic Grid
disjoint with: Active Zone Dense Projection
definition: Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004).

Pre-synaptic Active Zone Component
type: Class
curation status: uncurated
sao ID: sao1911631652
subclass of: Pre-synaptic Component

has Molecular Constituent
type: ObjectProperty
range: Molecule
domain: Class
  union of: Membrane Surface
  union of: FiatObjectPart
  union of: ObjectAggregate
  union of: Object
sub property of: has Part
inverse of: is Molecular Constituent Of
sao ID: sao152994059

Pre-synaptic Grid
type: Class
sao ID: sao1730664005
definition: 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).
disjoint with: Active Zone Dense Projection
disjoint with: Pre-synaptic Dense Body
subclass of: Pre-synaptic Active Zone Component
curation status: uncurated

Active Zone Dense Projection
type: Class
definition: Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004).
sao ID: sao494258938
subclass of: Pre-synaptic Active Zone Component
curation status: uncurated

IP3R Type 3
type: Class
sao ID: sao2003006393
curation status: uncurated
subclass of: Inositol 1 4 5 Trisphosphate Receptor

Inositol 1 4 5 Trisphosphate Receptor
type: Class
umls ID: C0063592
sao ID: sao2115096416
curation status: uncurated
subclass of: Intracellular Calcium Channel

Cochlear Outer Hair Cell
type: Class
cell ontology ID: CL:0000601
curation status: uncurated
subclasses disjoint: true
definition: 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)
disjoint with: Cochlear Inner Hair Cell
umls ID: C0206513
sao ID: sao1582628662
subclass of: Cochlear Hair Cell

Cochlear Inner Hair Cell
type: Class
subclass of: Cochlear Hair Cell
curation status: uncurated
umls ID: C0018497
definition: 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)
subclasses disjoint: true
sao ID: sao429277527
cell ontology ID: CL:0000589
definition source: UMLS

Cochlear Hair Cell
type: Class
subclass of: hair cell
curation status: uncurated
sao ID: sao630986029
subclasses disjoint: true

Intercalated Disk
type: Class
sao ID: sao1152983960
definition: 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).
subclass of: Cell Cell Contact Zone
curation status: uncurated
disjoint with: Peg And Socket Contact

Peg And Socket Contact
type: Class
curation status: uncurated
subclass of: Cell Cell Contact Zone
sao ID: sao1943947957
definition: 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).

Cerebellar Golgi Cell
type: Class
disjoint with: mitral cell
disjoint with: Cortical Bipolar Cell
disjoint with: Chandelier Cell
subclass of: Restriction
  on property: anatomical Location General
  has value: cerebellar cortex
disjoint with: Spherical Bushy Cell
disjoint with: Cerebellar Granule Cell
disjoint with: hair cell
disjoint with: Cortical Stellate Cell
sao ID: sao1415726815
disjoint with: Cerebellar Basket Cell
disjoint with: Pyramidal Cell
curation status: uncurated
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Substantia Nigra Dopaminergic Cell
disjoint with: Globular Bushy Cell
subclass of: Neuron
definition: 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.
disjoint with: Random Cell
subclass of: Restriction
  on property: circuit Type
  has value: local circuit neuron
disjoint with: Double Bouquet Cell
disjoint with: Olfactory Granule Cell
disjoint with: Motor Neuron
disjoint with: Photoreceptor Cell
subclasses disjoint: true

Chandelier Cell
type: Class
subclass of: Restriction
  has value: false
  on property: is spiny
disjoint with: Cortical Bipolar Cell
sao ID: sao1267578530
curation status: uncurated
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
subclass of: Restriction
  some values from: GABA
  on property: has Neurotransmitter
disjoint with: Spherical Bushy Cell
disjoint with: Double Bouquet Cell
subclass of: Neuron
disjoint with: Cerebellar Granule Cell
disjoint with: mitral cell
disjoint with: Photoreceptor Cell
definition: 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.
disjoint with: Motor Neuron
subclass of: Restriction
  has value: cerebral cortex
  on property: anatomical Location General
subclasses disjoint: true
disjoint with: Cortical Stellate Cell
disjoint with: Olfactory Granule Cell
disjoint with: Random Cell
disjoint with: Substantia Nigra Dopaminergic Cell
disjoint with: Pyramidal Cell

Cerebellar Granule Cell
type: Class
subclasses disjoint: true
disjoint with: Cortical Bipolar Cell
disjoint with: Spherical Bushy Cell
disjoint with: Photoreceptor Cell
curation status: uncurated
disjoint with: Motor Neuron
subclass of: Restriction
  cardinality: 1
  on property: Number of Axons
sao ID: sao1736323572
disjoint with: Olfactory Granule Cell
subclass of: Restriction
  some values from: Glutamate
  on property: has Neurotransmitter
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Cortical Stellate Cell
disjoint with: Double Bouquet Cell
definition: 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.
bonfire ID: BF_C000108
subclass of: Restriction
  on property: anatomical Location General
  has value: cerebellar cortex
subclass of: Neuron
disjoint with: Random Cell
disjoint with: Pyramidal Cell
disjoint with: mitral cell

hair cell
type: Class
subclasses disjoint: true
disjoint with: Cortical Bipolar Cell
disjoint with: Cortical Stellate Cell
disjoint with: Substantia Nigra Dopaminergic Cell
curation status: uncurated
disjoint with: Photoreceptor Cell
disjoint with: Double Bouquet Cell
disjoint with: Motor Neuron
disjoint with: Random Cell
disjoint with: Spherical Bushy Cell
disjoint with: Pyramidal Cell
disjoint with: mitral cell
cell ontology ID: CL:0000202
disjoint with: Chandelier Cell
subclass of: Neuron
disjoint with: Olfactory Granule Cell
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
sao ID: sao2046464388
disjoint with: Cerebellar Granule Cell
umls ID: C0018496
definition: 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).
label: Hair Cell

Cerebellar Basket Cell
type: Class
disjoint with: Spherical Bushy Cell
disjoint with: Pyramidal Cell
curation status: uncurated
subclass of: Restriction
  some values from: GABA
  on property: has Neurotransmitter
subclasses disjoint: true
sao ID: sao666951243
disjoint with: Random Cell
disjoint with: hair cell
definition: 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.
disjoint with: Cortical Stellate Cell
subclass of: Restriction
  on property: location CNS PNS
  has value: CNS
disjoint with: Cerebellar Granule Cell
disjoint with: mitral cell
disjoint with: Olfactory Granule Cell
disjoint with: Cortical Bipolar Cell
disjoint with: Chandelier Cell
subclass of: Neuron
subclass of: Restriction
  has value: local circuit neuron
  on property: circuit Type
disjoint with: Motor Neuron
subclass of: Restriction
  has value: multipolar
  on property: process Number
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Photoreceptor Cell
disjoint with: Double Bouquet Cell
disjoint with: Substantia Nigra Dopaminergic Cell

Principal Cells Medial Nucleus Trapezoid Body
type: Class
disjoint with: Random Cell
subclass of: Restriction
  on property: has Regional Part
  some values from: Dendrite
disjoint with: Double Bouquet Cell
subclass of: Restriction
  has value: multipolar
  on property: process Number
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: Glycine
sao ID: sao1918137235
disjoint with: Pyramidal Cell
subclass of: Restriction
  some values from: Neuronal Cell Body
  on property: has Regional Part
disjoint with: mitral cell
definition: Properties derived from Gersdorff and Borst (2002).
curation status: uncurated
subclass of: Restriction
  has value: medial nucleus of the trapezoid body
  on property: anatomical Location General
disjoint with: Olfactory Granule Cell
disjoint with: Spherical Bushy Cell
subclass of: Neuron
disjoint with: Photoreceptor Cell
disjoint with: Cortical Bipolar Cell
disjoint with: Motor Neuron
disjoint with: Cortical Stellate Cell
subclass of: Restriction
  has value: CNS
  on property: location CNS PNS
subclass of: Restriction
  some values from: Axon Collateral
  on property: has Regional Part
subclass of: Restriction
  cardinality: 1
  on property: Number of Axons
subclasses disjoint: true
subclass of: Restriction
  some values from: Axon
  on property: has Regional Part

Substantia Nigra Dopaminergic Cell
type: Class
curation status: uncurated
subclass of: Restriction
  on property: process Number
  has value: multipolar
disjoint with: Cortical Bipolar Cell
disjoint with: Pyramidal Cell
disjoint with: Olfactory Granule Cell
subclasses disjoint: true
subclass of: Restriction
  on property: Number of Axons
  cardinality: 1
sao ID: sao34994437
disjoint with: Cerebellar Granule Cell
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Motor Neuron
disjoint with: Cortical Stellate Cell
subclass of: Restriction
  on property: anatomical Location General
  has value: Substantia nigra pars compacta
subclass of: Restriction
  has value: false
  on property: is spiny
disjoint with: Random Cell
disjoint with: Double Bouquet Cell
disjoint with: Spherical Bushy Cell
subclass of: Neuron
subclass of: Restriction
  some values from: Dopamine
  on property: has Neurotransmitter
disjoint with: mitral cell
subclass of: Restriction
  on property: circuit Type
  has value: projection neuron
disjoint with: Photoreceptor Cell

Globular Bushy Cell
type: Class
curation status: uncurated
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Photoreceptor Cell
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: Glutamate
disjoint with: Cerebellar Granule Cell
disjoint with: Double Bouquet Cell
disjoint with: Motor Neuron
disjoint with: Pyramidal Cell
disjoint with: Cortical Bipolar Cell
disjoint with: Olfactory Granule Cell
disjoint with: hair cell
disjoint with: mitral cell
disjoint with: Cerebellar Basket Cell
sao ID: sao538050329
disjoint with: Cortical Stellate Cell
disjoint with: Chandelier Cell
disjoint with: Spherical Bushy Cell
disjoint with: Random Cell
subclasses disjoint: true
disjoint with: Substantia Nigra Dopaminergic Cell
subclass of: Neuron
subclass of: Restriction
  on property: anatomical Location General
  has value: anterior ventral cochlear nucleus

Regional Part Of Glia
type: Class
curation status: uncurated
sao ID: sao895885284
subclass of: Regional Part Of Cell

Regional Part Of Cell
type: Class
comment: 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).
disjoint with: Regional Part Of Cell Component
sao ID: sao340271629
subclass of: FiatObjectPart
curation status: uncurated

DNA
type: Class
definition: 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).
subclass of: Nucleic Acid
curation status: uncurated
umls ID: C0012854
sao ID: sao454034570

Terminal Loop
type: Class
sao ID: sao924713546
curation status: uncurated
definition: Portion of myelin-forming Schwann cell consisting of terminal cytoplasmic extensions adhered to the axon at the beginning and end of the myelin sheath.
subclass of: Regional Part Of Schwann Cell

Regional Part Of Schwann Cell
type: Class
subclass of: Regional Part Of Glia
disjoint with: Regional Part Of Astrocyte
disjoint with: Glial Subcompartment
sao ID: sao195217619
curation status: uncurated

Glial Limiting Endfoot
type: Class
sao ID: sao181458425
curation status: uncurated
definition: Process of astrocyte that extends to the surface of the central nervous system. Together, they form the glial limiting membrane or glial limitans.
subclass of: Endfoot
disjoint with: Perivascular Endfoot

Endfoot
type: Class
curation status: graph position temporary
curation status: uncurated
subclass of: Restriction
  on property: has Molecular Constituent
  some values from: Glial Fibrillary Acidic Protein
subclass of: Vellous Process
sao ID: sao388182739
definition: Terminal process of astrocyte abutting non-neuronal surfaces in the brain.

Perivascular Endfoot
type: Class
curation status: uncurated
subclass of: Restriction
  some values from: Vascular Endothelial Cell
  on property: associated Cellular Element
subclass of: Restriction
  some values from: Aquaporin 4
  on property: has Molecular Constituent
subclass of: Endfoot
subclass of: Restriction
  on property: has Molecular Constituent
  some values from: RSlo
sao ID: sao2048701763
comment: We are unclear why this is causing an inconsistency error.

Epithelial Cell
type: Class
curation status: uncurated
disjoint with: Microglia
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of Epithelial Cell
disjoint with: Vascular Cell
umls ID: C0014597
sao ID: sao441624014
cell ontology ID: CL:0000066
definition: Cell that line the inner and outer surfaces of the body by forming cellular layers (epithelium) or masses (MSH).
subclass of: Cell
disjoint with: Nerve Cell
disjoint with: Macrophage

Regional Part Of Epithelial Cell
type: Class
umls ID: C0932419
curation status: uncurated
subclass of: Non Neural Cell Compartment
sao ID: sao1974433376
disjoint with: Regional Part Of Tanycyte

Vascular Cell
type: Class
umls ID: C0225336
sao ID: sao197110912
disjoint with: Macrophage
disjoint with: Microglia
disjoint with: Nerve Cell
curation status: uncurated
subclass of: Cell
definition: Cells that line the inner and outer surfaces of the body (MSH).

Macrophage
type: Class
disjoint with: Microglia
disjoint with: Nerve Cell
curation status: uncurated
subclass of: Cell
definition: 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).
sao ID: sao185843373
cell ontology ID: CL:0000235

F-actin
type: Class
sao ID: sao856608566
disjoint with: G-actin
curation status: uncurated
subclass of: Actin

G-actin
type: Class
umls ID: C0016890
sao ID: sao251535222
curation status: uncurated
subclass of: Actin

Regional Part Of Oligodendrocyte
type: Class
subclass of: Regional Part Of Glia
sao ID: sao831502550
curation status: uncurated
disjoint with: Glial Subcompartment
disjoint with: Regional Part Of Schwann Cell
disjoint with: Regional Part Of Astrocyte

Glial Subcompartment
type: Class
subclass of: Regional Part Of Glia
disjoint with: Regional Part Of Astrocyte
curation status: uncurated
sao ID: sao1253297813

Regional Part Of Astrocyte
type: Class
curation status: uncurated
subclass of: Regional Part Of Glia
sao ID: sao685712019

Organotypic Slice
type: Class
sao ID: sao1596955138
subclass of: Slice Preparation

Slice Preparation
type: Class
sao ID: sao832793084
subclass of: In Vitro

Cis Face
type: Class
sao ID: sao632188024
subclass of: Regional Part Of Golgi
curation status: uncurated

Phosphatase
type: Class
sao ID: sao1202737159
definition: 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)
subclass of: Enzyme
disjoint with: ATP Synthase
disjoint with: Kinase
curation status: uncurated
umls ID: C0031686

ATP Synthase
type: Class
subclass of: Enzyme
curation status: uncurated
disjoint with: Kinase
sao ID: sao1794895660

Kinase
type: Class
curation status: uncurated
subclass of: Enzyme
sao ID: sao743185455

Axolemma
type: Class
sao ID: sao250772229
curation status: uncurated
subclass of: Plasma Membrane
definition: 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).
gene ontology ID: 0030673

Neuron Protrusion
type: Class
subclass of: Regional Part Of Neuron
sao ID: sao-250931889
curation status: uncurated
disjoint with: Regional Part Of Neuron Protrusion
disjoint with: Neuron Process

Regional Part Of Neuron Protrusion
type: Class
subclass of: Regional Part Of Neuron
curation status: uncurated
sao ID: sao-750951932
disjoint with: Neuron Process

NMDA Receptor
type: Class
umls ID: C0080093
subclass of: Glutamate Receptor
curation status: uncurated
sao ID: sao794753833
disjoint with: AMPA Receptor
definition: 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).

Glutamate Receptor
type: Class
disjoint with: Acetylcholine Receptor
sao ID: sao1164727693
umls ID: C0061465
subclass of: Neurotransmitter Receptor
definition: 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).
curation status: uncurated

Orthogonal Array
type: Class
synonym: square array
curation status: uncurated
subclass of: Restriction
  some values from: Aquaporin 4
  on property: has Molecular Constituent
subclass of: Cell Component Aggregate Object
sao ID: sao1747012216
definition: Square arrays of closely spaced intramembrane particles, 4-6 nm in size seen in astrocyte processes, now known to contain aquaporins.

Aquaporin 4
type: Class
umls ID: C0292777
sao ID: sao1548226791
curation status: uncurated
subclass of: Water Channel
abbreviation: AQP4

Cell Component Aggregate Object
type: Class
sao ID: sao991156472
subclass of: ObjectAggregate
disjoint with: Cell Regional Part Aggregate Object
disjoint with: Junction Complex
disjoint with: Supra Cellular Structure

Nucleus Type
type: Class
definition: The shape of the nucleus, e.g., round, lobulated, indented
disjoint with: Chemical Synapse Type
curation status: uncurated
contributor: Maryann Martone
subclass of: Morphological Type
sao ID: sao343486489
disjoint with: Spine Type
disjoint with: Axon Type
disjoint with: Vesicle Type
disjoint with: Cristae Type
disjoint with: Mitochondrial Type

Vesicle Type
type: Class
disjoint with: Axon Type
sao ID: sao1863391630
disjoint with: Spine Type
disjoint with: Chemical Synapse Type
subclass of: Morphological Type
curation status: uncurated
disjoint with: Cristae Type
disjoint with: Mitochondrial Type
abbreviation: Refers to the morphology of a vesicle.

Nuclear Outer Membrane
type: Class
curation status: uncurated
definition: 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).
gene ontology ID: 0005640
sao ID: sao1617136075
subclass of: Nuclear Membrane
subclass of: Restriction
  on property: continuous With
  some values from: Endoplasmic Reticulum

Nuclear Membrane
type: Class
gene ontology ID: 0031965
subclass of: Nuclear Subcomponent
disjoint with: Nuclear Body
curation status: uncurated
disjoint with: Nuclear Lamina
disjoint with: Nucleolus
definition: Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology).
umls ID: C0028584
sao ID: sao1687101204
disjoint with: Interchromatin Granule

Centriole
type: Class
subclass of: Non Membrane Bound Organelle
definition: 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).
curation status: uncurated
gene ontology ID: 0005814
umls ID: C0007708
disjoint with: Nucleolus
sao ID: sao95019936

Anatomical Coordinate
type: Class
definition: Anatomical location which specifies the relationship between one or more physical anatomical entities in terms of...
subclass of: Anatomical Location
curation status: uncurated
birnlex definition source: FMA
sao ID: sao-843826795
birnlex external source: FMA

Anatomical Location
type: Class
curation status: uncurated
sao ID: sao1426984192
subclass of: Anatomical Relationship
definition: Spatial association relationship which describes the containment, adjacency, and anatomical coordinates of physical anatomical entities. Examples: anatomical containment, anatomical adjacency, anatomical coordinate (FMA).

Regional Part Of Spiny Dendrite
type: Class
sao ID: sao1590928667
subclass of: Subregional Part Of Neuron Process
curation status: uncurated

Synantocyte
type: Class
comment: 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.
externally sourced definition: 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).
subclasses disjoint: true
curation status: graph position temporary
created date: 2007-01-13
sao ID: sao-408886955
disjoint with: Bipolar Progenitor Cell
subclass of: NG2 Cell
definition: NG2 cell characterized by a differentiated, stellate appearance that lack expression of most differentiated glial cell-type specific markers.

Bipolar Progenitor Cell
type: Class
subclasses disjoint: true
definition: A type of NG2 positive cell that resemble oligodendrocyte precursors
externally sourced definition: Ligon et al PNAS 2006, PMID: 16682644
sao ID: sao1492258085
subclass of: NG2 Cell

NG2 Cell
type: Class
subclass of: Macroglia
curation status: uncurated
disjoint with: Astrocyte
disjoint with: Pectin Glial Cell
disjoint with: Ependymoglial Cell
temp definition: 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
sao ID: sao265591209
subclasses disjoint: true
disjoint with: Modified Astrocyte
disjoint with: Schwann Cell
disjoint with: Oligodendrocyte

KIF3A
type: Class
curation status: uncurated
sao ID: sao483834130
subclass of: Molecular Motor
umls ID: C0255106

Protoplasmic Astrocyte
type: Class
definition: Astrocyte characterized by spongy appearance and many vellous processes; often found in gray matter.
sao ID: sao374942934
subclass of: Astrocyte
subclass of: Restriction
  all values from: Regional Part Of Astrocyte
  on property: has Regional Part
umls ID: C0228089
subclasses disjoint: true
synonym: Passive Astrocyte
synonym: GluT Astrocyte
curation status: uncurated

Potassium Channel
type: Class
subclass of: Ion Channel
umls ID: C0032824
definition: 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).
sao ID: sao666200564
curation status: uncurated

Round Clear
type: Class
sao ID: sao967304317
disjoint with: Pleomorphic
curation status: uncurated
subclass of: Vesicle Type

Pleomorphic
type: Class
subclass of: Vesicle Type
curation status: uncurated
sao ID: sao854959971
definition: Characterized by many shapes in glutaraldehyde fixed tissue.

GluR2
type: Class
subclass of: AMPA Receptor
umls ID: C0536483
sao ID: sao1390810994
disjoint with: GlurR3
curation status: uncurated

Extracellular Space
type: Class
curation status: uncurated
disjoint with: Apical Pole Of Neuron
subclass of: Site
disjoint with: Cellular Space
gene ontology ID: 0005616
disjoint with: Mitochondrial Site
disjoint with: Basal Pole Of Neuron
disjoint with: Node Related Site
disjoint with: Cell Interior
disjoint with: Spine Related Site
disjoint with: Regional Part Of Neuronal Cell Body
definition: That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid (Gene Ontology).
disjoint with: Intercellular Junction Site
disjoint with: Cell Cell Contact Zone
sao ID: sao1425028079

Mitochondrial Site
type: Class
subclass of: Site
sao ID: sao-1367457321
disjoint with: Node Related Site
disjoint with: Cell Interior
disjoint with: Basal Pole Of Neuron
disjoint with: Regional Part Of Neuronal Cell Body
disjoint with: Intercellular Junction Site
disjoint with: Cell Cell Contact Zone
disjoint with: Cellular Space
disjoint with: Apical Pole Of Neuron

Spine Related Site
type: Class
disjoint with: Regional Part Of Neuronal Cell Body
disjoint with: Mitochondrial Site
subclass of: Site
disjoint with: Cell Cell Contact Zone
disjoint with: Intercellular Junction Site
disjoint with: Node Related Site
disjoint with: Cellular Space
sao ID: sao553711217
disjoint with: Basal Pole Of Neuron
disjoint with: Apical Pole Of Neuron
disjoint with: Cell Interior

Intercellular Junction Site
type: Class
disjoint with: Cell Interior
disjoint with: Apical Pole Of Neuron
disjoint with: Basal Pole Of Neuron
disjoint with: Node Related Site
disjoint with: Regional Part Of Neuronal Cell Body
definition: The site of cell-cell contact containing a morphologically identified junctional complex joining the two cells.
disjoint with: Cell Cell Contact Zone
sao ID: sao1922892319
comment: 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.
subclass of: Site
gene ontology ID: 0005911
disjoint with: Cellular Space
curation status: definition incomplete

Alpha Actinin
type: Class
umls ID: C0917705
curation status: uncurated
sao ID: sao1659393491
subclass of: Actin Binding Protein
definition: Cytoskeletal protein present in Z lines of muscle fibrils and at sites of non-muscle cell contact with a substrate (CSP).

Actin Binding Protein
type: Class
sao ID: sao1785445428
umls ID: C0001239
curation status: uncurated
definition: 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).
subclass of: Actin Associated Protein

Sorting Endosome
type: Class
definition: 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.
curation status: uncurated
sao ID: sao1028571114
subclass of: Endosome

Post-synaptic Site
type: Class
subclass of: Synaptic Site
subclass of: Restriction
  some values from: Post-synaptic Density
  on property: has Location Of
sao ID: sao1074198261

Post-synaptic Density
type: Class
sao ID: sao1196688972
gene ontology ID: 0014069
definition: 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).
bonfire ID: BF_C000103
subclass of: Post-synaptic Component

has Location Of
type: ObjectProperty
range: Class
  union of: ObjectAggregate
  union of: Object
inverse of: located in
domain: Site
sao ID: sao9371595441

Cell Process
type: Class
disjoint with: Non Neural Cell Compartment
disjoint with: Cell Protrusion
disjoint with: Regional Part Of Glia
disjoint with: Regional Part Of Neuron
sao ID: sao-1828894864
subclass of: Regional Part Of Cell
curation status: uncurated

Non Neural Cell Compartment
type: Class
disjoint with: Regional Part Of Glia
disjoint with: Cell Protrusion
subclass of: Regional Part Of Cell
curation status: uncurated
sao ID: sao1843719868

Cell Protrusion
type: Class
sao ID: sao-82111036
disjoint with: Regional Part Of Glia
subclass of: Regional Part Of Cell
curation status: uncurated

Perivascular Astrocyte
type: Class
disjoint with: Fibrous Astrocyte
subclass of: Astrocyte
curation status: graph position temporary
disjoint with: Protoplasmic Astrocyte
sao ID: sao1239389
disjoint with: Radial Astrocyte
subclasses disjoint: true
disjoint with: Sub-ependymal Astrocyte
definition: 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)

Fibrous Astrocyte
type: Class
curation status: uncurated
umls ID: C0228090
subclass of: Astrocyte
disjoint with: Radial Astrocyte
disjoint with: Protoplasmic Astrocyte
sao ID: sao2078084673
subclasses disjoint: true
definition: Astrocytes characterized by high content of intermediate filaments and few vellous processes; often found in white matter.

Sub-ependymal Astrocyte
type: Class
disjoint with: Fibrous Astrocyte
disjoint with: Protoplasmic Astrocyte
subclass of: Marginal Astrocyte
sao ID: sao399295448
definition: Large astrocyte that forms a layer that lies beneath the ependymal layer.
curation status: uncurated
subclasses disjoint: true

PSD95
type: Class
sao ID: sao642625418
curation status: uncurated
subclass of: Scaffolding Protein

Scaffolding Protein
type: Class
disjoint with: Membrane Receptor
disjoint with: PDZ Containing Protein
disjoint with: Membrane Pump
disjoint with: Molecular Motor
disjoint with: Enzyme
disjoint with: Extracellular Matrix Protein
disjoint with: Clathrin
disjoint with: Synapse Associated Protein
disjoint with: Myelin Associated Protein
disjoint with: Connexin
subclass of: Protein
curation status: uncurated
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: GTPases
disjoint with: Neurotransmitter Associated Protein
disjoint with: Respiratory Chain Complex
sao ID: sao1280179455
disjoint with: Transporter Protein
disjoint with: Cytoskeletal Associated Protein
disjoint with: Ion Channel
disjoint with: Cytokine
disjoint with: Cell Adhesion Molecule
disjoint with: Transcription Factor
disjoint with: Calcium Binding Protein
disjoint with: Growth Factor
disjoint with: Cytoskeletal Protein

Nuclear Inner Membrane
type: Class
gene ontology ID: 0005637
subclass of: Nuclear Membrane
definition: The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology).
sao ID: sao1612527463
curation status: uncurated
disjoint with: Nuclear Outer Membrane
disjoint with: Smooth Membrane

Smooth Membrane
type: Class
curation status: uncurated
definition: Characterized by a nuclear membrane with no indentations.
disjoint with: Nuclear Outer Membrane
subclass of: Nuclear Membrane
sao ID: sao1845602529

Dense Material
type: Class
subclass of: Regional Part Of Spine Apparatus
curation status: uncurated
sao ID: sao1004601938

Regional Part Of Spine Apparatus
type: Class
disjoint with: Regional Part Of RER
disjoint with: Regional Part Of Nucleolus
disjoint with: Regional Part Of Mitochondria
disjoint with: Regional Part Of Mitochondrial Membrane
disjoint with: Regional Part Of Golgi
sao ID: sao1682692988
curation status: uncurated
subclass of: Regional Part Of Cell Component

has Neurotransmitter
type: ObjectProperty
inverse of: is Neurotransmitter Of
sub property of: has Part
range: Molecule
comment: Neurotransmitter associated with neuronal class
domain: Neuron
sao ID: sao1490541696

Polarity
type: Class
comment: Need to define property with "reference point"
curation status: uncurated
subclass of: Quality
sao ID: sao349337269
disjoint with: Measurement
disjoint with: Anatomical Pattern

Endoplasmic Reticulum Exit Site
type: Class
curation status: uncurated
definition: 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).
subclass of: Regional Part Of RER
sao ID: sao124393998

Regional Part Of RER
type: Class
subclass of: Regional Part Of Cell Component
curation status: uncurated
disjoint with: Regional Part Of Mitochondrial Membrane
disjoint with: Regional Part Of Mitochondria
definition: 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).
sao ID: sao2019617624

Cell Body Referent Polarity
type: Class
curation status: uncurated
subclass of: Polarity
sao ID: sao311075036

Simple
type: Class
disjoint with: Filopodial
definition: 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).
subclass of: Spine Type
curation status: uncurated
sao ID: sao614188547

Filopodial
type: Class
sao ID: sao1141340175
definition: 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.
subclass of: Spine Type
curation status: uncurated

Gap Junction
type: Class
disjoint with: Zonula Occludens
gene ontology ID: 0005921
disjoint with: Zonula Adhaerens
curation status: uncurated
disjoint with: Septate Junction
sao ID: sao118541872
umls ID: C0206117
disjoint with: Macular Adhaerentia
subclass of: Intercellular Junction Site
disjoint with: Synaptic Site
definition: 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).

Zonula Occludens
type: Class
disjoint with: Septate Junction
gene ontology ID: 0005923
curation status: uncurated
disjoint with: Zonula Adhaerens
definition: 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).
disjoint with: Macular Adhaerentia
subclass of: Intercellular Junction Site
synonym: tight junction
sao ID: sao1939999134

Zonula Adhaerens
type: Class
sao ID: sao1400623473
subclass of: Intercellular Junction Site
definition: Adherent, symmetrical junction characterized by widened extracellular space and filamentous material (Peters, Palay and Webster, 1991).
curation status: uncurated
synonym: fascia adhaerens

Septate Junction
type: Class
disjoint with: Zonula Adhaerens
disjoint with: Macular Adhaerentia
subclass of: Intercellular Junction Site
definition: 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
gene ontology ID: 0005918
sao ID: sao427941916
curation status: graph position temporary

Macular Adhaerentia
type: Class
sao ID: sao1956738165
pending action note: Look into the relationship of Macular and zonula adhaerentia and determine whether they are all subclasses of adhaerent junction
subclass of: Intercellular Junction Site
curation status: uncurated
disjoint with: Zonula Adhaerens

Pre-synaptic Part
type: Class
curation status: uncurated
synonym: Pre-synaptic compartment
subclass of: Part Of Synapse
sao ID: sao2044996357
disjoint with: Junctional Part

located in
type: ObjectProperty
domain: Class
  union of: ObjectAggregate
  union of: Object
inverse of: has Location Of
range: Site
sao ID: sao4245285112

Glycogen
type: Class
curation status: uncurated
umls ID: C0017911
sao ID: sao196990275
subclass of: Carbohydrate

Microtubule Mediated Motility
type: Class
subclass of: Motility
definition: Refers to the transport of a structure via microtubules and microtubule-associated motors.
sao ID: sao1301290450

Neurotransmitter Receptor
type: Class
disjoint with: G Coupled Receptor
disjoint with: Synthetic Enzyme
definition: 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).
curation status: uncurated
subclass of: Membrane Receptor
sao ID: sao587592318
umls ID: C0034828

Calreticulin
type: Class
disjoint with: ERp57
disjoint with: Endoplasmin
curation status: uncurated
umls ID: C0054543
sao ID: sao2060855807
definition: 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).
subclass of: Calcium Binding Protein

ERp57
type: Class
subclass of: Calcium Binding Protein
sao ID: sao698543279
curation status: uncurated
umls ID: C0528009

Endoplasmin
type: Class
subclass of: Calcium Binding Protein
curation status: uncurated
umls ID: C0059259
disjoint with: ERp57
sao ID: sao1951490568

Thin
type: Class
subclass of: Pedunculated
curation status: uncurated
definition: 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).
sao ID: sao1643644091
disjoint with: Simple
disjoint with: Filopodial

Pedunculated
type: Class
subclass of: Spine Type
curation status: graph position temporary
disjoint with: Simple
disjoint with: Filopodial
sao ID: sao2045795635
definition: 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.
comment: May need to do more reading to determine whether this should be a parent of mushroom and thin.

Electrotonic Synapse
type: Class
subclass of: Synapse
curation status: uncurated
synonym: Electrical Synapse
sao ID: sao1311109124
disjoint with: Mixed Synapse
disjoint with: Chemical Synapse
definition: 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).

Synapse
type: Class
disjoint with: Gap Junction Plaque
sao ID: sao914572699
curation status: uncurated
definition: 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).
gene ontology ID: 0045202
subclass of: Intercellular Junction

Mixed Synapse
type: Class
curation status: uncurated
definition: Synaptic contact characterized by both electrical and chemical synaptic junctions.
definition: Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991).
subclass of: Synapse
sao ID: sao1506103497
disjoint with: Chemical Synapse

Trans Face
type: Class
subclass of: Regional Part Of Golgi
definition: The concave side of the Golgi apparatus, from which secretory vesicles emerge (Gene Ontology).
sao ID: sao1039242387
disjoint with: Cis Face
gene ontology ID: 0005802
curation status: uncurated

Glomerulus
type: Class
definition: Large synaptic bouton found in areas like olfactory bulb, cerebellar cortex and thalamus, that contacts many post-synaptic targets.
sao ID: sao587858733
curation status: uncurated
subclass of: Neuropil

Neuropil
type: Class
curation status: uncurated
definition: 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).
umls ID: C0228081
subclass of: Supra Cellular Structure
disjoint with: Intercellular Junction
disjoint with: Pinceau
sao ID: sao205380252

Syndecan-2
type: Class
curation status: uncurated
synonym: fibroglycan
subclass of: Syndecan
umls ID: C0174307
sao ID: sao1504920769

Neuronal Cell Body
type: Class
disjoint with: Regional Part Of Neuron Process
umls ID: C0599444
disjoint with: Neuron Protrusion
subclass of: Restriction
  some values from: Oval
  on property: has Morphological Type
subclass of: Restriction
  on property: has Morphological Type
  some values from: Fusiform
subclass of: Restriction
  all values from: Class
    union of: Fusiform
    union of: Spherical
    union of: Oval
    union of: Pyramidal
  on property: has Morphological Type
sao ID: sao1044911821
subclass of: Restriction
  on property: has Morphological Type
  some values from: Pyramidal
definition: Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA).
subclass of: Restriction
  some values from: Class
    union of: Axon
    union of: Somatic Spine
    union of: Regional Part Of Neuron
    union of: Subregional Part Of Neuron Process
    union of: Dendrite
  on property: continuous With
disjoint with: Regional Part Of Spine
curation status: uncurated
subclass of: Regional Part Of Neuron
subclass of: Restriction
  on property: has Morphological Type
  some values from: Spherical
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of Neuronal Cell Body
disjoint with: Neuron Process
disjoint with: Regional Part Of Neuron Protrusion
synonym: soma

Fusiform
type: Class
disjoint with: Oval
disjoint with: Pyramidal
disjoint with: Spherical
definition: Elongated shape that tapers at both ends
curation status: curation complete
subclass of: Soma Type
synonym: Spindle
sao ID: sao542875575

Pyramidal
type: Class
sao ID: sao-1465673360
subclass of: Soma Type
definition: Generally triangular-shaped soma with a dendrite emerging from the apical pole and basilar dendrites emerging from two or more basal poles
curation status: curation complete
disjoint with: Oval
disjoint with: Spherical

Somatic Spine
type: Class
subclass of: Spine
subclass of: Restriction
  on property: continuous With
  some values from: Neuronal Cell Body
definition: Spine emanating from the cell soma.
curation status: uncurated
sao ID: sao2048514053

Hippocampal CA1 Pyramidal Neuron
type: Class
subclass of: Restriction
  has value: hippocampal area CA1
  on property: anatomical Location General
disjoint with: Hippocampal CA3 Pyramidal Neuron
subclass of: Restriction
  cardinality: 1
  on property: Number of Axons
subclass of: Restriction
  on property: has Regional Part
  some values from: Dendritic Spine
subclass of: Restriction
  on property: has Regional Part
  some values from: Recurrent Collateral
curation status: uncurated
subclass of: Restriction
  on property: has Regional Part
  some values from: Neuronal Cell Body
subclass of: Hippocampal Pyramidal Neuron
subclasses disjoint: true
subclass of: Restriction
  on property: has Regional Part
  some values from: Apical Dendrite
sao ID: sao830368389

Number of Axons
type: FunctionalProperty
range: int
type: DatatypeProperty
sao ID: sao1384659949
domain: Neuron
comment: 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.
label: number Of Axons

Dendritic Spine
type: Class
sao ID: sao1799103720
definition: 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).
curation status: uncurated
gene ontology ID: 0043197
subclass of: Spine
subclass of: Restriction
  on property: is Regional Part Of
  some values from: Dendritic Shaft
umls ID: C0872341
disjoint with: Somatic Spine

Recurrent Collateral
type: Class
curation status: uncurated
definition: Axon collateral that ramifies in the area of the soma of the cell of origin.
subclass of: Axon Collateral
disjoint with: Schaffer Collateral
sao ID: sao1642494436

Apical Dendrite
type: Class
curation status: uncurated
sao ID: sao273773228
subclass of: Dendrite
bonfire ID: BF_C000112

Acetylcholine
type: Class
disjoint with: Dopamine
disjoint with: Serotonin
umls ID: C0001041
sao ID: sao185580330
curation status: uncurated
definition: 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).
subclass of: Molecule

Attachment
type: Class
curation status: uncurated
sao ID: sao1179195262
subclass of: Connectivity
umls ID: C0923872

Connectivity
type: Class
subclass of: Spatial Relationship
curation status: uncurated
sao ID: sao1211239798
umls ID: C0925206

Nucleolus-associated Heterochromatin
type: Class
definition: Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974).
curation status: uncurated
subclass of: Nuclear Body
subclass of: Restriction
  some values from: Nucleolus
  on property: associated Cell Component
sao ID: sao1210952635

associated Cell Component
type: ObjectProperty
sub property of: associated With
sao ID: sao1356746816
range: Cellular Component
domain: Class
  union of: Site
  union of: Cellular Subcomponent
comment: Used to describe a physical relationship between two or more cellular components

Fused Vesicle
type: Class
disjoint with: Round Clear
disjoint with: Pleomorphic
curation status: uncurated
definition: Synaptic vesicle that is fused to the pre-synaptic membrane, forming the characteristic omega profile.
subclass of: Vesicle Type
sao ID: sao128105491
synonym: Omega profile

Alpha Tanycyte
type: Class
subclass of: Tanycyte
subclasses disjoint: true
sao ID: sao971374186
curation status: uncurated

Tanycyte
type: Class
disjoint with: Pectin Glial Cell
subclass of: Restriction
  has value: CNS
  on property: location CNS PNS
curation status: uncurated
disjoint with: Pigment Epithelial Cell
subclass of: Ependymoglial Cell
synonym: Stretch cells
subclass of: Restriction
  all values from: Regional Part Of Tanycyte
  on property: has Regional Part
sao ID: sao1149261773
umls ID: C0926518
disjoint with: Radial Glia
subclasses disjoint: true
disjoint with: Ependymal Cell
definition: 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.
cell ontology ID: CL:0000643
disjoint with: Choroid Epithelial Cell

Anaphase
type: Class
sao ID: sao21946128
subclass of: Cell Cyle Phase
gene ontology ID: 0051322
umls ID: C0002788
definition: 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).

Regional Part Of Dendritic Tree
type: Class
sao ID: sao553876173
curation status: uncurated
subclass of: Obsolete class

Alpha Motor Neuron
type: Class
synonym: lower motor neuron
definition: 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.
disjoint with: Gamma Motor Neuron
sao ID: sao1154704263
curation status: uncurated
subclass of: Motor Neuron
definition source: Wikipedia
subclasses disjoint: true

Gamma Motor Neuron
type: Class
sao ID: sao1438006234
subclasses disjoint: true
umls ID: C0026610
subclass of: Motor Neuron
curation status: uncurated
synonym: fusimotor neuron
cell ontology ID: CL:0000717
definition: 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).

Vascular Endothelial Cell
type: Class
comment: This cell class is not contained in the Cell Type Ontology
curation status: uncurated
subclass of: Vascular Cell
sao ID: sao1543450574

associated Cellular Element
type: ObjectProperty
domain: Class
  union of: Supracellular Object Part
  union of: Regional Part Of Cell
  union of: Cell
range: Class
  union of: Regional Part Of Cell
  union of: Cell
sao ID: sao180517057
sub property of: associated With
comment: Cellular element derived from another cell associated with a compartment, e.g., myelin

RSlo
type: Class
curation status: uncurated
subclass of: Calcium Activated Potassium Channel
sao ID: sao618069210

Branched Spine
type: Class
disjoint with: Sessile
definition: Characterized by two or more heads (Harris et. al 1992) that emerge from the same origin (Sorra KE and Harris KM, 2000).
disjoint with: Filopodial
subclass of: Spine Type
disjoint with: Simple
disjoint with: Mushroom
sao ID: sao268063700
disjoint with: Stubby
disjoint with: Thin
curation status: uncurated
disjoint with: Pedunculated

Sessile
type: Class
disjoint with: Filopodial
disjoint with: Pedunculated
disjoint with: Simple
disjoint with: Thin
curation status: uncurated
sao ID: sao941226261
definition: Also refers to a stubby spine.
subclass of: Spine Type

Mushroom
type: Class
definition: Characterized by the diameter of the head being much greater than that of the neck (Harris et. al 1992).
curation status: uncurated
subclass of: Pedunculated
disjoint with: Simple
disjoint with: Filopodial
disjoint with: Thin
disjoint with: Sessile
sao ID: sao1983595164

Stubby
type: Class
disjoint with: Simple
sao ID: sao1786354232
disjoint with: Filopodial
subclass of: Spine Type
disjoint with: Sessile
disjoint with: Mushroom
definition: Characterized by the diameter of the neck being similar to that of the head (Harris et. al 1992).
disjoint with: Pedunculated
disjoint with: Thin
curation status: uncurated

Membranous Inclusion
type: Class
curation status: uncurated
subclass of: Obsolete class
sao ID: sao673040867

Glial Filament
type: Class
subclass of: Intermediate Filament
disjoint with: Neurofilament
sao ID: sao-1863852493
curation status: uncurated

Intermediate Filament
type: Class
sao ID: sao952483289
curation status: uncurated
gene ontology ID: 0005882
definition: 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).
subclass of: Cytoskeletal Element
umls ID: C0021770
disjoint with: Microtubule
disjoint with: Microfilament

Neurofilament
type: Class
sao ID: sao1316272517
umls ID: C0027834
gene ontology ID: 0005883
definition: 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).
curation status: uncurated
subclass of: Intermediate Filament

Spectrin
type: Class
disjoint with: Glial Fibrillary Acidic Protein
disjoint with: Tubulin
subclass of: Cytoskeletal Protein
curation status: uncurated
umls ID: C0037799
disjoint with: Myosin
definition: 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).
sao ID: sao536287099
bonfire ID: 0008091
gene ontology ID: 0008091
disjoint with: Neurofilament Protein
disjoint with: Actin

Glial Fibrillary Acidic Protein
type: Class
definition: The major component of glia-specific intermediate filament primarily found in astrocytes and Bergmann glia.
disjoint with: Tubulin
disjoint with: Neurofilament Protein
curation status: uncurated
disjoint with: Actin
subclass of: Cytoskeletal Protein
sao ID: sao333741607
disjoint with: Myosin
umls ID: C0017626
abbreviation: GFAP

Myosin
type: Class
subclass of: Cytoskeletal Protein
umls ID: C0027096
definition: 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).
sao ID: sao1810043179
disjoint with: Actin
disjoint with: Neurofilament Protein
disjoint with: Tubulin
curation status: uncurated

Ribosome
type: Class
umls ID: C0035553
definition: 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).
disjoint with: Nucleolus
disjoint with: Centriole
gene ontology ID: 0005840
subclass of: Non Membrane Bound Organelle
curation status: uncurated
sao ID: sao1429207766

MAP2
type: Class
umls ID: C0024773
curation status: uncurated
sao ID: sao1707694834
subclass of: Microtubule Associated Protein

Microtubule Associated Protein
type: Class
umls ID: C0026042
disjoint with: Actin Associated Protein
definition: Proteins found in the microtubules (MSH).
sao ID: sao1174532162
curation status: uncurated
subclass of: Cytoskeletal Associated Protein

Radial Glia
type: Class
disjoint with: Schwann Cell
synonym: radial glial cell
cell ontology ID: CL:0000681
disjoint with: Oligodendrocyte
umls ID: C0815005
disjoint with: Pigment Epithelial Cell
disjoint with: Ependymal Cell
definition: 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).
sao ID: sao621772985
disjoint with: Astrocyte
subclasses disjoint: true
disjoint with: NG2 Cell
subclass of: Ependymoglial Cell
disjoint with: Pectin Glial Cell
disjoint with: Modified Astrocyte
curation status: uncurated
disjoint with: Choroid Epithelial Cell

Pigment Epithelial Cell
type: Class
subclasses disjoint: true
sao ID: sao-423426544
disjoint with: Ependymal Cell
disjoint with: Choroid Epithelial Cell
definition: Located in the sub-retinal space, these cells form the sub-retinal blood-brain barrier and contain light-absorbing melanin pigment granules
comment: There is a visual pigment cell in the cell type ontology but we are not sure if this is the same cell
subclass of: Ependymoglial Cell

Ependymal Cell
type: Class
sao ID: sao1714094301
definition: 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).
curation status: graph position temporary
definition: A neurectoderm derived cell that lines the neural lumen (Cell Ontology).
cell ontology ID: CL:0000065
subclasses disjoint: true
comment: We are not sure whether ependymal cells should be considered a type of ependymoglial cell
umls ID: C0228092
subclass of: Ependymoglial Cell

Ependymoglial Cell
type: Class
subclass of: Macroglia
definition: 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)
subclasses disjoint: true
disjoint with: Schwann Cell
sao ID: sao3593465546

Choroid Epithelial Cell
type: Class
disjoint with: Ependymal Cell
subclass of: Ependymoglial Cell
curation status: uncurated
subclasses disjoint: true
sao ID: sao1541570510
definition: Cuboidal shaped epithelial cell forming one of the components of the choroid plexus (Peters, Palay and Webster, 1991).

Dendritic Branch
type: Class
curation status: uncurated
sao ID: sao884265541
disjoint with: Branch Point Of Dendrite
disjoint with: Trunk
disjoint with: Terminal Specialization
subclass of: Regional Part Of Dendrite
definition: Refers to dendrites arising from another dendrite.

Branch Point Of Dendrite
type: Class
disjoint with: Trunk
disjoint with: Terminal Specialization
curation status: uncurated
subclass of: Regional Part Of Dendrite
sao ID: sao-1348591767

S100 beta
type: Class
sao ID: sao1022370595
subclass of: Calcium Binding Protein
curation status: uncurated
umls ID: C0654870
disjoint with: Calsequestrin
disjoint with: Calreticulin
disjoint with: ERp57
disjoint with: Endoplasmin

Calsequestrin
type: Class
disjoint with: ERp57
disjoint with: Calreticulin
disjoint with: Endoplasmin
umls ID: C0006787
curation status: uncurated
sao ID: sao1508721375
definition: 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).
subclass of: Calcium Binding Protein

Rho GTPase
type: Class
subclass of: GTPases
umls ID: C0174045
curation status: uncurated
definition: 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).
sao ID: sao908816138

GTPases
type: Class
disjoint with: Myelin Associated Protein
disjoint with: Clathrin
disjoint with: Membrane Pump
disjoint with: Ion Channel
definition: Enzymes that hydrolyze GTP to GDP. EC 3.6.1.- (MSH).
disjoint with: Calcium Binding Protein
disjoint with: Cytokine
disjoint with: PDZ Containing Protein
subclass of: Protein
disjoint with: Cytoskeletal Associated Protein
disjoint with: Synapse Associated Protein
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: Extracellular Matrix Protein
disjoint with: Respiratory Chain Complex
umls ID: C0018296
disjoint with: Transporter Protein
disjoint with: Connexin
disjoint with: Membrane Receptor
disjoint with: Neurotransmitter Associated Protein
disjoint with: Molecular Motor
disjoint with: Enzyme
disjoint with: Transcription Factor
sao ID: sao271459227
disjoint with: Cell Adhesion Molecule
disjoint with: Growth Factor
curation status: uncurated

Cortical Spiny Stellate Cell
type: Class
subclasses disjoint: true
subclass of: Cortical Stellate Cell
subclass of: Restriction
  on property: is spiny
  has value: true
sao ID: sao1236796660
curation status: uncurated
bonfire ID: BF_T0000036
definition: 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).

is spiny
type: FunctionalProperty
comment: Denotes whether a neuron or dendrite is characterized by at least one spine.
range: boolean
domain: Class
  union of: Dendritic Shaft
  union of: Neuron
  union of: Dendrite
sao ID: sao1863785805
type: DatatypeProperty
label: is Spiny

Living Animal
type: Class
sao ID: sao1694199019
definition: Indicates that the feature was observed in the living animal.
subclass of: In Vivo

Length
type: Class
disjoint with: Density
curation status: uncurated
disjoint with: Volume
disjoint with: Half Life
disjoint with: Speed
disjoint with: Cross Section Diameter Minor
subclass of: Measurement
sao ID: sao1217691568
disjoint with: Surface Area
disjoint with: Spacing

Non Myelinating Oligodendrocyte
type: Class
subclass of: Obsolete class
curation status: uncurated
sao ID: sao546569295

Vellous Process
type: Class
subclass of: Astrocyte Process
definition: Refers to the fine, veil-like terminal processes of protoplasmic astrocytes.
curation status: graph position temporary
curation status: uncurated
sao ID: sao1189060993
comment: is this the same as what is now termed the peripheral astrocyte process?

Beta Tubulin
type: Class
curation status: uncurated
sao ID: sao1202564066
umls ID: C0005290
subclass of: Tubulin
definition: One of two globular polypeptides forming microtubules.

Dopamine
type: Class
curation status: uncurated
sao ID: sao2050279787
umls ID: C0013030
subclass of: Monoamines
definition: 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).
disjoint with: Serotonin

Spiny Bracelet Of Nageotte
type: Class
sao ID: sao937871668
curation status: uncurated
subclass of: Regional Part Of Schwann Cell
definition: Paranodal terminations of Schwann cells that do not directly contact the paranodal axon membane. Usually found in thicker myelin. (Sosinsky et al., 2005)

Filopodium
type: Class
gene ontology ID: 0030175
sao ID: sao-1046371754
subclass of: Neuron Protrusion
curation status: uncurated
disjoint with: Excrescence
definition: 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)

Excrescence
type: Class
sao ID: sao-961694769
curation status: uncurated
subclass of: Neuron Protrusion

Neurotrophin-4
type: Class
subclass of: Neurotrophin
umls ID: C0166894
curation status: uncurated
sao ID: sao692404013

Neurotrophin
type: Class
sao ID: sao1473913158
umls ID: C0132298
curation status: uncurated
disjoint with: Platelet Derived Growth Factor
subclass of: Growth Factor
definition: 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).

SERCA3
type: Class
subclass of: SERCA
disjoint with: SERCA2
curation status: uncurated
umls ID: C0916181
sao ID: sao1127560844

SERCA2
type: Class
umls ID: C0916183
sao ID: sao1016012060
curation status: uncurated
subclass of: SERCA

Myelin Subcompartment
type: Class
curation status: uncurated
sao ID: sao359916506
subclass of: Obsolete class

Pinceau
type: Class
curation status: uncurated
sao ID: sao732341560
subclass of: Supra Cellular Structure
definition: 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.

Supra Cellular Structure
type: Class
sao ID: sao508165343
disjoint with: Cell Regional Part Aggregate Object
definition: A morphological or functional domain formed by parts of two or more cells, e.g., neuropil, dendritic bundles.
curation status: uncurated
subclass of: ObjectAggregate
subclass of: Restriction
  some values from: Regional Part Of Cell
  on property: has Aggregate Part

Nuclear DNA
type: Class
sao ID: sao1785015039
subclass of: DNA
disjoint with: Mitochondrial DNA
curation status: uncurated

Mitochondrial DNA
type: Class
definition: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial genome is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins (MSH).
umls ID: C0012929
curation status: uncurated
sao ID: sao529397229
subclass of: DNA

Proximal End
type: Class
definition: Ending of a process closest to the cell soma.
curation status: uncurated
sao ID: sao812067870
disjoint with: Distal End
subclass of: Cell Body Referent Polarity

Distal End
type: Class
sao ID: sao783483540
curation status: uncurated
definition: Ending of a process furthest from the cell soma.
subclass of: Cell Body Referent Polarity

Juxta Paranode Axon
type: Class
curation status: uncurated
sao ID: sao1191319089
definition: Region of axon immediately adjacent to the paranode.
disjoint with: Paranode Axon
subclass of: Restriction
  some values from: Paranode Axon
  on property: continuous With
subclass of: Regional Part Of Myelinated Axon

Paranode Axon
type: Class
sao ID: sao936144858
subclass of: Restriction
  some values from: Juxta Paranode Axon
  on property: continuous With
subclass of: Regional Part Of Myelinated Axon
curation status: uncurated

Regional Part Of Myelinated Axon
type: Class
sao ID: sao1791490892
disjoint with: Regional Part Of Spiny Dendrite
subclass of: Subregional Part Of Neuron Process
curation status: uncurated

Gap Junction Plaque
type: Class
subclass of: Intercellular Junction
comment: Need to determine what is the proper relationships between an electrotonic synapse and a gap junction
definition: 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.
sao ID: sao700839054

Intercellular Junction
type: Class
subclass of: Supra Cellular Structure
disjoint with: Pinceau
sao ID: sao1395777368

Biological Occurrent
type: Class
comment: "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).
curation status: uncurated
sao ID: sao1070274187
subclass of: Obsolete class

Inter-Golgi Transport Vesicle
type: Class
subclass of: Transport Vesicle
sao ID: sao1382918459
gene ontology ID: 0030143
curation status: uncurated
definition: A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack) (Gene Ontology).

Mitochondrial Membrane
type: Class
disjoint with: Endosomal Membrane
disjoint with: Vesicle Membrane
sao ID: sao1045389829
subclass of: Intracellular Membrane
curation status: uncurated

Ciliary Ganglion Neuron
type: Class
disjoint with: hair cell
disjoint with: Cortical Bipolar Cell
subclass of: Neuron
disjoint with: Globular Bushy Cell
disjoint with: mitral cell
subclass of: Restriction
  on property: anatomical Location General
  has value: ciliary ganglion
disjoint with: Cerebellar Granule Cell
sao ID: sao1366775348
subclasses disjoint: true
subclass of: Restriction
  has value: unipolar
  on property: process Number
subclass of: Restriction
  all values from: Class
    union of: Neuronal Cell Body
    union of: Somatic Spine
  on property: has Regional Part
subclass of: Restriction
  on property: Number of Primary Dendrites
  has value: 0
umls ID: C0229060
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Cortical Stellate Cell
disjoint with: Pyramidal Cell
disjoint with: Olfactory Granule Cell
subclass of: Restriction
  on property: circuit Type
  has value: projection neuron
disjoint with: Random Cell
disjoint with: Motor Neuron
disjoint with: Spherical Bushy Cell
disjoint with: Photoreceptor Cell
curation status: uncurated
disjoint with: Cerebellar Golgi Cell
subclass of: Restriction
  on property: has Regional Part
  some values from: Neuronal Cell Body
subclass of: Restriction
  some values from: Somatic Spine
  on property: has Regional Part
disjoint with: Double Bouquet Cell
disjoint with: Cerebellar Basket Cell
disjoint with: Substantia Nigra Dopaminergic Cell
disjoint with: Chandelier Cell

Number of Primary Dendrites
type: FunctionalProperty
sao ID: sao950829914
range: int
type: DatatypeProperty
comment: Refers to the minimum number of primary dendrites arising from the cell soma
domain: Neuron
label: number Primary Dendrites Min

Actin Associated Protein
type: Class
subclass of: Cytoskeletal Associated Protein
curation status: uncurated
sao ID: sao811908115

Ribosomal RNA
type: Class
definition: 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)
umls ID: C0035701
sao ID: sao2114723559
subclass of: RNA
curation status: uncurated
gene ontology ID: 0003735

RNA
type: Class
curation status: uncurated
umls ID: C0035668
sao ID: sao1843715402
definition: 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)
disjoint with: DNA
subclass of: Nucleic Acid

Vesicle Coat
type: Class
definition: Refers to any specialized coating present on a vesicle membrane, e.g., clathrin.
sao ID: sao1177708494
gene ontology ID: 0030120
disjoint with: Vesicle Cargo
umls ID: C1166749
subclass of: Vesicle Subcomponent

Vesicle Subcomponent
type: Class
subclass of: Cellular Subcomponent
sao ID: sao1455064842

Neurotransmitter Associated Protein
type: Class
disjoint with: Growth Factor
disjoint with: Extracellular Matrix Protein
disjoint with: Ion Channel
disjoint with: Cytoskeletal Associated Protein
disjoint with: Respiratory Chain Complex
disjoint with: Calcium Binding Protein
disjoint with: Myelin Associated Protein
disjoint with: Enzyme
disjoint with: Membrane Receptor
disjoint with: Molecular Motor
disjoint with: Synaptic Vesicle Associated Protein
disjoint with: PDZ Containing Protein
disjoint with: Transporter Protein
disjoint with: Clathrin
disjoint with: Synapse Associated Protein
disjoint with: Cytokine
subclass of: Protein
disjoint with: Membrane Pump
disjoint with: Transcription Factor
disjoint with: Cell Adhesion Molecule
disjoint with: Connexin
curation status: uncurated
sao ID: sao1440704204

Tau
type: Class
umls ID: C0085401
disjoint with: MAP2
subclass of: Microtubule Associated Protein
curation status: uncurated
definition: 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).
sao ID: sao1077731745

Cortical Smooth Stellate Cell
type: Class
curation status: uncurated
definition: A non-pyramidal neuron class found primarily in layer IV of mammalian neocortex characterized by relatively smooth dendrites (While and Rock, 1980).
subclass of: Cortical Stellate Cell
subclass of: Restriction
  has value: false
  on property: is spiny
disjoint with: Cortical Spiny Stellate Cell
subclasses disjoint: true
sao ID: sao770302354

Golgi Lamellae
type: Class
curation status: uncurated
subclass of: Golgi Subcomponent
sao ID: sao561419532

Golgi Subcomponent
type: Class
sao ID: sao624292949
subclass of: Cellular Subcomponent
curation status: uncurated

Nuclear Inclusion
type: Class
disjoint with: Nuclear Body
disjoint with: Nuclear Lamina
curation status: uncurated
sao ID: sao238602892
disjoint with: Nucleolus
definition: Cellular inclusion found in the nucleus.
subclass of: Obsolete class
disjoint with: Nuclear Membrane
disjoint with: Nucleoplasm
disjoint with: Interchromatin Granule

Nucleoplasm
type: Class
sao ID: sao661522542
disjoint with: Interchromatin Granule
disjoint with: Nuclear Body
disjoint with: Nucleolus
disjoint with: Nuclear Lamina
subclass of: Nuclear Subcomponent
definition: That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology).
gene ontology ID: 0005654
disjoint with: Nuclear Membrane
curation status: uncurated
umls ID: C0682537

Varicose Axon
type: Class
sao ID: sao1746802704
subclass of: Axon Type

Pars Granulosa
type: Class
definition: 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).
sao ID: sao1217793903
curation status: uncurated
umls ID: C0230580
subclass of: Regional Part Of Nucleolus

Regional Part Of Nucleolus
type: Class
curation status: uncurated
subclass of: Regional Part Of Cell Component
disjoint with: Regional Part Of Golgi
disjoint with: Regional Part Of RER
disjoint with: Regional Part Of Mitochondrial Membrane
disjoint with: Regional Part Of Mitochondria
sao ID: sao113580911

Membrane Bound Ribosome
type: Class
definition: A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it.
subclass of: Ribosome
curation status: uncurated
sao ID: sao1291545653

Spiny
type: Class
subclass of: Dendrite Type
curation status: uncurated
definition: Characterized by a high density of dendritic spines.
sao ID: sao638749545

Dendrite Type
type: Class
disjoint with: Chemical Synapse Type
subclass of: Morphological Type
disjoint with: Bouton Type
definition: Characterization based on high or low density of classical spines on dendrites.
disjoint with: Vesicle Type
sao ID: sao1959705051
disjoint with: Spine Type
disjoint with: Cristae Type
disjoint with: Mitochondrial Type
disjoint with: Nucleus Type
disjoint with: Axon Type
curation status: uncurated

Post-synaptic Part
type: Class
synonym: Post-synaptic compartment
curation status: uncurated
subclass of: Part Of Synapse
sao ID: sao1607047124
disjoint with: Pre-synaptic Part
disjoint with: Junctional Part
comment: 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.

Part Of Synapse
type: Class
subclass of: Supracellular Object Part
curation status: uncurated
sao ID: sao941107815

Junctional Part
type: Class
curation status: uncurated
sao ID: sao1423758634
subclass of: Part Of Synapse

SERCA2a
type: Class
curation status: uncurated
sao ID: sao833348185
subclass of: SERCA2
disjoint with: SERCA2b

SERCA2b
type: Class
curation status: uncurated
sao ID: sao1091808058
subclass of: SERCA2

Velate Astrocyte
type: Class
umls ID: C0926509
subclasses disjoint: true
curation status: uncurated
sao ID: sao1309473597
definition: A protoplasmic astrocyte with extremely thin veil-like (vellous) processes.
subclass of: Protoplasmic Astrocyte

Golgi-associated Vesicle
type: Class
subclass of: Golgi Subcomponent
umls ID: C0230767
definition: 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).
sao ID: sao819927218
disjoint with: Golgi Lamellae
gene ontology ID: 0005798
curation status: uncurated

Varicose Dendrite
type: Class
subclass of: Dendrite Type
curation status: uncurated
definition: Characterized by numerous swellings or varicosities along their length.
sao ID: sao1706854098

IP3R Type 1
type: Class
curation status: uncurated
sao ID: sao383990749
subclass of: Inositol 1 4 5 Trisphosphate Receptor

Golgi Lumen
type: Class
sao ID: sao1956231674
disjoint with: Mitochondrial Space
disjoint with: RER Lumen
disjoint with: Endosomal Lumen
disjoint with: Vesicle Lumen
disjoint with: Schmidtt-Lanterman Cleft
curation status: uncurated
subclass of: Cellular Space

Pial Cell
type: Class
curation status: uncurated
subclass of: Meninges Cell
sao ID: sao783352775

Meninges Cell
type: Class
curation status: uncurated
sao ID: sao1847837612
comment: This needs to be extensively investigated
disjoint with: Ventricular Epithelial Cell
disjoint with: Choroid Epithelial Cell
definition: Cell that comprises the meninges
subclass of: Epithelial Cell

Neurofilament 68kd
type: Class
sao ID: sao460214456
definition: Neurofilament protein with molecular weight approximately 68 kd.
subclass of: Neurofilament Protein
subclass of: Restriction
  on property: molecular weight
  has value: 68 kd
disjoint with: Neurofilament 150kd
disjoint with: Neurofilament 200kd
curation status: uncurated

molecular weight
type: FunctionalProperty
domain: Molecule
range: string
sao ID: sao1220772118
type: DatatypeProperty
label: molecular Weight

Neurofilament 150kd
type: Class
sao ID: sao1845865352
subclass of: Neurofilament Protein
subclass of: Restriction
  has value: 150 kd
  on property: molecular weight
definition: Neurofilmanet protein with molecular weight 150 kd.
curation status: uncurated

Neurofilament 200kd
type: Class
disjoint with: Neurofilament 150kd
sao ID: sao1200165704
definition: Neurofilament protein with molecular weight 200 kd.
subclass of: Neurofilament Protein
subclass of: Restriction
  on property: molecular weight
  has value: 200 kd
curation status: uncurated

Nematosome
type: Class
subclass of: Cellular Inclusion
curation status: uncurated
definition: 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)
sao ID: sao138430598

Synaptic Cleft
type: Class
sao ID: sao243541954
umls ID: C0682685
definition: The narrow gap that separates the presynaptic and postsynaptic membranes, into which a neurotransmitter is released (Gene Ontology).
gene ontology ID: 0043083
subclass of: Extracellular Space
curation status: uncurated

Node Of Ranvier Axon
type: Class
definition: 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.
curation status: uncurated
sao ID: sao-188049490
subclass of: Restriction
  some values from: Class
    union of: Subplasmalemmal Coating
    union of: Voltage Gated Sodium Channel
  on property: has Molecular Constituent
subclass of: Regional Part Of Myelinated Axon
disjoint with: Paranode Axon
disjoint with: Internode Axon
disjoint with: Juxta Paranode Axon

Voltage Gated Sodium Channel
type: Class
sao ID: sao785001660
definition: A sodium channel in a cell membrane whose opening is governed by the membrane potential (Gene Ontology).
subclass of: Sodium Channel
umls ID: C1153465
gene ontology ID: 0001518
curation status: uncurated

Internode Axon
type: Class
subclass of: Regional Part Of Myelinated Axon
sao ID: sao830092290
curation status: uncurated
disjoint with: Paranode Axon
disjoint with: Juxta Paranode Axon

Vesicular Component
type: Class
sao ID: sao138219748
subclass of: Regional Part Of Golgi
disjoint with: Trans Face
disjoint with: Trans Golgi Network
disjoint with: Cis Face
curation status: uncurated

Trans Golgi Network
type: Class
disjoint with: Trans Face
disjoint with: Cis Face
gene ontology ID: 0005802
umls ID: C0887838
subclass of: Regional Part Of Golgi
curation status: uncurated
sao ID: sao9456487
definition: 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).

Smooth Nucleus
type: Class
curation status: uncurated
sao ID: sao47950958
subclass of: Nucleus Type
definition: Nucleus with smooth membrane and no large folds or lobules.
disjoint with: Lobulated Nucleus
disjoint with: Indented Nucleus

Lobulated Nucleus
type: Class
definition: Nucleus with heavily indented nuclear membrane, giving the appearance of one or more lobes.
sao ID: sao301169922
subclass of: Nucleus Type
curation status: uncurated

Indented Nucleus
type: Class
definition: Nucleus with one or more indentations in the nuclear membrane.
curation status: uncurated
sao ID: sao1277586470
subclass of: Nucleus Type
disjoint with: Lobulated Nucleus

Regional Part Of Cell Component
type: Class
sao ID: sao-1819020575
curation status: uncurated
subclass of: FiatObjectPart

Regional Part Of Mitochondrial Membrane
type: Class
sao ID: sao-1686050947
disjoint with: Regional Part Of Mitochondria
subclass of: Regional Part Of Cell Component
curation status: uncurated

Regional Part Of Mitochondria
type: Class
curation status: uncurated
sao ID: sao903454364
subclass of: Obsolete class

Mitochondrial Membrane Inner
type: Class
gene ontology ID: 0005743
sao ID: sao1371347282
umls ID: C0230840
subclass of: Mitochondrial Membrane
subclass of: Restriction
  some values from: Mitochondrial Matrix
  on property: boundary Of
definition: 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).
curation status: uncurated

Mitochondrial Matrix
type: Class
sao ID: sao1804523077
definition: 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).
umls ID: C0230843
subclass of: Restriction
  some values from: Mitochondrial Membrane Inner
  on property: has Boundary
subclass of: Mitochondrial Subcomponent
disjoint with: Cristae
gene ontology ID: 0005759
curation status: uncurated

boundary Of
type: FunctionalProperty
sao ID: sao923422536
type: ObjectProperty
domain: Class
  union of: Object
  union of: ObjectBoundary
inverse of: has Boundary
range: Class
  union of: Site
  union of: Object
comment: Indicates that the structure forms the boundary for another structure, e.g., membrane of endoplasmic reticulum is boundary of lumen of endoplasmic reticulum

Dentate Gyrus Granule Cell
type: Class
sao ID: sao2007319345
disjoint with: Cerebellar Basket Cell
disjoint with: Cortical Bipolar Cell
subclass of: Restriction
  on property: Number of Axons
  cardinality: 1
disjoint with: mitral cell
subclass of: Restriction
  has value: CNS
  on property: location CNS PNS
disjoint with: Spherical Bushy Cell
disjoint with: Photoreceptor Cell
disjoint with: Cerebellar Granule Cell
disjoint with: Random Cell
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: Glutamate
disjoint with: Cortical Stellate Cell
disjoint with: hair cell
subclass of: Neuron
disjoint with: Cerebellar Golgi Cell
disjoint with: Motor Neuron
subclass of: Restriction
  on property: is spiny
  has value: true
disjoint with: Cholinergic Striatal Neuron
disjoint with: Substantia Nigra Dopaminergic Cell
curation status: uncurated
disjoint with: Olfactory Granule Cell
disjoint with: Double Bouquet Cell
disjoint with: Dorsal Root Ganglion Cell
disjoint with: Chandelier Cell
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Pyramidal Cell
subclass of: Restriction
  on property: anatomical Location General
  has value: dentate gyrus
disjoint with: Cerebellar Stellate Cell
subclass of: Restriction
  on property: circuit Type
  has value: local circuit neuron
disjoint with: Ciliary Ganglion Neuron
disjoint with: Globular Bushy Cell
subclasses disjoint: true
disjoint with: Medium Spiny Cell
disjoint with: Purkinje Cell

Cholinergic Striatal Neuron
type: Class
subclasses disjoint: true
disjoint with: Globular Bushy Cell
disjoint with: Cortical Bipolar Cell
disjoint with: Double Bouquet Cell
disjoint with: Photoreceptor Cell
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
subclass of: Restriction
  has value: false
  on property: is spiny
disjoint with: Cortical Stellate Cell
disjoint with: Chandelier Cell
disjoint with: Random Cell
disjoint with: Substantia Nigra Dopaminergic Cell
disjoint with: Pyramidal Cell
disjoint with: Ciliary Ganglion Neuron
disjoint with: hair cell
disjoint with: mitral cell
disjoint with: Cerebellar Granule Cell
subclass of: Neuron
disjoint with: Olfactory Granule Cell
sao ID: sao1866881837
disjoint with: Cerebellar Golgi Cell
subclass of: Restriction
  some values from: Acetylcholine
  on property: has Neurotransmitter
disjoint with: Purkinje Cell
disjoint with: Motor Neuron
disjoint with: Cerebellar Basket Cell
definition: Large cholinergic interneuron in the caudate nucleus, putamen and nucleus accumbens.
disjoint with: Spherical Bushy Cell
curation status: uncurated

Dorsal Root Ganglion Cell
type: Class
subclass of: Neuron
definition: 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.
sao ID: sao1919499702
disjoint with: Cortical Stellate Cell
disjoint with: mitral cell
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Pyramidal Cell
disjoint with: Spherical Bushy Cell
subclass of: Restriction
  on property: process Number
  has value: unipolar
disjoint with: Cerebellar Granule Cell
disjoint with: Substantia Nigra Dopaminergic Cell
disjoint with: Ciliary Ganglion Neuron
disjoint with: Double Bouquet Cell
disjoint with: Olfactory Granule Cell
disjoint with: Random Cell
disjoint with: Purkinje Cell
curation status: uncurated
subclasses disjoint: true
subclass of: Restriction
  has value: Doral root ganglion
  on property: anatomical Location General
disjoint with: Photoreceptor Cell
disjoint with: Chandelier Cell
disjoint with: Cerebellar Golgi Cell
disjoint with: Motor Neuron
disjoint with: hair cell
disjoint with: Cortical Bipolar Cell
disjoint with: Cerebellar Basket Cell
disjoint with: Cholinergic Striatal Neuron
disjoint with: Globular Bushy Cell

Cerebellar Stellate Cell
type: Class
disjoint with: hair cell
disjoint with: Cholinergic Striatal Neuron
disjoint with: Cortical Stellate Cell
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
subclass of: Neuron
disjoint with: Cerebellar Granule Cell
subclass of: Restriction
  has value: CNS
  on property: location CNS PNS
subclasses disjoint: true
disjoint with: Pyramidal Cell
sao ID: sao2046525601
disjoint with: Globular Bushy Cell
disjoint with: Substantia Nigra Dopaminergic Cell
disjoint with: Spherical Bushy Cell
disjoint with: Double Bouquet Cell
disjoint with: Cerebellar Basket Cell
disjoint with: Motor Neuron
curation status: uncurated
disjoint with: Dorsal Root Ganglion Cell
disjoint with: Photoreceptor Cell
disjoint with: Olfactory Granule Cell
disjoint with: Ciliary Ganglion Neuron
disjoint with: Medium Spiny Cell
definition: Multipolar neuron found in cerebellar molecular layer.
disjoint with: Purkinje Cell
disjoint with: mitral cell
disjoint with: Random Cell
disjoint with: Cortical Bipolar Cell
disjoint with: Chandelier Cell
disjoint with: Cerebellar Golgi Cell

Medium Spiny Cell
type: Class
disjoint with: Cerebellar Basket Cell
disjoint with: Cerebellar Granule Cell
disjoint with: Substantia Nigra Dopaminergic Cell
subclass of: Restriction
  has value: neostriatum
  on property: anatomical Location General
disjoint with: Double Bouquet Cell
disjoint with: Spherical Bushy Cell
disjoint with: Olfactory Granule Cell
subclasses disjoint: true
curation status: uncurated
disjoint with: Photoreceptor Cell
disjoint with: Ciliary Ganglion Neuron
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
subclass of: Restriction
  on property: is spiny
  has value: true
disjoint with: hair cell
disjoint with: Globular Bushy Cell
disjoint with: Cerebellar Golgi Cell
disjoint with: Dorsal Root Ganglion Cell
disjoint with: mitral cell
subclass of: Restriction
  on property: circuit Type
  has value: projection neuron
bonfire ID: BF_C000100
disjoint with: Purkinje Cell
disjoint with: Pyramidal Cell
subclass of: Restriction
  has value: multipolar
  on property: process Number
disjoint with: Motor Neuron
disjoint with: Cortical Bipolar Cell
disjoint with: Cortical Stellate Cell
subclass of: Neuron
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: GABA
synonym: Medium Spiny Neuron
disjoint with: Cholinergic Striatal Neuron
disjoint with: Random Cell
sao ID: sao68203136
disjoint with: Chandelier Cell
subclass of: Restriction
  on property: location CNS PNS
  has value: CNS

Purkinje Cell
type: Class
sao ID: sao471801888
definition: Large branching neurons of the middle layer of cerebellar cortex, characterized by vast arrays of dendrites; involved in controlling complex movements (CSP).
curation status: uncurated
disjoint with: Globular Bushy Cell
subclass of: Neuron
disjoint with: Olfactory Granule Cell
subclass of: Restriction
  on property: Number of Axons
  cardinality: 1
disjoint with: Double Bouquet Cell
subclass of: Restriction
  on property: has Neurotransmitter
  some values from: GABA
cell ontology ID: CL:0000121
subclass of: Class
  union of: Restriction
    has value: 2
    on property: Number of Primary Dendrites
  union of: Restriction
    on property: Number of Primary Dendrites
    has value: 1
disjoint with: Cerebellar Granule Cell
disjoint with: Random Cell
disjoint with: mitral cell
disjoint with: hair cell
disjoint with: Pyramidal Cell
disjoint with: Cortical Bipolar Cell
umls ID: C0034143
disjoint with: Substantia Nigra Dopaminergic Cell
subclass of: Restriction
  on property: anatomical Location General
  has value: cerebellar cortex
synonym: Purkinje neuron
disjoint with: Spherical Bushy Cell
disjoint with: Cortical Stellate Cell
disjoint with: Photoreceptor Cell
disjoint with: Chandelier Cell
subclass of: Restriction
  on property: is spiny
  has value: true
disjoint with: Ciliary Ganglion Neuron
disjoint with: Principal Cells Medial Nucleus Trapezoid Body
disjoint with: Motor Neuron
disjoint with: Cerebellar Golgi Cell
subclasses disjoint: true
subclass of: Restriction
  has value: projection neuron
  on property: circuit Type
disjoint with: Cerebellar Basket Cell

Branched Dendritic Spine
type: Class
curation status: uncurated
sao ID: sao-965204139
equivalent class: Class
  intersection of: Dendritic Spine
  intersection of: Restriction
    some values from: Branched Spine
    on property: has Morphological Type

Pinceau Fiber
type: Class
definition: Dense plexus formed by the descending collaterals of cerebellar basket cells tha wrap around the Purkinje cell axonal initial segment.
sao ID: sao109906988
disjoint with: Peri Cellular Basket
subclass of: Regional Part Of Basket Cell Axon
curation status: uncurated

Peri Cellular Basket
type: Class
subclass of: Regional Part Of Basket Cell Axon
definition: Ramification of basket cell axon surrounding cell bodies, forming the characteristic peri-cellular baskets from which the cell class derives its name.
sao ID: sao413722576
curation status: uncurated

Endocytic Zone
type: Class
subclass of: Spine Related Site
sao ID: sao517367952
definition: Region of the spine within several hundred nanometers of the post synaptic specialization characterized by the presence of coated pits. It is believed that this zone may be specialized for endocytosis. These coated pits are never observed in membrane associated with the post synaptic specialization (Blanpied and Ehlers, 2004).

Quiescent Oligodendrocyte Precursor Cell
type: Class
subclass of: Obsolete class
curation status: uncurated
sao ID: sao1352451787

Spine Mat
type: Class
definition: 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).
created date: 2007-02-09
subclass of: Cell Regional Part Aggregate Object
contributor: Maryann Martone
sao ID: sao2128156969

Cell Regional Part Aggregate Object
type: Class
subclass of: ObjectAggregate
sao ID: sao1970895398

Macroglia
type: Class
subclass of: Glial Cell
disjoint with: Precursor Cell
subclasses disjoint: true
comment: SAO classifies Schwann cells as a type of macroglia; Cell Type Ontology includes only astrocytes and oligodendroglia
curation status: uncurated
umls ID: C0228087
cell ontology ID: CL:0000126
sao ID: sao1895605722
synonym: macroglial cell

Glial Cell
type: Class
umls ID: C0027836
subclass of: Restriction
  all values from: Regional Part Of Glia
  on property: has Regional Part
sao ID: sao313023570
subclass of: Nerve Cell
comment: (Reichenbach and Wolburg)
externally sourced definition: Cell Type Ontology
definition: 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.
cell ontology ID: CL:0000125
curation status: uncurated
synonym: neuroglial cell

Precursor Cell
type: Class
subclass of: Glial Cell
synonym: progenitor cell
sao ID: sao467424240
curation status: uncurated

Transverse
type: Class
definition: Oriented orthogonal to the long axis.
subclass of: Orientation
sao ID: sao679027665
disjoint with: Radial
disjoint with: Random
disjoint with: Longitudinal
curation status: uncurated

Radial
type: Class
disjoint with: Random
disjoint with: Longitudinal
subclass of: Orientation
sao ID: sao2077793822
curation status: uncurated

Random
type: Class
sao ID: sao1143221302
definition: No particular orientation.
curation status: uncurated
subclass of: Orientation

Longitudinal
type: Class
definition: Oriented parallel to the long axis.
subclass of: Orientation
disjoint with: Random
curation status: uncurated
sao ID: sao430240391

Cytoplasmic Inclusion
type: Class
subclass of: Obsolete class
definition: Cellular inclusion found in the cytoplasm.
curation status: uncurated
sao ID: sao2092254444

Pre-synaptic Site
type: Class
subclass of: Synaptic Site
sao ID: sao2108323256

Fixed Tissue
type: Class
sao ID: sao1833377695
subclass of: In Vivo
definition: Indicates that the feature was observed in fixed tissue.

Calcium Activated Potassium Channel
type: Class
subclass of: Potassium Channel
umls ID: C0949653
curation status: uncurated
sao ID: sao1494484467
definition: Potassium channels whose activation is dependent on intracellular calcium concentrations (MSH).

Alpha 3 Acetylcholine Receptor
type: Class
subclass of: Nicotinic Acetylcholine Receptor
sao ID: sao99825125
curation status: uncurated

Synaptic Vesicle
type: Class
sao ID: sao1071221672
umls ID: C0039065
subclass of: Cytoplasmic Vesicle
disjoint with: Transport Vesicle
definition: 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).
gene ontology ID: 0008021
disjoint with: Granular Vesicle
curation status: uncurated
disjoint with: Vesicle Other

Dendritic Growth Cone
type: Class
curation status: uncurated
subclass of: Terminal Specialization
sao ID: sao1594955670
disjoint with: Dendriole

Dendriole
type: Class
curation status: uncurated
sao ID: sao295057932
subclass of: Terminal Specialization

Actin Filament
type: Class
sao ID: sao1588493326
curation status: uncurated
subclass of: Microfilament
definition: 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).
gene ontology ID: 0005884
umls ID: C0025979

Microfilament
type: Class
subclass of: Cytoskeletal Element
sao ID: sao2006047981
definition: 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)
curation status: uncurated
disjoint with: Microtubule
umls ID: C0025979

Coated Tip
type: Class
subclass of: Endosomal Subcomponent
definition: Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002).
sao ID: sao694815499
curation status: uncurated

Endosomal Subcomponent
type: Class
sao ID: sao1683772610
subclass of: Cellular Subcomponent
curation status: uncurated

has Inherent 3D Shape
type: DatatypeProperty
sao ID: sao1254683799
range: DataRange
  one of: false
  one of: true

Chemical Fixation
type: Class
sao ID: sao1554187262
definition: Indicates that the feature was observed in tissue prepared by chemical fixation.
subclass of: Fixed Tissue

IP3R Type 2
type: Class
subclass of: Inositol 1 4 5 Trisphosphate Receptor
sao ID: sao1920358312
curation status: uncurated

Condensed Chromatin
type: Class
subclass of: Chromatin
disjoint with: Extended Chromatin
curation status: uncurated
synonym: heterochromatin
sao ID: sao581845896
gene ontology ID: 0000792
definition: Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope.
definition: A compact and highly condensed form of chromatin (Gene Ontology).

Chromatin
type: Class
disjoint with: Barr Body
disjoint with: Nuclear Body
disjoint with: Nuclear Lamina
disjoint with: Nucleolus
umls ID: C0008546
disjoint with: Nuclear Pore
subclass of: Nuclear Subcomponent
definition: The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology).
disjoint with: Nuclear Membrane
disjoint with: Nuclear Inclusion
sao ID: sao1615953555
disjoint with: Nucleoplasm
disjoint with: Interchromatin Granule
gene ontology ID: 0000785
curation status: uncurated

Extended Chromatin
type: Class
sao ID: sao445485807
curation status: uncurated
subclass of: Chromatin
definition: A dispersed and relatively uncompacted form of chromatin (Gene Ontology).
gene ontology ID: 0000791
synonym: euchromatin

EAAT2
type: Class
subclass of: Glutamate Transporter
curation status: uncurated
sao ID: sao1585306176

Glutamate Transporter
type: Class
sao ID: sao1399894198
subclass of: Transporter Protein
curation status: uncurated
umls ID: C0061467

Membrane Stack
type: Class
subclass of: Cell Component Aggregate Object
sao ID: sao2114874506
definition: 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).
curation status: uncurated

Nissl Body
type: Class
definition: Stacks of rough endoplasmic reticulum that stain intensely with basophilic dyes.
sao ID: sao793088923
subclass of: Cell Component Aggregate Object
curation status: uncurated

Lipofuscin
type: Class
sao ID: sao941755985
definition: 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).
umls ID: C0023789
subclass of: Pigment
curation status: uncurated

Actin Based Motility
type: Class
subclass of: Motility
sao ID: sao656094176
definition: Mobility that is mediated by the actin cytoskeleton.

Bridge Contact Site
type: Class
curation status: uncurated
subclass of: Mitochondrial Site
definition: 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).
sao ID: sao1858501007

Basilar Dendrite
type: Class
disjoint with: Apical Dendrite
subclass of: Dendrite
synonym: Basal Dendrite
curation status: uncurated
sao ID: sao1079900774

Spinal Motor Neuron
type: Class
synonym: anterior horn cell
sao ID: sao1785599611
curation status: uncurated
subclass of: Obsolete class
subclass of: Restriction
  has value: multipolar
  on property: process Number

Perivascular Macrophage
type: Class
subclass of: Macrophage
curation status: uncurated
sao ID: sao1245187339

Pituicyte
type: Class
disjoint with: Astrocyte
cell ontology ID: CL:0000645
subclass of: Macroglia
disjoint with: NG2 Cell
disjoint with: Pectin Glial Cell
disjoint with: Ependymoglial Cell
curation status: uncurated
disjoint with: Radial Glia
disjoint with: Modified Astrocyte
disjoint with: Oligodendrocyte
subclasses disjoint: true
umls ID: C0229545
disjoint with: Schwann Cell
sao ID: sao1004082033

Microtubule Fascicle
type: Class
subclass of: Microtubule
curation status: uncurated
sao ID: sao1872343973
disjoint with: Neurotubule
definition: Refers to a bundle of closely apposed microtubules running parallel to each other.

Neurotubule
type: Class
definition: Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings.
subclass of: Microtubule
sao ID: sao248349196
curation status: uncurated

Muller Cell
type: Class
cell ontology ID: CL:0000636
externally sourced definition: 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
definition: Specialized glial cell of the retina that extends from the inner limiting membrane to the outer limiting membrane
curation status: graph position temporary
subclass of: Radial Glia
comment: 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.
subclasses disjoint: true
sao ID: sao1615912903

RIM1
type: Class
umls ID: C0171438
subclass of: Vesicle Binding Protein
sao ID: sao1798128207
disjoint with: Synapsin
curation status: uncurated

Synapsin
type: Class
definition: 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).
curation status: uncurated
sao ID: sao2143851382
umls ID: C0085252
subclass of: Vesicle Binding Protein

Real Boundary
type: Class
sao ID: sao1786656680
subclass of: Boundary
definition: A real boundary corresponds to its surface and designates a discontinuity between constitutional parts of anatomical entities (FMA: Mejino and Cornelius, ???)
curation status: uncurated

Boundary
type: Class
sao ID: sao1090974305
subclass of: Obsolete class
curation status: uncurated
definition: 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).

Stubby Dendritic Spine
type: Class
sao ID: sao317384566
curation status: uncurated
disjoint with: Sessile Dendritic Spine
disjoint with: Branched Dendritic Spine
disjoint with: Thin Dendritic Spine
disjoint with: Mushroom Dendritic Spine
equivalent class: Class
  intersection of: Dendritic Spine
  intersection of: Restriction
    on property: has Morphological Type
    some values from: Stubby

Sessile Dendritic Spine
type: Class
subclass of: Dendritic Spine
disjoint with: Thin Dendritic Spine
disjoint with: Branched Dendritic Spine
curation status: uncurated
sao ID: sao1536532595

Thin Dendritic Spine
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has Morphological Type
    some values from: Thin
  intersection of: Dendritic Spine
sao ID: sao1232858786
disjoint with: Branched Dendritic Spine
curation status: uncurated

Mushroom Dendritic Spine
type: Class
disjoint with: Sessile Dendritic Spine
disjoint with: Branched Dendritic Spine
disjoint with: Thin Dendritic Spine
equivalent class: Class
  intersection of: Restriction
    on property: has Morphological Type
    some values from: Mushroom
  intersection of: Dendritic Spine
sao ID: sao-876577163
curation status: uncurated

Lamellar Body
type: Class
sao ID: sao1379604862
curation status: uncurated
definition: 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).
subclass of: Cellular Inclusion
gene ontology ID: 0042599

Connexin 32
type: Class
sao ID: sao376700953
curation status: uncurated
umls ID: C0163743
subclass of: Connexin

Pinocytic Vesicle
type: Class
sao ID: sao1925368674
curation status: uncurated
disjoint with: Large Vesicle
subclass of: Endocytic Vesicle

Large Vesicle
type: Class
subclass of: Endocytic Vesicle
definition: Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating.
curation status: uncurated
sao ID: sao1241866791

Endocytic Vesicle
type: Class
disjoint with: Transport Vesicle
disjoint with: Synaptic Vesicle
gene ontology ID: 0030139
curation status: uncurated
disjoint with: Vesicle Other
sao ID: sao1362520468
subclass of: Cytoplasmic Vesicle
umls ID: C0887883
disjoint with: Coated Vesicle
definition: A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).
disjoint with: Granular Vesicle

Radius
type: Class
disjoint with: Cross Section Diameter Minor
disjoint with: Speed
sao ID: sao632949619
disjoint with: Distance From Soma
subclass of: Measurement
disjoint with: Half Life
disjoint with: Spacing
disjoint with: Surface Area
curation status: uncurated
disjoint with: Density
disjoint with: Width
disjoint with: Cross Section Diameter Major
disjoint with: Length
disjoint with: Volume

Distance From Soma
type: Class
disjoint with: Spacing
disjoint with: Half Life
disjoint with: Volume
disjoint with: Speed
sao ID: sao1779606731
disjoint with: Length
subclass of: Measurement
disjoint with: Cross Section Diameter Minor
definition: Distance, usually in linear microns, from soma where a feature is observed.
disjoint with: Surface Area
disjoint with: Density
curation status: uncurated

Width
type: Class
disjoint with: Speed
disjoint with: Density
disjoint with: Spacing
disjoint with: Half Life
disjoint with: Surface Area
disjoint with: Distance From Soma
disjoint with: Volume
disjoint with: Cross Section Diameter Minor
disjoint with: Length
curation status: uncurated
subclass of: Measurement
sao ID: sao888175480

Cross Section Diameter Major
type: Class
disjoint with: Surface Area
disjoint with: Spacing
disjoint with: Distance From Soma
sao ID: sao824839913
disjoint with: Volume
curation status: uncurated
disjoint with: Speed
definition: 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.
disjoint with: Cross Section Diameter Minor
disjoint with: Half Life
subclass of: Measurement
disjoint with: Density
disjoint with: Width
disjoint with: Length

Tufted
type: Class
curation status: uncurated
sao ID: sao754373097
subclass of: Dendrite Type
definition: Characterized by a terminal tuft.

Brainstem Motor Neuron
type: Class
curation status: uncurated
sao ID: sao1928362432
subclass of: Obsolete class

Post-synaptic Subcompartment
type: Class
subclass of: Obsolete class
sao ID: sao671299150

Mitochondrial Chromosome
type: Class
gene ontology ID: 0000262
subclass of: Mitochondrial Subcomponent
definition: A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology).
sao ID: sao1186327184
umls ID: C1166687
curation status: uncurated

Mitochondrial Subcomponent
type: Class
curation status: uncurated
subclass of: Cellular Subcomponent
sao ID: sao666410040

Acetylcholinesterase
type: Class
curation status: uncurated
definition: 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)
sao ID: sao1842089031
subclass of: Degradative Enzyme
umls ID: C0001044

Degradative Enzyme
type: Class
disjoint with: Neurotransmitter Receptor
disjoint with: Transporter
disjoint with: Synthetic Enzyme
sao ID: sao701966895
curation status: uncurated
subclass of: Neurotransmitter Associated Protein

NeurabinI
type: Class
sao ID: sao1535366556
curation status: uncurated
definition: PDZ containing proteins with F-actin binding protein activity.
subclass of: Actin Bundling Protein

Actin Bundling Protein
type: Class
sao ID: sao1281431356
curation status: uncurated
disjoint with: Actin Binding Protein
subclass of: Actin Associated Protein

Non Myelinating Schwann Cell
type: Class
subclass of: Obsolete class
curation status: uncurated
definition: Schwann cell that forms a simple ensheathment around axons.
sao ID: sao528084208

Dendritic Segment
type: Class
sao ID: sao1039042901
curation status: uncurated
subclass of: Obsolete class
definition: Refers to dendrites emanating from the cell soma.

Connexon
type: Class
sao ID: sao445019788
definition source: Wikipedia
curation status: uncurated
subclass of: Restriction
  on property: has Molecular Constituent
  some values from: Connexin
definition: 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.
subclass of: Cell Component Aggregate Object
umls ID: C0230609
subclass of: Restriction
  some values from: Molecule
  on property: has Molecular Constituent
disjoint with: Orthogonal Array
gene ontology ID: 0005922
synonym: hemichannel, connexon complex

Marginal Astrocyte
type: Class
disjoint with: Perivascular Astrocyte
subclasses disjoint: true
curation status: graph position temporary
disjoint with: Protoplasmic Astrocyte
sao ID: sao-1865064409
disjoint with: Radial Astrocyte
comment: There is some discussion about whether all marginal glia are astrocytes.
definition: 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
disjoint with: Fibrous Astrocyte
subclass of: Astrocyte

Neurosecretory Vesicle
type: Class
definition: 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).
sao ID: sao2031592629
subclass of: Granular Vesicle
curation status: uncurated

Basal
type: Class
sao ID: sao-282380853
curation status: uncurated
subclass of: Anatomical Coordinate

Junction Complex
type: Class
disjoint with: Supra Cellular Structure
disjoint with: Cell Regional Part Aggregate Object
subclass of: Restriction
  on property: located in
  all values from: Synaptic Site
subclass of: ObjectAggregate
sao ID: sao-301233507

Flattened
type: Class
sao ID: sao1785495506
subclass of: Vesicle Type
disjoint with: Round Clear
disjoint with: Pleomorphic
disjoint with: Fused Vesicle
curation status: uncurated
definition: Characterized by a flattened shape in glutaraldehyde fixed tissue.

Tuft
type: Class
disjoint with: Dendriole
disjoint with: Dendritic Growth Cone
subclass of: Terminal Specialization
curation status: uncurated
definition: Refers to the terminal specialization found in some types of dendrites consisting of numerous small terminal branches, giving the dendrite a tufted appearance.
sao ID: sao1340260079

Vestibular Hair Cell
type: Class
definition source: UMLS
cell ontology ID: CL:0000609
umls ID: C0206511
subclass of: hair cell
sao ID: sao709770772
curation status: uncurated
definition: 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.
subclasses disjoint: true
disjoint with: Cochlear Hair Cell

Barr Body
type: Class
disjoint with: Nucleoplasm
disjoint with: Nuclear Pore
disjoint with: Nuclear Inclusion
disjoint with: Nuclear Membrane
disjoint with: Nuclear Lamina
curation status: uncurated
disjoint with: Interchromatin Granule
disjoint with: Nuclear Body
disjoint with: Nucleolus
sao ID: sao1571698684
subclass of: Nuclear Subcomponent

Nuclear Pore
type: Class
definition: 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).
disjoint with: Interchromatin Granule
disjoint with: Nucleolus
curation status: uncurated
disjoint with: Nuclear Lamina
disjoint with: Nuclear Inclusion
umls ID: C0028587
sao ID: sao220861693
disjoint with: Nuclear Body
gene ontology ID: 0005643
disjoint with: Nuclear Membrane
disjoint with: Nucleoplasm
subclass of: Nuclear Subcomponent

Pre-synaptic Active Zone
type: Class
subclass of: Restriction
  on property: has Component
  all values from: Pre-synaptic Active Zone Component
subclass of: Pre-synaptic Site
definition: A specialized presynaptic plasma membrane region where synaptic vesicles dock and fuse (Gene Ontology).
curation status: uncurated
sao ID: sao792027222
gene ontology ID: 0048786

Atlas Location
type: Class
sao ID: sao2052625281
curation status: graph position temporary
subclass of: Anatomical Coordinate

Intracristal Space
type: Class
definition: The space bounded by the cristae membrane
subclass of: Mitochondrial Space
sao ID: sao508958414
curation status: uncurated
disjoint with: Mitochondrial Lumen
subclasses disjoint: true
disjoint with: Mitochondrial Intermembrane Space
subclass of: Restriction
  on property: has Boundary
  some values from: Cristae Membrane

Mitochondrial Intermembrane Space
type: Class
comment: 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.
disjoint with: Mitochondrial Lumen
subclasses disjoint: true
definition: The region between the inner and outer lipid bilayers of the mitochondrial envelope. (Gene Ontology).
gene ontology ID: 0005758
subclass of: Mitochondrial Space
sao ID: sao118944228
umls ID: C1166886
curation status: graph position temporary

has Boundary
type: ObjectProperty
sao ID: sao1844377738
comment: Refers to a structure that defines the boundary of a given structure
range: Class
  union of: Object
  union of: ObjectBoundary
domain: Class
  union of: Site
  union of: Object
inverse of: boundary Of

Cristae Membrane
type: Class
curation status: uncurated
subclass of: Obsolete class
sao ID: sao614641003

Dopamine Transporter Type 1
type: Class
definition: Sodium dependent transport protein, located on presynaptic terminals, involved in the uptake of dopamine; site at which cocaine exerts rewarding/ reinforcing effects (CSP).
sao ID: sao285839036
umls ID: C0114838
curation status: uncurated
subclass of: Transporter

Transporter
type: Class
sao ID: sao791350993
curation status: uncurated
disjoint with: Neurotransmitter Receptor
disjoint with: Synthetic Enzyme
subclass of: Neurotransmitter Associated Protein

Mitochondrial Membrane Outer
type: Class
definition: The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology).
subclass of: Mitochondrial Membrane
curation status: uncurated
gene ontology ID: 0005741
sao ID: sao1289741256
disjoint with: Mitochondrial Membrane Inner
umls ID: C0230839

Tyrosine Kinase Receptor
type: Class
curation status: uncurated
definition: A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH).
disjoint with: Neurotransmitter Receptor
disjoint with: G Coupled Receptor
subclass of: Membrane Receptor
umls ID: C0206364
sao ID: sao1048004962

Docked Vesicle
type: Class
disjoint with: Amorphous Vesicle
sao ID: sao403156667
subclass of: Vesicle Other
curation status: uncurated
definition: Synaptic vesicle docked at the pre-synaptic active zone.

Extracellular Surface
type: Class
subclass of: Membrane Surface
curation status: uncurated
sao ID: sao2135015805

Membrane Surface
type: Class
subclass of: ObjectBoundary
sao ID: sao1329750433
curation status: uncurated

Anterograde Transport
type: Class
definition: Transport in the direction away from the cell soma.
umls ID: C0598952
subclass of: Microtubule Mediated Motility
sao ID: sao992129328

Fast Frozen Freeze Substituted
type: Class
subclass of: Fixed Tissue
sao ID: sao1693353776
definition: Indicates that feature was described in tissue prepared by fast freezing followed by freeze substitution.

Capillary Endothelial Cell
type: Class
curation status: uncurated
sao ID: sao1540081501
subclass of: Vascular Endothelial Cell

Oligodendrocyte Precursor Cell
type: Class
acronym: OPC
subclass of: Precursor Cell
sao ID: sao1213292244
curation status: uncurated

Apical
type: Class
sao ID: sao1703115805
subclass of: Anatomical Coordinate
curation status: uncurated

Junctional Connectivity
type: Class
sao ID: sao1392266325
curation status: uncurated
subclass of: Connectivity

Stellate
type: Class
definition: Generally star shaped multipoloar cell shpae with spherically extending processes
subclass of: Cell Morphological Type
curation status: uncurated
sao ID: sao9271919883

Cell Morphological Type
type: Class
subclass of: Morphological Type
sao ID: sao1278200674

Activated Oligodendrocyte Precursor Cell
type: Class
sao ID: sao484101752
curation status: uncurated
synonym: oligodendrocyte progenitor cell
subclass of: Obsolete class

Intercellular Gap Junction Channel
type: Class
subclass of: Junction Complex
creator: Maryann Martone
definition: Junctional complex consisting of two connexons that come together to form a communicating pore between two cells
sao ID: sao-1778046445

Synaptic Connectivity
type: Class
definition: Implies that a morphologically identified synapse exists between two cell components where release of transmitter from cell influences cell B.
subclass of: Junctional Connectivity
curation status: uncurated
sao ID: sao223845603

Regional Part Of SER
type: Class
subclass of: Regional Part Of Cell Component
sao ID: sao-699412220
curation status: uncurated

Active Zone Cytomatrix
type: Class
definition: Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004).
disjoint with: Active Zone Dense Projection
disjoint with: Active Zone Plasma Membrane
disjoint with: Pre-synaptic Grid
curation status: uncurated
subclass of: Pre-synaptic Active Zone Component
sao ID: sao1470121605

Skeletal Muscle Cell
type: Class
sao ID: sao1741889714
subclass of: Striated Muscle Cell
cell ontology ID: CL:0000188
disjoint with: Cardiac Muscle Cell
curation status: uncurated

Cardiac Muscle Cell
type: Class
subclass of: Striated Muscle Cell
cell ontology ID: CL:0000746
sao ID: sao658938043
synonym: cardiac myocyte
definition: Striated muscle cells found in the heart. They are derived from cardiac myoblasts (myoblasts, cardiac (MSH).
umls ID: C0225828
curation status: uncurated

Platelet Derived Growth Factor
type: Class
definition: 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).
abbreviation: PDGF
umls ID: C0032200
subclass of: Growth Factor
curation status: uncurated
sao ID: sao603947546

Axon Microtubule Fascicle
type: Class
definition: Refers to the bundled configuration of microtubules in the axon hillock and initial segment.
subclass of: Microtubule Fascicle
curation status: uncurated
sao ID: sao707332678

Reactive Microglia
type: Class
subclass of: Obsolete class
curation status: uncurated
disjoint with: Resting Microglia
sao ID: sao1448451779

Resting Microglia
type: Class
curation status: uncurated
subclass of: Obsolete class
sao ID: sao172764364

Retrograde Transport
type: Class
sao ID: sao31662418
subclass of: Microtubule Mediated Motility
definition: Transport in the direction towards the cell soma.
umls ID: C0598953

Oligodendrocyte Compact Myelin
type: Class
sao ID: sao1186642361
definition: 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).
curation status: uncurated
gene ontology ID: 0043218
subclass of: Oligodendrocyte Myelin Sheath

Oligodendrocyte Myelin Sheath
type: Class
gene ontology ID: 0043209
umls ID: C0026973
curation status: uncurated
subclass of: Regional Part Of Oligodendrocyte
sao ID: sao1279474730
definition: 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).

Condensed
type: Class
disjoint with: Orthodox
sao ID: sao1152497626
definition: Morphological state characterized by a contracted matrix and expanded intracristal space; observed experimentally when added ADP is used up (Mannella et al., 2001).
subclass of: Mitochondrial Type
curation status: uncurated

Orthodox
type: Class
definition: Morphological state characterized by an expanded matrix space and contracted intracristal space; observed experimentally when ADP is added (Mannella et al., 2001).
sao ID: sao358853874
subclass of: Mitochondrial Type
curation status: uncurated

Mitochondrion
type: Class
subclass of: Restriction
  all values from: Cristae
  on property: has Regional Part
subclass of: Restriction
  on property: has Regional Part
  some values from: Cristae
subclass of: Restriction
  some values from: Mitochondrial Type
  on property: has Morphological Type
sao ID: sao1860313010
disjoint with: Lysosome
disjoint with: Golgi Apparatus
disjoint with: Endoplasmic Reticulum
subclass of: Membrane Bound Organelle
disjoint with: Nucleus
disjoint with: Multivesicular Body
disjoint with: Peroxisome
umls ID: C0026237
gene ontology ID: 0005739
disjoint with: Spine Apparatus
definition: 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).
disjoint with: Endosome
curation status: uncurated

Cristae
type: Class
sao ID: sao333328131
subclass of: Regional Part Of Mitochondrial Membrane
subclass of: Restriction
  on property: has Morphological Type
  all values from: Cristae Type
umls ID: C0230844
definition: Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology)
curation status: uncurated
gene ontology ID: 0030061

Spine Apparatus
type: Class
disjoint with: Endoplasmic Reticulum
disjoint with: Lysosome
subclass of: Restriction
  all values from: Regional Part Of Spine Apparatus
  on property: has Regional Part
definition: A specialization of the endomembrane system found in some classes of spines consisting of two or more closely apposed lamellae with interspersed dense material.
disjoint with: Endosome
disjoint with: Peroxisome
curation status: uncurated
disjoint with: Nucleus
sao ID: sao725931194
subclass of: Membrane Bound Organelle
disjoint with: Multivesicular Body
disjoint with: Golgi Apparatus
umls ID: C0230810

Axocruciform
type: Class
subclass of: Synaptic Configuration
curation status: uncurated
definition: Synaptic arrangement where the axon courses orthogonal to and forms a synapse with a portion of dendrite.
sao ID: sao1062287912

Dynamin
type: Class
sao ID: sao1565708461
subclass of: Molecular Motor
definition: 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).
curation status: uncurated
umls ID: C0058836
disjoint with: KIF3A

Regional Part Of Cell Cell Contact Zone
type: Class
comment: 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.
subclass of: Obsolete class
curation status: graph position temporary
sao ID: sao2081625415

Spine
type: Class
sao ID: sao1145756102
subclass of: Neuron Protrusion
curation status: uncurated
disjoint with: Excrescence
disjoint with: Filopodium
comment: Do spines only have a post synaptic density
comment: 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.

is Regional Part Of
type: ObjectProperty
sao ID: sao1239937685
inverse of: has Regional Part
domain: FiatObjectPart
sub property of: is Part Of
range: IndependentContinuant

Sparsely Spiny
type: Class
curation status: uncurated
definition: Characterized by a low density of dendritic spines.
sao ID: sao1288413465
subclass of: Dendrite Type

Pyramidal Neuronal Cell Body
type: Class
sao ID: sao-820130069
curation status: uncurated
subclass of: Neuronal Cell Body
subclass of: Restriction
  on property: has Morphological Type
  some values from: Pyramidal

Lumenal Surface
type: Class
sao ID: sao120818728
subclass of: Membrane Surface
curation status: uncurated
disjoint with: Extracellular Surface
disjoint with: Cytoplasmic Surface

Cytoplasmic Surface
type: Class
sao ID: sao1514682949
disjoint with: Extracellular Surface
curation status: uncurated
subclass of: Membrane Surface

Clathrin Coat
type: Class
subclass of: Vesicle Coat
gene ontology ID: 0030118
curation status: uncurated
definition: 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).
umls ID: C1166728
sao ID: sao879919129

Primary Lysosome
type: Class
subclass of: Lysosome
gene ontology ID: 0005766
curation status: uncurated
definition: A lysosome before it has fused with a vesicle or vacuole (Gene Ontology).
sao ID: sao1140587416
umls ID: C0230814
disjoint with: Secondary Lysosome

Smooth Endoplasmic Reticulum
type: Class
umls ID: C0230789
definition: 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).
subclass of: Endoplasmic Reticulum
curation status: uncurated
gene ontology ID: 0005790
sao ID: sao710427438

Sub-surface Cisternae
type: Class
subclass of: Hypolemmal Cisternae
curation status: uncurated
sao ID: sao128470897
definition: 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).

Hypolemmal Cisternae
type: Class
sao ID: sao1634374950
subclass of: Regional Part Of SER
curation status: uncurated
definition: Specialized part of the smooth endoplasmic reticulum that closely underlies the plasma membrane, usually within 60 nm or closer (Peters, Palay and Webster, 1991).

Cell Line
type: Class
subclass of: In Vitro
sao ID: sao938874695

In Vitro
type: Class
subclass of: Experimental Condition
definition: Indicates that the feature was observed in cells in culture or in isolated subcellular fractions.
sao ID: sao1649728317

Tubular
type: Class
curation status: uncurated
subclass of: Cristae Type
disjoint with: Lamellar
definition: Refers to crisate with a roughly circular profile in cross section.
sao ID: sao2110170574

Lamellar
type: Class
subclass of: Cristae Type
definition: Refers to cristae with a flattened, extended appearance.
curation status: uncurated
sao ID: sao1995010823

Serotonin
type: Class
curation status: uncurated
sao ID: sao711465902
umls ID: C0036751
subclass of: Monoamines
definition: 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).

Peripheral Astrocyte Process
type: Class
disjoint with: Vellous Process
definition: Thin terminal processes of astrocytes found in sheathing, axon terminals, blood vessels, and pial surface of the brain.
subclass of: Astrocyte Process
sao ID: sao1573004591
comment: This comes from derouiche et al. J. Physol. Paris 2002 96:177 PubMedID:12445894
comment: It is not clear whether peripheral astrocyte process only refers to the processes surrounding synapses or also refers to the endfeet
curation status: 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.
curation status: graph position temporary

Astrocyte Process
type: Class
curation status: uncurated
subclass of: Regional Part Of Astrocyte
sao ID: sao1630537580
definition: Refers to processes of astrocytes extending from the cell soma that wrap around neurons and conform to cellular components in the neuropil.

SAP90
type: Class
umls ID: C0213974
sao ID: sao1232021729
curation status: uncurated
disjoint with: PSD95
subclass of: Scaffolding Protein

Acute Slice
type: Class
sao ID: sao819188787
subclass of: Slice Preparation

Initial Segment
type: Class
gene ontology ID: 0043194
curation status: uncurated
disjoint with: Axonal Growth Cone
sao ID: sao256000789
definition: 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).
subclass of: Restriction
  on property: has Molecular Constituent
  some values from: Voltage Gated Sodium Channel
disjoint with: Main Axon
disjoint with: Regional Part Of Basket Cell Axon
subclass of: Regional Part Of Axon
disjoint with: Axon Collateral
disjoint with: Axon Hillock
disjoint with: Axon Terminal

Main Axon
type: Class
disjoint with: Regional Part Of Basket Cell Axon
disjoint with: Axonal Growth Cone
curation status: uncurated
disjoint with: Axon Hillock
disjoint with: Axon Terminal
sao ID: sao1596975044
disjoint with: Axon Collateral
definition: Used to refer to the main axonal trunk, as opposed to the collaterals.
subclass of: Regional Part Of Axon

Rough Endoplasmic Reticulum
type: Class
subclass of: Endoplasmic Reticulum
curation status: uncurated
synonym: Nissl substance
umls ID: C0230779
sao ID: sao1881364067
definition: 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).
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of RER
gene ontology ID: 0005791
disjoint with: Smooth Endoplasmic Reticulum

Supra-organismal Occurrent
type: Class
subclass of: Biological Occurrent
sao ID: sao211804939

Supracellular Object Part
type: Class
sao ID: sao85163621
subclass of: Obsolete class
disjoint with: Regional Part Of Cell
disjoint with: Regional Part Of Cell Component
definition: Parts of a supracellular object, e.g., synapse.
comment: We have not yet decided whether they are regional parts of some other sort. So for now, they are just parts.

Type I/II Oligodendrocyte
type: Class
subclasses disjoint: true
disjoint with: Type III/IV Oligodendrocyte
subclass of: Interfascicular Oligodendrocyte
curation status: definition incomplete
definition: Interfascicular oligodendrocyte which can support myelin volumes of approximately 500 cubic microns and is associated with small diameter axons
sao ID: sao-32901633
label: Type I II Oligodendrocyte

Biological Continuant
type: Class
subclass of: Obsolete class
sao ID: sao1950472752
curation status: uncurated
comment: "Continuant" refers to the participants of occurrent processes and are entities that endure during the period of their existence (Rosse C et a., 2005).

Voltage Gated Potassium Channel
type: Class
definition: 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).
gene ontology ID: 0008076
disjoint with: Calcium Activated Potassium Channel
umls ID: C0814023
sao ID: sao371494298
curation status: uncurated
subclass of: Potassium Channel

Sodium Channel
type: Class
umls ID: C0037492
subclass of: Ion Channel
definition: Cell membrane glycoproteins selective for sodium ions. Fast sodium current is associated with the action potential in neural membranes (MSH).
sao ID: sao1797800540
disjoint with: Potassium Channel
disjoint with: Calcium Channel
curation status: uncurated

Neural Stem Cell
type: Class
subclass of: Nerve Cell
disjoint with: Glial Cell
umls ID: C1113654
synonym: Nerve stem cell
curation status: uncurated
sao ID: sao938060309
definition: Embryonic cell that develops into a neuron (CSP).

EAAT1
type: Class
subclass of: Glutamate Transporter
disjoint with: Water Channel
disjoint with: EAAT2
curation status: uncurated
sao ID: sao2016979058

Water Channel
type: Class
definition: 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).
sao ID: sao992093782
curation status: uncurated
disjoint with: EAAT2
subclass of: Protein
umls ID: C0599635

Spinophliln
type: Class
disjoint with: NeurabinI
sao ID: sao2023460124
synonym: neurabinII
curation status: uncurated
subclass of: Actin Bundling Protein

SER Subcomponent
type: Class
sao ID: sao1842028314
subclass of: Cellular Subcomponent
curation status: uncurated

Mitochondrial Adhaerens Complex
type: Class
definition: 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).
subclass of: Mitochondrial Subcomponent
disjoint with: Mitochondrial Chromosome
curation status: uncurated
sao ID: sao1933817066

Pathological
type: Class
subclass of: Cellular Inclusion
curation status: uncurated
definition: Cellular inclusions associated with pathological conditions.
sao ID: sao74391158

SERCA1
type: Class
disjoint with: SERCA3
disjoint with: SERCA2
umls ID: C0916182
subclass of: SERCA
curation status: uncurated
sao ID: sao229773618

SER Lumen
type: Class
disjoint with: Golgi Lumen
disjoint with: Schmidtt-Lanterman Cleft
subclass of: Restriction
  some values from: SER Membrane
  on property: has Boundary
sao ID: sao927884761
disjoint with: Mitochondrial Space
synonym: smooth endoplasmic reticulum lumen
gene ontology ID: 0048238
disjoint with: RER Lumen
curation status: uncurated
subclass of: Cellular Space
disjoint with: Vesicle Lumen
definition: The volume enclosed by the membranes of the smooth endoplasmic reticulum (Gene Ontology).
disjoint with: Endosomal Lumen

Schwann Cell Paranodal Termination
type: Class
definition: 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 ID: sao-1067215520
subclass of: Schwann Cell Myelin Sheath
curation status: uncurated

Schwann Cell Myelin Sheath
type: Class
subclass of: Regional Part Of Schwann Cell
sao ID: sao-593830697
definition: 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).
curation status: uncurated

Intranuclear Membrane Space
type: Class
subclass of: Cellular Space
sao ID: sao1908934319
disjoint with: Vesicle Lumen
disjoint with: Mitochondrial Space
disjoint with: Schmidtt-Lanterman Cleft
disjoint with: Endosomal Lumen
disjoint with: SER Lumen
disjoint with: Golgi Lumen
definition: The space between the inner and outer nuclear membranes
disjoint with: RER Lumen
curation status: uncurated

Anatomical Part
type: Class
subclass of: Anatomical Relationship
curation status: uncurated
comment: 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.
sao ID: sao1968590282

Layer 5 Pyramidal Neuron
type: Class
sao ID: sao840814183
subclass of: Cortical Pyramidal Neuron
curation status: uncurated
subclasses disjoint: true
definition: Pyramidal neuron whose cell soma resides in layer 5 or whose connectivity patterns resemble layer 5 neurons.

Tissue Plasminogen Activator
type: Class
abbreviation: tPA
umls ID: C0032143
sao ID: sao681020632
definition: Extracellular tissue protease that degrades a wide spectrum of extracellular matrix proteins.
subclass of: Extracellular Matrix Protein
curation status: uncurated

Tumor Necrosis Factor Alpha
type: Class
curation status: uncurated
abbreviation: TNF-alpha
subclass of: Cytokine
sao ID: sao220868685
umls ID: C0041368
definition: 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).
disjoint with: Interleukin-1

Interleukin-1
type: Class
umls ID: C0021755
sao ID: sao950082944
curation status: uncurated
subclass of: Cytokine
abbreviation: IL-1
definition: 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).

Axonal Spine
type: Class
sao ID: sao18239917
definition: Refers to spine that originates from the axon, usually the initial segment (Peters, Palay and Webster, 1991).
subclass of: Spine
disjoint with: Dendritic Spine
disjoint with: Somatic Spine
curation status: uncurated

Oligodendrocyte Paranodal Termination
type: Class
definition: 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
synonym: Paranodal loop
subclass of: Restriction
  on property: continuous With
  some values from: Oligodendrocyte Compact Myelin
subclass of: Oligodendrocyte Myelin Sheath
sao ID: sao1354781919
curation status: uncurated

Juxtaparanode
type: Class
sao ID: sao758620702
subclass of: Node Related Site
definition: Region of nodal complex adjacent to the paranode

Internode
type: Class
subclass of: Node Related Site
sao ID: sao-206157942
definition: Part of nodal complex located underneath the compact myelin in between nodes of Ranvier

Granule
type: Class
curation status: uncurated
subclass of: Cell Morphological Type
comment: small numerous cell
sao ID: sao6934064108

Age Associated
type: Class
sao ID: sao2017162875
curation status: uncurated
subclass of: Cellular Inclusion

is Molecular Constituent Of
type: ObjectProperty
sao ID: sao1939689633
inverse of: has Molecular Constituent
domain: Molecule
range: Class
  union of: Membrane Surface
  union of: FiatObjectPart
  union of: ObjectAggregate
  union of: Object
sub property of: is Part Of

Kv3.2
type: Class
umls ID: C0906849
curation status: uncurated
sao ID: sao1482557638
subclass of: Kv3

Kv3
type: Class
definition: Shaw-like family of voltage gated potassium channels.
subclass of: Voltage Gated Potassium Channel
curation status: uncurated
sao ID: sao1120423785

Ventricular Epithelial Cell
type: Class
sao ID: sao855466308
subclass of: Obsolete class
disjoint with: Choroid Epithelial Cell
curation status: uncurated
definition: Epithelial cell lining the ventricles.

Ventricular Cardiac Muscle Cell
type: Class
synonym: ventricular myocyte
subclass of: Cardiac Muscle Cell
definition: Cardiac muscle cell comprising the ventricles
curation status: uncurated
sao ID: sao1011026882

Dendritic Microtubule
type: Class
disjoint with: Neurotubule
disjoint with: Microtubule Fascicle
sao ID: sao110773650
subclass of: Restriction
  some values from: MAP2
  on property: has Molecular Constituent
subclass of: Microtubule
curation status: uncurated

Myelin Basic Protein
type: Class
umls ID: C0014063
curation status: uncurated
sao ID: sao775011514
subclass of: Myelin Associated Protein
definition: 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)

Free Ribosome
type: Class
disjoint with: Membrane Bound Ribosome
sao ID: sao1139385046
subclass of: Ribosome
curation status: uncurated

Connexin 43
type: Class
umls ID: C0110613
sao ID: sao1089608116
disjoint with: Connexin 32
subclass of: Connexin
curation status: uncurated
definition: 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).

Tubular Endosome
type: Class
subclass of: Endosome
sao ID: sao1570660411
curation status: uncurated
disjoint with: Sorting Endosome
definition: 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.

Beta Tanycyte
type: Class
sao ID: sao647178911
disjoint with: Alpha Tanycyte
subclasses disjoint: true
curation status: uncurated
subclass of: Tanycyte

MRNA
type: Class
subclass of: RNA
sao ID: sao116515730
disjoint with: Ribosomal RNA
curation status: uncurated
definition: 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).
umls ID: C0035696

SAP97
type: Class
curation status: uncurated
umls ID: C0295347
sao ID: sao885184181
disjoint with: PSD95
disjoint with: SAP90
subclass of: Scaffolding Protein

Clathrin Coated Endocytic Vesicle
type: Class
subclass of: Restriction
  on property: has Component
  some values from: Clathrin Coat
subclass of: Endocytic Vesicle
sao ID: sao1243595998
gene ontology ID: 0045334
curation status: uncurated
disjoint with: Large Vesicle
disjoint with: Pinocytic Vesicle
definition: A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).

Microvilli
type: Class
subclass of: Regional Part Of Epithelial Cell
sao ID: sao671419673
curation status: uncurated

Inner Bounding Mitochondrial Membrane
type: Class
subclass of: Regional Part Of Mitochondrial Membrane
sao ID: sao18461326
disjoint with: Cristae Membrane
curation status: uncurated
definition: Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane

Virtual Boundary
type: Class
disjoint with: Real Boundary
sao ID: sao1825296048
definition: 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).
subclass of: Boundary
curation status: uncurated

Alpha Tubulin
type: Class
sao ID: sao335197072
curation status: uncurated
subclass of: Tubulin
definition: One of two globular polypeptides forming microtubules.
disjoint with: Beta Tubulin
umls ID: C0002318

Alpha 7 Acetylcholine Receptor
type: Class
sao ID: sao138926812
subclass of: Nicotinic Acetylcholine Receptor
disjoint with: Alpha 3 Acetylcholine Receptor
curation status: uncurated

Component Part Of
type: Class
subclass of: Anatomical Part
sao ID: sao818838791
curation status: definition incomplete

Perineuronal Oligodendrocyte
type: Class
umls ID: C0949376
comment: It is unclear to us whether perineuronal oligodendrocytes should be considered a separate class.
subclasses disjoint: true
definition: Oligodendrocyte found in gray matter in close association with neurons (Peters, Palay and Webster, 1991).
curation status: graph position temporary
sao ID: sao1353298471
subclass of: Oligodendrocyte
subclass of: Restriction
  some values from: Neuronal Cell Body
  on property: associated Cellular Element

Filamentous Inclusion
type: Class
definition: Cellular inclusion containing filamentous structures.
curation status: uncurated
subclass of: Obsolete class
sao ID: sao2081684219

Synaptic Bouton
type: Class
disjoint with: Calyx
definition: Terminal pre-synaptic ending of an axon or axon collateral.
curation status: uncurated
subclass of: Restriction
  on property: has Morphological Type
  all values from: Bouton Type
subclass of: Axon Terminal
sao ID: sao187426937

Post-synaptic Component
type: Class
subclass of: Synaptic Component
sao ID: sao1507566336

Dendritic Tree
type: Class
sao ID: sao172297168
subclass of: Cell Regional Part Aggregate Object
subclass of: Restriction
  on property: has Regional Part
  all values from: Regional Part Of Dendritic Tree
disjoint with: Spine Mat
curation status: uncurated
definition: The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches.
bonfire ID: BF_C000102

Puncta Adhaerentia
type: Class
definition: A small version of the zonula adharens type junction, characterized by a symmetrical adherent point between two cells.
sao ID: sao257629430
subclass of: Zonula Adhaerens
curation status: uncurated

Cell Cell Contact
type: Class
subclass of: Supra-organismal Occurrent
sao ID: sao2023779072

Polyribosome
type: Class
disjoint with: Connexon
disjoint with: Orthogonal Array
definition: 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).
umls ID: C0032592
subclass of: Cell Component Aggregate Object
curation status: uncurated
sao ID: sao1038025871

Precursor
type: Class
disjoint with: Degradative Enzyme
disjoint with: Synthetic Enzyme
disjoint with: Transporter
disjoint with: Neurotransmitter Receptor
subclass of: Neurotransmitter Associated Protein
sao ID: sao2146594471
curation status: uncurated
umls ID: C0033665

Regional Part Of
type: Class
sao ID: sao1120063482
curation status: definition incomplete
subclass of: Anatomical Part

Organismal Continuant
type: Class
curation status: uncurated
sao ID: sao1863115908
comment: "Continuant" refers to the participants of occurrent processes and are entities that endure during the period of their existence (Rosse C et a., 2005).
subclass of: Biological Continuant

Interlaminar Astrocyte
type: Class
contributor: Eric Bushong
sao ID: sao-1220620412
disjoint with: Velate Astrocyte
definition: Glial cell type unique to primates which extend long processes throughout cortical lamina forming pallisades.
comment: We need to create an object property that allows us to assign taxonomy information to classes that are only seen in certain taxa
subclasses disjoint: true
subclass of: Protoplasmic Astrocyte

ANT-2
type: Class
sao ID: sao369353782
subclass of: Adenine Nucleotide Transporter
curation status: uncurated

Adenine Nucleotide Transporter
type: Class
curation status: uncurated
umls ID: C1153655
subclass of: Transporter Protein
sao ID: sao2077117136
definition: Transports adenine nucleotides (AMP, ADP, and ATP) across membranes (Gene Ontology).
gene ontology ID: 0000295
disjoint with: Glutamate Transporter

Neuromelanin
type: Class
curation status: uncurated
umls ID: C0068608
subclass of: Pigment
sao ID: sao1996310556
disjoint with: Lipofuscin

Layer 2 3 Pyramidal Neuron
type: Class
disjoint with: Layer 3 Pyramidal Neuron
disjoint with: Layer 5 Pyramidal Neuron
subclasses disjoint: true
subclass of: Cortical Pyramidal Neuron
curation status: uncurated
sao ID: sao816233655

Layer 3 Pyramidal Neuron
type: Class
sao ID: sao1123695773
disjoint with: Layer 5 Pyramidal Neuron
definition: Pyramidal neuron whose cell soma resides in layer 3 of neocortex.
subclass of: Cortical Pyramidal Neuron
curation status: uncurated
subclasses disjoint: true

Crista Junction
type: Class
subclass of: Mitochondrial Site
curation status: uncurated
definition: Tubular structures of relatively uniform size that connect mitochondrial cristae to the inner mitchondrial membrane (Perkins and Ellisman, 2003).
sao ID: sao1825845900

Laminated Body
type: Class
curation status: uncurated
subclass of: Cellular Inclusion
sao ID: sao506721981

Aspiny
type: Class
sao ID: sao128827344
subclass of: Dendrite Type
definition: A dendrite characterized by few or no recognizable dendritic spines.
curation status: uncurated

Fibrillary Inclusion
type: Class
curation status: uncurated
sao ID: sao967812059
definition: 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)
subclass of: Cellular Inclusion

Dense Core Vesicle
type: Class
umls ID: C0887944
disjoint with: Neurosecretory Vesicle
subclass of: Granular Vesicle
sao ID: sao772007592
definition: 40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991).
curation status: uncurated

Pre-synaptic Subcomponent
type: Class
subclass of: Obsolete class
sao ID: sao503947499
curation status: uncurated

Ryanodine Receptor
type: Class
sao ID: sao960745141
subclass of: Intracellular Calcium Channel
disjoint with: Inositol 1 4 5 Trisphosphate Receptor
curation status: uncurated
umls ID: C0054493
definition: 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)

Schwann Cell Compact Myelin
type: Class
sao ID: sao-1123256993
subclass of: Schwann Cell Myelin Sheath
curation status: uncurated
definition: 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).

GluR1
type: Class
disjoint with: GluR2
disjoint with: GlurR3
subclass of: AMPA Receptor
sao ID: sao1322219701
curation status: uncurated

Cell Secretion
type: Class
sao ID: sao627060194
subclass of: Organismal Occurrent

Asymmetrical
type: Class
curation status: curation complete
comment: see example at: http://synapse-web.org/anatomy/chemical/asymh.htm
subclass of: Chemical Synapse Type
synonym: Gray's Type 1
definition: 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.
sao ID: sao2047438300

retinal rod cell
type: Class
cell ontology ID: CL:0000604
synonym: rod cell
curation status: uncurated
definition: 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.
subclasses disjoint: true
disjoint with: Retinal Cone Cell
umls ID: C0206427
subclass of: Eye Photoreceptor Cell
sao ID: sao1458938856
label: Retinal Rod Cell

Retinal Cone Cell
type: Class
cell ontology ID: CL:0000573
sao ID: sao1103104164
definition: 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)
subclass of: Eye Photoreceptor Cell
umls ID: C0206428
subclasses disjoint: true
curation status: uncurated
synonym: Cone cell
definition source: UMLS

Schwann Cell Microvillus
type: Class
sao ID: sao1890444066
curation status: uncurated
definition: 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)
subclass of: Regional Part Of Schwann Cell

Satellite Cell
type: Class
subclasses disjoint: true
sao ID: sao792373294
subclass of: Restriction
  on property: associated Cellular Element
  some values from: Neuronal Cell Body
subclass of: Schwann Cell
definition: Schwann cell that apposes or encapsulates neuronal perikarya (Peters, Palay and Webster, 1991).
curation status: uncurated

Calyx Of Held
type: Class
sao ID: sao1684283879
subclass of: Calyx
curation status: uncurated

Contact Site
type: Class
subclass of: Mitochondrial Site
subclass of: Restriction
  some values from: Mitochondrion
  on property: has Location Of
subclass of: Restriction
  some values from: Endoplasmic Reticulum
  on property: associated Cell Component
curation status: uncurated
sao ID: sao447856407
definition: Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000).

Pericyte
type: Class
subclass of: Vascular Cell
definition: 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).
synonym: Mural Cell
umls ID: C0598800
subclass of: Restriction
  on property: process Number
  has value: bipolar
synonym: Rouget Cell
disjoint with: Vascular Endothelial Cell
sao ID: sao1355908696
cell ontology ID: CL:0000184
curation status: uncurated

Ensheathing Process
type: Class
definition: Refers to the process of the Schwann cell that surrounds an unmyelinated axon or cell soma.
subclass of: Regional Part Of Schwann Cell
curation status: uncurated
sao ID: sao1376748732

Beta Neurexin
type: Class
subclass of: Neurexin
sao ID: sao149790201
curation status: uncurated

Betz Cell
type: Class
umls ID: C0228073
subclass of: Restriction
  has value: primate
  on property: species
subclass of: Restriction
  has value: motor cortex
  on property: anatomical Location General
subclass of: Layer 5 Pyramidal Neuron
curation status: uncurated
sao ID: sao786552500
subclasses disjoint: true
definition: Giant pyramidal neuron found in primate motor cortex.

species
type: FunctionalProperty
sao ID: sao1185641609
type: DatatypeProperty
range: string
domain: Class
  union of: Subregional Part Of Neuron Process
  union of: Nerve Cell
  union of: Regional Part Of Neuron
comment: Indicates the species of organism from which an observation derives

Primary Culture
type: Class
subclass of: In Vitro
sao ID: sao73984422

Post-synaptic Subcomponent
type: Class
sao ID: sao627589531
curation status: uncurated
subclass of: Obsolete class

Symmetrical
type: Class
synonym: Gray's Type 2
sao ID: sao1583093969
subclass of: Chemical Synapse Type
definition: Type of chemical synapse characterized by a thin post-synaptic density relatively equal in density to the pre-synaptic specialization giving the junction a symmetric appearance. This type of synapse is also characterized by flattened or pleiomorphic vesicles in the pre-synaptic terminal when fixed with aldehydes.
curation status: curation complete
comment: see example at: http://synapse-web.org/anatomy/chemical/symh.htm
disjoint with: Asymmetrical

Node Of Ranvier
type: Class
sao ID: sao571652273
subclass of: Node Related Site
subclass of: Restriction
  some values from: Paranode
  on property: continuous With
umls ID: C0034667
curation status: uncurated
definition: 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).

Paranode
type: Class
subclass of: Node Related Site
sao ID: sao-234066064
definition: Region of nodal complex adjacent to the nodal region

Subcellular Fraction
type: Class
subclass of: In Vitro
sao ID: sao1180716477

ANT-1
type: Class
sao ID: sao607850352
subclass of: Adenine Nucleotide Transporter
curation status: uncurated
disjoint with: ANT-2

Interphase
type: Class
gene ontology ID: 0051325
subclass of: Cell Cyle Phase
sao ID: sao727427771
definition: 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).
umls ID: C0021798

EAAT4
type: Class
curation status: uncurated
subclass of: Glutamate Transporter
sao ID: sao696157048
disjoint with: EAAT2
disjoint with: EAAT1
disjoint with: Water Channel

Myelinating Oligodendrocyte
type: Class
sao ID: sao841915587
definition: Oligodendrocyte that forms compact myelin sheath.
curation status: uncurated
umls ID: C0129447
subclass of: Obsolete class

Pars Fibrosa
type: Class
sao ID: sao1841764412
umls ID: C0230581
subclass of: Regional Part Of Nucleolus
definition: Portion of the nucleolus composed of densely matted filaments with scattered dark granules (Palay and Chan-Palay, 1974).
disjoint with: Pars Granulosa
curation status: uncurated

Mesaxon
type: Class
curation status: uncurated
sao ID: sao2127666702
definition: 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).
subclass of: Regional Part Of Schwann Cell

is Component Of
type: ObjectProperty
domain: Class
  union of: Object
  union of: FiatObjectPart
inverse of: has Component
sub property of: is Part Of
range: Object
sao ID: sao138767806

is Part Of
type: ObjectProperty
inverse of: has Part
sao ID: sao9906015852

continuous With Centrifugal
type: ObjectProperty
sao ID: sao1454173298
sub property of: continuous With

has Vesicle Component
type: ObjectProperty
domain: Vesicle
sub property of: has Component
range: Class
  union of: Vesicle Subcomponent
  union of: Object
inverse of: inverse of has Component 6
sao ID: sao3762365186

inverse of has Component 6
type: ObjectProperty
sub property of: is Component Of
inverse of: has Vesicle Component
domain: Class
  union of: Vesicle Subcomponent
  union of: Object
range: Vesicle
sao ID: sao7291254923

has Property
type: ObjectProperty
domain: IndependentContinuant
sao ID: sao2103390115
range: DependentContinuant
comment: refers to a set of property classes that reflect unique aspects of a given structure, e.g., orientation, stability

is Morphological Type Of
type: ObjectProperty
inverse of: has Morphological Type
domain: Morphological Type
range: Class
  union of: Mitochondrion
  union of: Regional Part Of Cell
  union of: Intercellular Junction Site
  union of: Cellular Component
  union of: Cell
sao ID: sao3610809721

has Part
type: ObjectProperty
inverse of: is Part Of
sao ID: sao5598458770

associated With
type: ObjectProperty
comment: Indicates that there is a spatial relationship other than containment or parthood between cellular regional parts or components (e.g. microtuble associates with mitochondria)
sao ID: sao2047323768

contains Site
type: ObjectProperty
range: Class
  union of: Mitochondrial Space
  union of: Site
  union of: Mitochondrial Site
domain: Class
  union of: Mitochondrion
  union of: Site
sao ID: sao554204175

is Intercellular Junction Compartment Of
type: ObjectProperty
sao ID: sao45720944
range: Class
  union of: Cell Cell Contact Zone
  union of: Regional Part Of Neuron
  union of: Subregional Part Of Neuron Process
  union of: Intercellular Junction Site
inverse of: intercellular Junction Compartment
domain: Class
  union of: Regional Part Of Cell Cell Contact Zone
  union of: Intercellular Junction Site
sub property of: is Part Of

intercellular Junction Compartment
type: ObjectProperty
range: Class
  union of: Regional Part Of Cell Cell Contact Zone
  union of: Intercellular Junction Site
comment: participates in one or more types of intercellular junctions
domain: Class
  union of: Cell Cell Contact Zone
  union of: Regional Part Of Neuron
  union of: Subregional Part Of Neuron Process
  union of: Intercellular Junction Site
sub property of: has Part
sao ID: sao733319732
inverse of: is Intercellular Junction Compartment Of

is Aggregate Part of
type: ObjectProperty
inverse of: has Aggregate Part
range: ObjectAggregate
sub property of: is Part Of
domain: Class
  union of: IndependentContinuant
  union of: Thing
sao ID: sao2422696582

continuous With Centripetal
type: ObjectProperty
sub property of: continuous With
sao ID: sao158083006

anatomical Location
type: ObjectProperty
sao ID: sao7122682114

is Neurotransmitter Of
type: InverseFunctionalProperty
sao ID: sao924725934
inverse of: has Neurotransmitter
range: Neuron
domain: Molecule
type: ObjectProperty
sub property of: is Part Of

morphometrics
type: ObjectProperty
range: Measurement
sub property of: has Property
domain: IndependentContinuant
sao ID: sao872346836
comment: Measurement associated with compartment

anatomical Location Specific
type: ObjectProperty
sub property of: anatomical Location
domain: Class
  union of: Supra Cellular Structure
  union of: Subregional Part Of Neuron Process
  union of: Nerve Cell
  union of: Regional Part Of Neuron
  union of: Glial Subcompartment
sao ID: sao548011359
comment: Refers to the specific location of an instance of a cell

synapse Type
type: DatatypeProperty
sao ID: sao99760531
comment: Classification of synaptic type according to Gray, except using the symmetrical (Gray's Type 2) and asymmetrical (Gray's Type 1) designations
range: DataRange
  one of: asymmetrical
  one of: symmetrical
domain: Class
  union of: Synapse
  union of: Intercellular Junction Site
  union of: Regional Part Of Cell Cell Contact Zone

maximum
type: DatatypeProperty
domain: Measurement
comment: maximum value in a range
sao ID: sao395752640
range: float

has Mass
type: DatatypeProperty
range: DataRange
  one of: false
  one of: true
sao ID: sao1077517916

observation Conditions
type: DatatypeProperty
comment: Indicates under what conditions the observation was made
range: string
domain: Nerve Cell
sao ID: sao1429489883

minimum
type: DatatypeProperty
domain: Measurement
comment: Minimum value in a range
sao ID: sao643761283
range: float

point Of Measurement
type: DatatypeProperty
sao ID: sao1669593695
comment: Indicates the point at which a described measurement was taken
domain: Measurement
range: DataRange
  one of: proximal
  one of: distal

PSD morphology
type: DatatypeProperty
domain: Post-synaptic Density
range: DataRange
  one of: perforated
  one of: macular
  one of: asymmetric
  one of: symmetric
comment: 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).
sao ID: sao1056822429
label: psd Morphology

presence
type: DatatypeProperty
definition: 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.
comment: This property should be updated when we switch to OBR relations to the "lacks" relationship
domain: Class
  union of: Intercellular Junction Site
  union of: General Cell Subcompartment
  union of: Glial Subcompartment
  union of: Subregional Part Of Neuron Process
  union of: Regional Part Of Glia
  union of: Nerve Cell
  union of: Molecule
  union of: Regional Part Of Neuron
  union of: Cellular Subcomponent
  union of: Regional Part Of Cell Cell Contact Zone
range: DataRange
  one of: not found
curation status: graph position temporary
sao ID: sao2372462654

is Continuant
type: DatatypeProperty
comment: 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.
range: DataRange
  one of: false
  one of: true
sao ID: sao1798215493

value Type
type: FunctionalProperty
range: DataRange
  one of: range
  one of: less than or equal to
  one of: estimate
  one of: greater than or equal to
  one of: greater than
  one of: average
  one of: less than
  one of: direct
  one of: absolute
domain: Class
  union of: Measurement
  union of: Subregional Part Of Neuron Process
comment: Describes whether the reported values are averages, estimates, ranges, or absolute values
type: DatatypeProperty
sao ID: sao375065056

maximum Branch Order
type: FunctionalProperty
sao ID: sao925977276
type: DatatypeProperty
range: int
domain: Class
  union of: Dendrite
  union of: Dendritic Tree
comment: Refers to the maximum branch order of the dendritic tree

density
type: FunctionalProperty
domain: Molecule
type: DatatypeProperty
sao ID: sao382106499
range: float

Atlas Coordinate A-P
type: FunctionalProperty
domain: Atlas Location
sao ID: sao2048509857
type: DatatypeProperty
comment: Coordiante along the anteior-posterior axis
range: string
label: atlas Coordinate A-P

standard Error
type: FunctionalProperty
comment: Standard error (+/-)
type: DatatypeProperty
domain: Measurement
range: float
sao ID: sao1620782974

Atlas Coordinate M-L
type: FunctionalProperty
comment: Coordinate along the medial-lateral axis
type: DatatypeProperty
domain: Atlas Location
sao ID: sao1804901442
range: string
label: atlas Coordinate M-L

number Primary Dendrites Max
type: FunctionalProperty
range: int
domain: Dendritic Tree
type: DatatypeProperty
comment: Refers to the maximum number of primary dendrites generally seen in a particulary neuronal class
sao ID: sao1936650489

number Of Branches
type: FunctionalProperty
domain: Dendritic Tree
type: DatatypeProperty
sao ID: sao1746944408
range: string

total Dendritic Length
type: FunctionalProperty
range: float
type: DatatypeProperty
comment: Cumulative length of all dendrites in the dendritic tree
sao ID: sao528500906

sex Of Animal
type: FunctionalProperty
domain: Class
  union of: Subregional Part Of Neuron Process
  union of: Nerve Cell
  union of: Regional Part Of Neuron
range: DataRange
  one of: Female
  one of: Male
  one of: Unspecified
comment: Indicates the sex of the animal in which the observation was made.
type: DatatypeProperty
sao ID: sao392224970

Age of Animal
type: FunctionalProperty
type: DatatypeProperty
comment: Indicates the age of the animal in which the observation was made
domain: Class
  union of: Subregional Part Of Neuron Process
  union of: Nerve Cell
  union of: Regional Part Of Neuron
range: string
sao ID: sao2134236783
label: age Of Animal

Atlas Reference
type: FunctionalProperty
comment: Name and edition of atlas used to derive coordinates
type: DatatypeProperty
sao ID: sao244654816
range: string
domain: Atlas Location
label: atlas Reference

functional Type
type: FunctionalProperty
range: DataRange
  one of: inhibitory
  one of: modulatory
  one of: excitatory
type: DatatypeProperty
domain: Regional Part Of Schwann Cell
sao ID: sao1608074544
comment: functional categorization of cell, e.g., motor, sensory, secretory, myelinating

population Object
type: FunctionalProperty
type: DatatypeProperty
sao ID: sao1428515021
domain: Class
  union of: Regional Part Of Cell Cell Contact Zone
  union of: Intercellular Junction Site
  union of: General Cell Subcompartment
  union of: Non Neural Cell Compartment
  union of: Subregional Part Of Neuron Process
  union of: Regional Part Of Glia
  union of: Nerve Cell
  union of: Molecule
  union of: Regional Part Of Neuron
  union of: Glial Subcompartment
  union of: Extracellular Space
range: DataRange
  one of: Yes
  one of: No
comment: 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.

isoform
type: FunctionalProperty
domain: Molecule
type: DatatypeProperty
sao ID: sao1267375031
range: string

Atlas reference point
type: FunctionalProperty
type: DatatypeProperty
domain: Atlas Location
range: string
comment: Reference point of the coordinate system used, e.g., bregma
sao ID: sao1945565347
label: atlas Reference Point

orientation Reference To
type: FunctionalProperty
type: DatatypeProperty
comment: Element with reference to which orientation is defined
range: string
sao ID: sao2110623092

ccdb ID
type: FunctionalProperty
sao ID: sao796296921
range: string
definition: Unique identifier of an instance found in the CCDB.
type: DatatypeProperty

branch Order
type: FunctionalProperty
comment: A property of branching structures such as axons and dendrites
range: DataRange
  one of: 3
  one of: >3
  one of: 2
  one of: >2
type: DatatypeProperty
sao ID: sao996727841

Anatomical location: atlas
type: FunctionalProperty
domain: Class
  union of: Regional Part Of Neuron
  union of: Nerve Cell
type: ObjectProperty
range: Atlas Location
comment: Location of a cell in a specific coordinate system
sao ID: sao1597912566
sub property of: anatomical Location
label: anatomical Location Atlas

attached To
type: FunctionalProperty
sub property of: associated With
pending action note: 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
type: ObjectProperty
sao ID: sao1896476612
comment: Indicates an intimate contact between two anatomical entities, each with their own real boundaries

value
type: FunctionalProperty
domain: Measurement
type: DatatypeProperty
comment: measurement value
range: float
sao ID: sao655061336

number
type: FunctionalProperty
range: int
domain: Class
  union of: Mitochondrion
  union of: Intercellular Junction Site
  union of: Regional Part Of Neuron
  union of: Subregional Part Of Neuron Process
  union of: General Cell Subcompartment
  union of: Synapse
type: DatatypeProperty
sao ID: sao267012610

polarity Reference To
type: FunctionalProperty
range: string
sao ID: sao431495567
domain: Polarity
type: DatatypeProperty
comment: Reference to which polarity is defined

shape
type: FunctionalProperty
comment: Used to describe generic shape of a component or compartment
domain: Class
  union of: Organelle
  union of: Vesicle
  union of: Regional Part Of Neuron
sao ID: sao166035570
type: DatatypeProperty
range: DataRange
  one of: convex
  one of: concave
  one of: spherical
  one of: elliptical
  one of: spindle-shaped
  one of: round
  one of: flat
  one of: cylindrical

unit
type: FunctionalProperty
range: DataRange
  one of: angstroms
  one of: microns
  one of: spines per micron
  one of: cubic microns
  one of: microns squared
domain: Class
  union of: Gap Junction
  union of: Measurement
comment: unit of measurement
sao ID: sao40919963
type: DatatypeProperty

Cell ID
type: FunctionalProperty
sao ID: sao1981606713
comment: 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.
type: DatatypeProperty
domain: Nerve Cell
range: DataRange
  one of: Asserted
  one of: concrete
  one of: abstract
label: parent Cell Identity

Atlas Coordinate D-V
type: FunctionalProperty
type: DatatypeProperty
range: string
comment: Coordinate along the dorsal ventral axis
sao ID: sao833783433
domain: Atlas Location
label: atlas Coordinate D-V