NIF-Subcellular: contains cell parts and subcellular structures from SAO-CORE
type: Ontology

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

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

Intracellular Membrane
type: Class
curation status: uncurated
disjoint with: sao237754030
subclass of: Cellular Membrane
sao ID: sao830981606

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

Nucleolus
type: Class
sao ID: sao1820400233
subclass of: Nuclear Subcomponent
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).
gene ontology ID: 0005730
umls ID: C0007609
curation status: uncurated

Nuclear Lamina
type: Class
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).
sao ID: sao1455996588
gene ontology ID: 0005652
umls ID: C1136039
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).
disjoint with: Interchromatin Granule
disjoint with: Nucleolus
subclass of: Nuclear Subcomponent
curation status: uncurated

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

Intracristal Space
type: Class
definition: The space bounded by the cristae membrane
disjoint with: Mitochondrial Intermembrane Space
sao ID: sao508958414
subclass of: Mitochondrial Space
subclasses disjoint: true
curation status: uncurated
disjoint with: Mitochondrial Lumen

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

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

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

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

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

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

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

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

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

Core
type: Class
sao ID: sao6587439252
subclass of: Regional Part Of Lewy Body
definition: The center portion of the Lewy Body. In Parkinson's Disease, it contains a matted meshwork of filaments.
curation status: uncurated
contributor: Sarah M. Maynard

Regional Part Of Lewy Body
type: Class
contributor: Sarah M. Maynard
subclass of: Regional Part Of Cell Component
sao ID: sao1894609662
curation status: uncurated

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

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

Spine Mat
type: Class
sao ID: sao2128156969
subclass of: Cell Regional Part Aggregate Object
contributor: Maryann Martone
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

Initial Segment
type: Class
disjoint with: Axon Terminal
disjoint with: Main Axon
disjoint with: Axonal Growth Cone
sao ID: sao256000789
disjoint with: Axon Collateral
curation status: uncurated
gene ontology ID: 0043194
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: Regional Part Of Axon
disjoint with: Axon Hillock
disjoint with: Regional Part Of Basket Cell Axon

Axon Terminal
type: Class
curation status: uncurated
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).
subclass of: Regional Part Of Axon

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

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

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

Axon Hillock
type: Class
sao ID: sao627227260
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: Axon Terminal
curation status: uncurated
subclass of: Regional Part Of Axon
disjoint with: Regional Part Of Basket Cell Axon
gene ontology ID: 0043203
umls ID: C0228079
disjoint with: Axonal Growth Cone

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

Node Of Ranvier
type: Class
subclass of: Node Related Site
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).
umls ID: C0034667
curation status: uncurated
sao ID: sao571652273

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

Post-synaptic Site
type: Class
subclass of: Synaptic Site
sao ID: sao1074198261
comment: Before replacing the is_Location_Of property with RO's contained_in and the site_Contained_In property with RO's contained_in, we had the two restrictions: 1) is_Location_Of some Post-synaptic Density and 2) site_Contained_In some Post-synatpic Density. Thus, now we just have one restriction: contained_in some Post-synaptic Density.

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

Barr Body
type: Class
disjoint with: Interchromatin Granule
disjoint with: Nucleolus
disjoint with: Nuclear Membrane
sao ID: sao1571698684
disjoint with: Nucleoplasm
disjoint with: Nuclear Lamina
disjoint with: Nuclear Pore
disjoint with: sao238602892
disjoint with: Nuclear Body
curation status: uncurated
subclass of: Nuclear Subcomponent

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

Nuclear Pore
type: Class
sao ID: sao220861693
disjoint with: Nucleoplasm
disjoint with: Nuclear Membrane
disjoint with: Nucleolus
disjoint with: sao238602892
umls ID: C0028587
disjoint with: Interchromatin Granule
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: Nuclear Body
curation status: uncurated
subclass of: Nuclear Subcomponent
gene ontology ID: 0005643
disjoint with: Nuclear Lamina

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

Cortical Lewy Body
type: Class
definition: Lesion that is less well defined than a Classical Lewy Body and lacks a halo.
contributor: Sarah M. Maynard
subclass of: Lewy Body
curation status: uncurated
sao ID: sao4040591221
comment: has Regional Part some Regional_Part_of_Lewy_Body restriction violated because Cortical Lewy Body lacks halo.

Lewy Body
type: Class
contributor: Sarah M. Maynard
curation status: uncurated
definition: Neuronal inclusion commonly found in damaged neurons. A spherical mass that dispaces other cells composed of abnormally phosphorylated, neurofilament proteins aggregated with ubiquitin and alpha-synuclein. They are intracytoplasmic.
subclass of: Cellular Inclusion
note: there are two morphological types: classical (brain stem) and cortical Lewy bodies
sao ID: sao4933778419

Pyramidal Neuronal Cell Body
type: Class
subclass of: Neuronal Cell Body
sao ID: sao-820130069
curation status: uncurated

Neuronal Cell Body
type: Class
sao ID: sao1044911821
umls ID: C0599444
disjoint with: Regional Part Of Neuronal Cell Body
disjoint with: Neuron Process
definition: Cell body which consists of the plasma membrane and the cytoplasm surrounding the nucleus of the neuron (FMA).
disjoint with: Regional Part Of Spine
disjoint with: Neuron Protrusion
subclass of: Regional Part Of Neuron
curation status: uncurated
disjoint with: sao-750951932
synonym: soma
disjoint with: Regional Part Of Neuron Process

Juxta Paranode Axon
type: Class
curation status: uncurated
disjoint with: Internode Axon
sao ID: sao1191319089
definition: Region of axon immediately adjacent to the paranode.
disjoint with: Paranode Axon
subclass of: Regional Part Of Myelinated Axon
disjoint with: Node Of Ranvier Axon

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

Paranode Axon
type: Class
curation status: uncurated
sao ID: sao936144858
subclass of: Regional Part Of Myelinated Axon
disjoint with: Internode Axon
disjoint with: Node Of Ranvier Axon
disjoint with: Juxta Paranode Axon

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

Node Of Ranvier Axon
type: Class
subclass of: Regional Part Of Myelinated Axon
curation status: uncurated
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.
sao ID: sao-188049490
disjoint with: Juxta Paranode Axon
disjoint with: Internode Axon
disjoint with: Paranode Axon

Active Zone Plasma Membrane
type: Class
curation status: uncurated
subclass of: Pre-synaptic Active Zone Component
disjoint with: Pre-synaptic Grid
disjoint with: Active Zone Dense Projection
sao ID: sao2038461087
definition: Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004).

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

Pre-synaptic Grid
type: Class
subclass of: Pre-synaptic Active Zone Component
curation status: uncurated
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: Pre-synaptic Dense Body
disjoint with: Active Zone Dense Projection

Active Zone Dense Projection
type: Class
curation status: uncurated
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

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

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

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

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

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

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

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

Synaptic Component
type: Class
disjoint with: Cellular Inclusion
disjoint with: Cilium
sao ID: sao1784069613
disjoint with: Coated Pit
disjoint with: Cytoskeletal Element
disjoint with: Cellular Subcomponent
disjoint with: Subplasmalemmal Coating
disjoint with: Glycogen Granule
disjoint with: Cytosol
disjoint with: Intracellular Membrane
disjoint with: Basal Lamina
disjoint with: sao237754030
disjoint with: Vesicle
subclass of: Cellular Component
disjoint with: Plasma Membrane

Regional Part Of Neuron Process
type: Class
subclass of: Regional Part Of Neuron
sao ID: sao-420949334
disjoint with: Neuron Process
disjoint with: Neuron Protrusion
curation status: uncurated
disjoint with: Regional Part Of Neuronal Cell Body
disjoint with: Neuronal Cell Body
disjoint with: Regional Part Of Spine
disjoint with: sao-750951932

Regional Part Of Neuron
type: Class
curation status: uncurated
disjoint with: Cell Protrusion
sao ID: sao864921383
subclass of: Regional Part Of Cell
synonym: neuron compartment
disjoint with: sao1843719868
disjoint with: Regional Part Of Glial Cell

Neuron Process
type: Class
disjoint with: Regional Part Of Neuronal Cell Body
subclass of: Regional Part Of Neuron
disjoint with: Neuronal Cell Body
synonym: Neurite
disjoint with: Neuron Protrusion
disjoint with: sao-750951932
sao ID: sao-867568886
disjoint with: Regional Part Of Neuron Process
disjoint with: Regional Part Of Spine

Neuron Protrusion
type: Class
subclass of: Regional Part Of Neuron
curation status: uncurated
sao ID: sao-250931889
disjoint with: sao-750951932
disjoint with: Neuronal Cell Body
disjoint with: Regional Part Of Neuronal Cell Body
disjoint with: Neuron Process
disjoint with: Regional Part Of Spine
disjoint with: Regional Part Of Neuron Process

Regional Part Of Neuronal Cell Body
type: Class
disjoint with: Basal Pole Of Neuron
disjoint with: sao-750951932
sao ID: sao1049717962
disjoint with: Neuron Protrusion
disjoint with: Cell Interior
curation status: uncurated
disjoint with: Apical Pole Of Neuron
disjoint with: Cell Cell Contact Zone
disjoint with: Regional Part Of Neuron Process
subclass of: Regional Part Of Neuron
disjoint with: Neuron Process
disjoint with: Node Related Site
disjoint with: Regional Part Of Spine
disjoint with: Neuronal Cell Body

Regional Part Of Spine
type: Class
curation status: uncurated
disjoint with: Regional Part Of Neuronal Cell Body
subclass of: Regional Part Of Neuron
disjoint with: Neuronal Cell Body
sao ID: sao866168499
disjoint with: Neuron Process
disjoint with: sao-750951932
disjoint with: Regional Part Of Neuron Process
disjoint with: Neuron Protrusion

Rough Endoplasmic Reticulum
type: Class
sao ID: sao1881364067
curation status: uncurated
disjoint with: Smooth Endoplasmic Reticulum
umls ID: C0230779
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: Endoplasmic Reticulum
gene ontology ID: 0005791
synonym: Nissl substance

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

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

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

Dendrite
type: Class
gene ontology ID: 0030425
umls ID: C0011305
sao ID: sao1211023249
subclass of: Neuron Process
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.
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).
curation status: uncurated

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

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

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

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

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

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

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

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

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

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

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

Mitochondrial Matrix
type: Class
gene ontology ID: 0005759
umls ID: C0230843
curation status: uncurated
disjoint with: Cristae
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).
subclass of: Mitochondrial Subcomponent
sao ID: sao1804523077

Cristae
type: Class
umls ID: C0230844
subclass of: Regional Part Of Mitochondrial Membrane
sao ID: sao333328131
gene ontology ID: 0030061
curation status: uncurated
definition: Any of the inward folds of the mitochondrial inner membrane. (Gene Ontology)

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

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

Endocytic Vesicle
type: Class
disjoint with: Transport Vesicle
subclass of: Cytoplasmic Vesicle
sao ID: sao1362520468
disjoint with: Synaptic Vesicle
umls ID: C0887883
disjoint with: Granular Vesicle
curation status: uncurated
gene ontology ID: 0030139
disjoint with: sao1985096626
disjoint with: Vesicle Other
definition: A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology).

Large Vesicle
type: Class
sao ID: sao1241866791
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

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

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

Cytoskeletal Element
type: Class
disjoint with: Intracellular Membrane
disjoint with: sao237754030
disjoint with: Vesicle
curation status: uncurated
sao ID: sao1635329413
subclass of: Cellular Component

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

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

Regional Part Of RER
type: Class
disjoint with: sao903454364
disjoint with: Regional Part Of Mitochondrial Membrane
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 Cell Component
sao ID: sao2019617624

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

Vesicle
type: Class
gene ontology ID: 0031982
subclass of: Cellular Component
disjoint with: Intracellular Membrane
sao ID: sao221389602
disjoint with: sao237754030
umls ID: C0042219
curation status: uncurated
definition: Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology).

Paired Helical Filament
type: Class
definition: Two threads of tau protein that are wound around each other.
contributor: Sarah M. Maynard
synonym: PHF
sao ID: sao6603990120
subclass of: Filament

Filament
type: Class
curation status: uncurated
contributor: Sarah M. Maynard
comment: This is a placeholder. This refers to a protein configuration, but we think it belongs elsewhere. A fibril is actually a minute fiber or filament. Filament could refer to protein filament. A long chain of proteins, such as those found in hair, muscle, or in flagella
sao ID: sao7561423738
synonym: Protein Filament
subclass of: Aggregate Object

Aggregate Object
type: Class
sao ID: sao3826089237
subclass of: ObjectAggregate
curation status: uncurated
contributor: Sarah Maynard

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

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

Cellular Subcomponent
type: Class
disjoint with: Intracellular Membrane
curation status: uncurated
disjoint with: Cytoskeletal Element
sao ID: sao628508602
subclass of: Cellular Component
disjoint with: Vesicle
disjoint with: sao237754030

Endfoot
type: Class
sao ID: sao388182739
subclass of: Vellous Process
definition: Terminal process of astrocyte abutting non-neuronal surfaces in the brain.
curation status: uncurated
curation status: graph position temporary

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

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

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

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

Spine Neck
type: Class
curation status: uncurated
disjoint with: Spine Head
synonym: neck
sao ID: sao1642908940
subclass of: Regional Part Of Spine
synonym: pedicle
disjoint with: Spinule

Spine Head
type: Class
disjoint with: Spinule
sao ID: sao952643730
subclass of: Regional Part Of Spine
curation status: uncurated

Spinule
type: Class
subclass of: Regional Part Of Spine
curation status: uncurated
sao ID: sao553737851

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

Schwann Cell Microvillus
type: Class
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
sao ID: sao1890444066
curation status: uncurated

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

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

Plasma Membrane
type: Class
disjoint with: Cellular Inclusion
disjoint with: sao237754030
sao ID: sao1663586795
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).
gene ontology ID: 0005886
subclass of: Cellular Membrane
disjoint with: Cilium
curation status: uncurated
disjoint with: Cellular Subcomponent
umls cui: C0007603
disjoint with: Cytoskeletal Element
disjoint with: Vesicle
disjoint with: Intracellular Membrane
synonym: cell membrane

Cellular Inclusion
type: Class
disjoint with: Cellular Subcomponent
curation status: uncurated
disjoint with: sao237754030
disjoint with: Vesicle
sao ID: sao120573470
subclass of: Cellular Component
synonym: Inclusion Body
disjoint with: Intracellular Membrane
disjoint with: Cytoskeletal Element
definition: A nuclear or cytoplasmic aggregate of stainable substances, usually proteins.

Cellular Membrane
type: Class
subclass of: Cellular Component
sao ID: sao6433132645

Cilium
type: Class
curation status: uncurated
subclass of: Cellular Component
disjoint with: Intracellular Membrane
disjoint with: Cellular Inclusion
gene ontology ID: 0005929
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).
sao ID: sao787716553
disjoint with: Vesicle
disjoint with: Cellular Subcomponent
umls ID: C0008778
disjoint with: sao237754030
disjoint with: Cytoskeletal Element

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
sao ID: sao1210952635

Synaptic Bouton
type: Class
disjoint with: Calyx
subclass of: Axon Terminal
definition: Terminal pre-synaptic ending of an axon or axon collateral.
curation status: uncurated
sao ID: sao187426937

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

Alpha-Synuclein Fibril
type: Class
definition: Insoluble fibrils that form in pathological conditions characterized by Lewy bodies, such as Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Alpha-synuclein is the primary structural component.
contributor: Sarah M. Maynard
subclass of: Fibril
sao ID: sao7474011676
curation status: uncurated

Fibril
type: Class
comment: This is a placeholder.
sao ID: sao5051906853
curation status: uncurated
contributor: Sarah M. Maynard
definition: A minute fibril or filament.
subclass of: Filament

Dark Material
type: Class
curation status: uncurated
sao ID: sao1122901839
subclass of: Protein Aggregate
definition: Irregularly shaped clumps of denatured or misfolded proteins observed in some neurons after a period of ischemia that stain heavily with osmium in electon microscopic preparations.
contributor: Sarah M. Maynard

Protein Aggregate
type: Class
subclass of: Aggregate Object
curation status: uncurated
contributor: Sarah M. Maynard
sao ID: sao7016027781
definition: An insoluble mass of misfolded proteins.

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

Chemical Synapse
type: Class
curation status: uncurated
subclass of: Synapse
sao ID: sao289211478

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

Synapse
type: Class
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
sao ID: sao914572699
curation status: uncurated
disjoint with: Gap Junction Plaque

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).

Mitochondrial Membrane Inner
type: Class
umls ID: C0230840
gene ontology ID: 0005743
subclass of: Mitochondrial Membrane
sao ID: sao1371347282
curation status: uncurated
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).

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

Classical Lewy Body
type: Class
sao ID: sao4749542545
curation status: uncurated
definition: Eosinophilic cytoplasmic lesion, 5 to 15 micrometers in diameter, with a dense eosinphilic core surrounded by a halo of 10 to 20 nm wide radially oriented alpha-synuclein fibrils.
contributor: Sarah M. Maynard
subclass of: Lewy Body

Hypolemmal Cisternae
type: Class
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).
sao ID: sao1634374950
subclass of: Regional Part Of SER
curation status: uncurated

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

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

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

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

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

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

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

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

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

Glycogen Granule
type: Class
sao ID: sao1081228141
disjoint with: Basal Lamina
curation status: uncurated
gene ontology ID: 0042587
subclass of: Cellular Component
disjoint with: sao237754030
disjoint with: Cilium
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: Cellular Subcomponent
disjoint with: Intracellular Membrane
disjoint with: Coated Pit
disjoint with: Cellular Inclusion
disjoint with: Cytoskeletal Element
umls ID: C0017911
disjoint with: Plasma Membrane
disjoint with: Vesicle

Basal Lamina
type: Class
disjoint with: Plasma Membrane
curation status: uncurated
disjoint with: Cellular Subcomponent
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
disjoint with: Cellular Inclusion
disjoint with: Vesicle
gene ontology ID: 0005605
subclass of: Extracellular Structure
disjoint with: Cilium
sao ID: sao1397492660
disjoint with: sao237754030
umls ID: C0242195

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

Coated Pit
type: Class
curation status: uncurated
disjoint with: Cilium
sao ID: sao1969557946
umls ID: C0009143
disjoint with: Plasma Membrane
disjoint with: Basal Lamina
subclass of: Cellular Component
disjoint with: Vesicle
disjoint with: Cytoskeletal Element
disjoint with: sao237754030
disjoint with: Intracellular Membrane
definition: Specialized sites on the plasma membrane exhibiting a clathrin coat; likely vesicles in the process of pinching off (Conner and Schmid, 2003).
disjoint with: Cellular Subcomponent
disjoint with: Cellular Inclusion

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

Neurotubule
type: Class
sao ID: sao248349196
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
curation status: uncurated

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

Mushroom Dendritic Spine
type: Class
disjoint with: Sessile Dendritic Spine
disjoint with: Thin Dendritic Spine
sao ID: sao-876577163
disjoint with: Branched Dendritic Spine
curation status: uncurated
subclass of: Dendritic Spine

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

Thin Dendritic Spine
type: Class
subclass of: Dendritic Spine
sao ID: sao1232858786
curation status: uncurated
disjoint with: Branched Dendritic Spine

Branched Dendritic Spine
type: Class
subclass of: Dendritic Spine
sao ID: sao-965204139
curation status: uncurated

Dendritic Spine
type: Class
disjoint with: Somatic Spine
sao ID: sao1799103720
subclass of: Spine
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).
gene ontology ID: 0043197
disjoint with: Axonal Spine
curation status: uncurated
umls ID: C0872341

Connexon
type: Class
disjoint with: Orthogonal Array
gene ontology ID: 0005922
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.
curation status: uncurated
synonym: hemichannel, connexon complex
definition source: Wikipedia
subclass of: Cell Component Aggregate Object
umls ID: C0230609
sao ID: sao445019788

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

Mitochondrion
type: Class
disjoint with: Nucleus
gene ontology ID: 0005739
disjoint with: Endoplasmic Reticulum
sao ID: sao1860313010
disjoint with: Multivesicular Body
umls ID: C0026237
disjoint with: Lysosome
curation status: uncurated
disjoint with: Endosome
disjoint with: Golgi Apparatus
disjoint with: Peroxisome
disjoint with: Spine Apparatus
subclass of: Membrane Bound Organelle
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).

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

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

Endosome
type: Class
disjoint with: Peroxisome
subclass of: Membrane Bound Organelle
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: Lysosome
curation status: uncurated
sao ID: sao1720343330
disjoint with: Multivesicular Body
gene ontology ID: 0005768
umls ID: C0034850

Golgi Apparatus
type: Class
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)
disjoint with: Endoplasmic Reticulum
disjoint with: Lysosome
subclass of: Membrane Bound Organelle
disjoint with: Multivesicular Body
curation status: uncurated
disjoint with: Peroxisome
sao ID: sao451912436
disjoint with: Endosome
umls ID: C0018042
synonym: golgi cisternae
gene ontology ID: 0005794

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

Spine Apparatus
type: Class
curation status: uncurated
disjoint with: Endosome
disjoint with: Nucleus
disjoint with: Multivesicular Body
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: Endoplasmic Reticulum
subclass of: Membrane Bound Organelle
disjoint with: Lysosome
umls ID: C0230810
disjoint with: Golgi Apparatus
disjoint with: Peroxisome
sao ID: sao725931194

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

Somatic Spine
type: Class
definition: Spine emanating from the cell soma.
curation status: uncurated
disjoint with: Axonal Spine
disjoint with: Dendritic Spine
sao ID: sao2048514053
subclass of: Spine

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

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

Axon
type: Class
subclass of: Neuron Process
disjoint with: Dendrite
sao ID: sao1770195789
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
gene ontology ID: 0030424
definition: Cell appendage of a neuron that consists of an axon hillock, an axon proper, axon collaterals and an axon terminal (FMA)
umls ID: C0004461

Glutamate Receptor
type: Class
sao ID: sao1164727693
curation status: uncurated
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).

Neurotransmitter Receptor
type: Class
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).
sao ID: sao587592318
subclass of: sao452970150
curation status: uncurated
disjoint with: sao1246280606
umls ID: C0034828

Autophagosome
type: Class
synonym: autophagic vacuole, initial autophagic vacuole (AVi)
subclass of: Vesicle
contributor: Sarah M. Maynard
curation status: uncurated
sao ID: sao8663416959
definition: A vesicle with a double membrance derived from the Endoplasmic Reticulum that encloses cytoplasmic material and organelles to be degraded. Its formation is the first step of the process of autophagy.

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

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

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

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

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

Neuritic Plaque
type: Class
comment: We need to check if any plaques do not amyloid and if amyloid is beta. We are not sure if there is a distinction between Neuritic plaque and Senile plaque.
sao ID: sao9515821206
curation status: uncurated
label: Neuritic plaque
subclass of: Plaque
contributor: Sarah M. Maynard
definition: A characteristic form of amyloid plaque. Has an extracellular core of amyloid fibrils surrounded by dystrophic dendrites and axons, some of which contain protein filaments, activated microglia and reactive astrocytes.

Plaque
type: Class
sao ID: sao9137852997
definition: A formation or growth of cells.
curation status: uncurated
contributor: Sarah M. Maynard
subclass of: Extracellular Structure

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

Lewy Neurite
type: Class
definition: Elongated neuronal process, described in brains of patients with Parkinson's disease, many of which exhibit side branches and have more than one branching point. Stains positively for ubiquitin in brainstem and forebrain regions affected in Parkinson's disease.
subclass of: Neuron Process
sao ID: sao601362597
curation status: uncurated

Extracellular Structure
type: Class
sao ID: sao9117790637
definition: Structure that exists outside the cell.
curation status: uncurated
subclass of: Object
contributor: Sarah M. Maynard

Population
type: Class
sao ID: sao2254405550
curation status: uncurated
subclass of: ObjectAggregate

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

Regional Part Of Nucleolus
type: Class
disjoint with: Regional Part Of Golgi
disjoint with: Regional Part Of RER
sao ID: sao113580911
subclass of: Regional Part Of Cell Component
curation status: uncurated
disjoint with: Regional Part Of Mitochondrial Membrane
disjoint with: sao903454364

Pars Granulosa
type: Class
subclass of: Regional Part Of Nucleolus
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

Age Associated
type: Class
sao ID: sao2017162875
curation status: uncurated
subclass of: Cellular Inclusion
comment: Need to look this one up and see what this really meant.

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

Regional Part Of Spine Apparatus
type: Class
subclass of: Regional Part Of Cell Component
disjoint with: Regional Part Of RER
sao ID: sao1682692988
curation status: uncurated
disjoint with: sao903454364
disjoint with: Regional Part Of Mitochondrial Membrane
disjoint with: Regional Part Of Golgi
disjoint with: Regional Part Of Nucleolus

Oligodendrocyte Compact Myelin
type: Class
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
sao ID: sao1186642361
subclass of: Oligodendrocyte Myelin Sheath
gene ontology ID: 0043218

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

Organelle
type: Class
disjoint with: Coated Pit
disjoint with: Subplasmalemmal Coating
curation status: uncurated
disjoint with: Intracellular Membrane
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: Dense Body
disjoint with: Cellular Inclusion
sao ID: sao1539965131
disjoint with: Cytosol
subclass of: Cellular Component
disjoint with: sao237754030
umls ID: C0029219
disjoint with: Basal Body
disjoint with: Cellular Subcomponent
disjoint with: Cilium
disjoint with: Plasma Membrane
disjoint with: Cytoskeletal Element
disjoint with: Basal Lamina
gene ontology ID: 0043226
disjoint with: sao1231384859
disjoint with: Synaptic Component
disjoint with: Vesicle
disjoint with: Glycogen Granule

Subplasmalemmal Coating
type: Class
disjoint with: Cytoskeletal Element
disjoint with: Intracellular Membrane
modified date: 2007-02-23
sao ID: sao1938587839
disjoint with: Coated Pit
curation status: core:definition incomplete
disjoint with: Cilium
disjoint with: Cellular Subcomponent
disjoint with: Cellular Inclusion
disjoint with: Basal Lamina
disjoint with: sao237754030
disjoint with: Plasma Membrane
subclass of: Cellular Component
disjoint with: Glycogen Granule
disjoint with: Vesicle
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

Dense Body
type: Class
disjoint with: Coated Pit
definition: An electron dense body, some of which contain granules (Peters, Palay and Webster (1991)
subclass of: Cellular Component
disjoint with: Cytosol
disjoint with: Glycogen Granule
comment: Not clear if this should be described as an organelle or an inclusion.
disjoint with: sao1231384859
disjoint with: Basal Lamina
disjoint with: Vesicle
disjoint with: Plasma Membrane
disjoint with: Cellular Subcomponent
disjoint with: sao237754030
disjoint with: Subplasmalemmal Coating
disjoint with: Synaptic Component
curation status: graph position temporary
disjoint with: Cilium
sao ID: sao730872736
disjoint with: Cytoskeletal Element
disjoint with: Cellular Inclusion
disjoint with: Intracellular Membrane

Cytosol
type: Class
subclass of: Cellular Component
disjoint with: Vesicle
disjoint with: Intracellular Membrane
disjoint with: Basal Lamina
definition: The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS).
disjoint with: Subplasmalemmal Coating
disjoint with: Cellular Inclusion
curation status: uncurated
disjoint with: Plasma Membrane
disjoint with: Cilium
disjoint with: Glycogen Granule
disjoint with: Cellular Subcomponent
sao ID: sao101633890
disjoint with: sao237754030
gene ontology ID: 0005829
umls ID: C0010854

Basal Body
type: Class
sao ID: sao11978067
disjoint with: sao237754030
disjoint with: Subplasmalemmal Coating
umls ID: C0230744
gene ontology ID: 0005932
disjoint with: Coated Pit
disjoint with: Cellular Subcomponent
disjoint with: Glycogen Granule
disjoint with: Cellular Inclusion
disjoint with: Plasma Membrane
disjoint with: sao1231384859
disjoint with: Cytosol
disjoint with: Dense Body
disjoint with: Basal Lamina
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: Vesicle
subclass of: Cellular Component
disjoint with: Cytoskeletal Element
disjoint with: Cilium
disjoint with: Synaptic Component
disjoint with: Intracellular Membrane
curation status: uncurated

Neuropil Thread
type: Class
subclass of: Aggregate Object
contributor: Sarah M. Maynard
definition: Abnormal structures located in distal dendrites. Filamentous bundles made up of straight and paried helical filaments which contain ubiquitin and tau.
curation status: uncurated
sao ID: sao9537723288

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

Schwann Cell Myelin Sheath
type: Class
curation status: uncurated
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).
subclass of: Regional Part Of Schwann Cell

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

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

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

Sub-surface Cisternae
type: Class
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).
subclass of: Hypolemmal Cisternae

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

Regional Part Of Mitochondrial Membrane
type: Class
curation status: uncurated
sao ID: sao-1686050947
subclass of: Regional Part Of Cell Component
disjoint with: sao903454364

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

Nuclear Outer Membrane
type: Class
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
curation status: uncurated

Junction Complex
type: Class
disjoint with: Cell Regional Part Aggregate Object
disjoint with: Supra Cellular Structure
subclass of: Aggregate Object
sao ID: sao-301233507

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

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

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

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

Coated Tip
type: Class
sao ID: sao694815499
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).
curation status: uncurated

Stubby Dendritic Spine
type: Class
sao ID: sao317384566
disjoint with: Thin Dendritic Spine
disjoint with: Sessile Dendritic Spine
disjoint with: Branched Dendritic Spine
disjoint with: Mushroom Dendritic Spine
curation status: uncurated
equivalent class: Class
  intersection of: Dendritic Spine
  intersection of: Restriction
    some values from: sao1786354232
    on property: sao5320776245

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

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

Microfilament
type: Class
subclass of: Cytoskeletal Element
umls ID: C0025979
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

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

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).
curation status: uncurated
sao ID: sao2031592629
subclass of: Granular Vesicle

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

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

Non Membrane Bound Organelle
type: Class
sao ID: sao1456184038
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
curation status: uncurated
gene ontology ID: 0043228

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

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

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

Regional Part Of Golgi
type: Class
curation status: uncurated
disjoint with: Regional Part Of Mitochondrial Membrane
disjoint with: sao903454364
disjoint with: Regional Part Of RER
subclass of: Regional Part Of Cell Component
sao ID: sao1546288504

Endocytic Zone
type: Class
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).
subclass of: Spine Related Site

Chromatin
type: Class
disjoint with: Nuclear Lamina
curation status: uncurated
disjoint with: Nucleolus
disjoint with: Barr Body
gene ontology ID: 0000785
disjoint with: Nuclear Body
disjoint with: Interchromatin Granule
sao ID: sao1615953555
disjoint with: Nuclear Membrane
subclass of: Nuclear Subcomponent
disjoint with: Nuclear Pore
umls ID: C0008546
definition: The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology).
disjoint with: sao238602892
disjoint with: Nucleoplasm

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

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

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

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

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

Nodal Complex
type: Class
subclass of: Supra Cellular Structure
sao ID: sao873654461

Somatic Portion
type: Class
definition: Portion of the tanycyte that lies within the ependyma and contains the nucleus (Peters, Palay and Webster, 1991).
disjoint with: Vascular Endfoot
sao ID: sao401910342
curation status: uncurated
subclass of: Regional Part Of Tanycyte

Vascular Endfoot
type: Class
subclass of: Regional Part Of Tanycyte
curation status: uncurated
sao ID: sao2064469343

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

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

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

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

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

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

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

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

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

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

Terminal Loop
type: Class
sao ID: sao924713546
subclass of: Regional Part Of Schwann Cell
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.
curation status: uncurated

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

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

Excrescence
type: Class
disjoint with: Spine
disjoint with: Filopodium
sao ID: sao-961694769
curation status: uncurated
subclass of: Neuron Protrusion

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

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

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

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

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

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

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

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

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

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

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

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

Fibrillary Inclusion
type: Class
subclass of: Cellular Inclusion
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)
curation status: uncurated

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

Peri Cellular Basket
type: Class
subclass of: Regional Part Of Basket Cell Axon
curation status: uncurated
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

Tail Portion
type: Class
disjoint with: Vascular Endfoot
sao ID: sao1749953771
curation status: uncurated
subclass of: Regional Part Of Tanycyte
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).
disjoint with: Somatic Portion

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

Neurofibrillary Tangle
type: Class
contributor: Sarah M. Maynard
curation status: uncurated
definition: Intracellular mass of paired, hellically wound protein filaments (PHF) lying in the cytoplasm of neuronal cell bodies and neuritic cell processes. They contain an abnormally phosporylated form of a microtuble associated with protein, tau.
sao ID: sao2409833926
subclass of: Cellular Inclusion

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

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

Clathrin Coat
type: Class
umls ID: C1166728
sao ID: sao879919129
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).

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

Schwann Cell Compact Myelin
type: Class
subclass of: Schwann Cell Myelin Sheath
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
sao ID: sao-1123256993

Cell Process
type: Class
curation status: uncurated
disjoint with: sao1843719868
disjoint with: Regional Part Of Neuron
disjoint with: Regional Part Of Glial Cell
disjoint with: Cell Protrusion
sao ID: sao-1828894864
subclass of: Regional Part Of Cell

Oligodendrocyte Paranodal Termination
type: Class
sao ID: sao1354781919
subclass of: Oligodendrocyte Myelin Sheath
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
curation status: uncurated

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

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

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

RER Membrane
type: Class
sao ID: sao3089754107
subclass of: Intracellular Membrane

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

Contact Site
type: Class
definition: Sites of close apposition of the inner and outer mitochondrial membrane (Perkins and Frey, 2000).
curation status: uncurated
subclass of: Mitochondrial Site
sao ID: sao447856407

Perivascular Endfoot
type: Class
curation status: uncurated
sao ID: sao2048701763
comment: We are unclear why this is causing an inconsistency error.
subclass of: Endfoot

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

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

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

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

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

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.
sao ID: sao1028571114
subclass of: Endosome
curation status: uncurated

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

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

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

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

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

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

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

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

Neck Portion
type: Class
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).
sao ID: sao901230115
subclass of: Regional Part Of Tanycyte

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

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

Tyrosine Kinase Receptor
type: Class
sao ID: sao1048004962
curation status: uncurated
definition: A class of cellular receptors that have an intrinsic protein-tyrosine kinase activity (MSH).
umls ID: C0206364
disjoint with: Neurotransmitter Receptor
subclass of: sao452970150

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

SER Membrane
type: Class
curation status: uncurated
sao ID: sao1596955044
gene ontology ID: 0030868
definition: The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology).
subclass of: Intracellular Membrane

Autolysosome
type: Class
contributor: Sarah M. Maynard
curation status: uncurated
subclass of: Secondary Lysosome
definition: A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases.
synonym: Autophagolysosome, degrading autophagic vacuole (AVd)
sao ID: sao8444068431

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

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

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

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

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

Dendritic Microtubule
type: Class
sao ID: sao110773650
subclass of: Microtubule
disjoint with: Microtubule Fascicle
disjoint with: Neurotubule
curation status: uncurated

Senile Plaque
type: Class
contributor: Sarah M. Maynard
curation status: uncurated
comment: We are not sure if there is a distinction between Neuritic plaque and Senile plaque.
subclass of: Plaque
sao ID: sao9615155060
synonym: amyloid plaques, senile druse, braindruse
definition: Extracellular deposits of Beta-amyloid / 8-10 nm amyloid fibrils that are polymers of amyloid-Beta protein. They are located in grey matter and associated with degenerative neural structures and an abundance of microglia and astrocytes.

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

Inner Bounding Mitochondrial Membrane
type: Class
subclass of: Regional Part Of Mitochondrial Membrane
definition: Part of mitochondrial inner membrane that runs parallel to the outer mitochondrial membrane
disjoint with: sao614641003
sao ID: sao18461326
curation status: uncurated

Neuromuscular Junction
type: Class
curation status: uncurated
gene ontology ID: 0031594
sao ID: sao1124888485
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).

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

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

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

Collagen Fibril
type: Class
definition: Delicate fibrils of collagen in connective tissue. It is composed of molecules of tropocollagen aggregated in linear array.
contributor: Sarah M. Maynard
curation status: uncurated
subclass of: Fibril
sao ID: sao7547390221

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

Amyloid Fibril
type: Class
contributor: Sarah M. Maynard
sao ID: sao1342297498
subclass of: Fibril
definition: A fibril composed of amyloid protein.

Extracellular Space
type: Class
disjoint with: Cell Cell Contact Zone
disjoint with: Spine Related Site
curation status: uncurated
disjoint with: Apical Pole Of Neuron
disjoint with: Mitochondrial Site
disjoint with: Node Related Site
disjoint with: Cell Interior
sao ID: sao1425028079
subclass of: Site
disjoint with: Regional Part Of Neuronal Cell Body
gene ontology ID: 0005616
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: Basal Pole Of Neuron
disjoint with: Cellular Space

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

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

Synaptic Cleft
type: Class
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
sao ID: sao243541954
curation status: uncurated
subclass of: Extracellular Space

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

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

Amyloid Aggregate
type: Class
curation status: uncurated
sao ID: sao4785563283
definition: Insoluble fibrous protein aggregation sharing specific structural traits.
contributor: Sarah M. Maynard
subclass of: Protein Aggregate

Corona
type: Class
curation status: uncurated
contributor: Sarah M. Maynard
sao ID: sao5764355747
definition: The periphery of the Lewy Body. In Parkinson's Disease, it contains sperical accumulations of filaments arrange in a loose, radiating array.
subclass of: Regional Part Of Lewy Body
synonym: Halo

Post synaptic density
type: Class
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Maryann_Martone
subclass of: birnlex 10
created date: 2006-07-15
modified date: 2006-09-28
bonfire ID: BF_C000103

Neurofilament
type: Class
created date: 2006-07-15
modified date: 2006-09-28
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#BIRN_OTF
subclass of: Intermediate filament

Intermediate filament
type: Class
created date: 2006-07-15
has external source: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#UMLS
subclass of: birnlex 878
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Maryann_Martone
umls cui: C0021770
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#pending_final_vetting
birnlex definition: Cytoskeletal element consisting of 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).
modified date: 2006-09-28
disjoint with: Microfilament
disjoint with: Microtubule

Node of Ranvier
type: Class
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Maryann_Martone
modified date: 2006-09-28
has external source: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#UMLS
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#pending_final_vetting
created date: 2006-07-15
subclass of: birnlex 3
umls cui: C0034667
birnlex definition: Specialized supracellular structures found in myelinated axons at the gaps between the myelin sheaths. The Node of Ranvier consists of the axonal membrane at the gap, the surrounding myelin processes and additional components such as astrocytic processes or basal lamina, depending upon whether the Node occurs in axons in the peripheral or central nervous system.

Microtubule
type: Class
disjoint with: Microfilament
modified date: 2006-09-28
disjoint with: Intermediate filament
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
subclass of: birnlex 878
has external source: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#UMLS
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Maryann_Martone
umls cui: C0026046
created date: 2006-07-15

Microfilament
type: Class
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
modified date: 2006-09-28
disjoint with: Intermediate filament
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#BIRN_OTF
subclass of: birnlex 878
created date: 2006-07-15
disjoint with: Microtubule

Neuropil
type: Class
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Maryann_Martone
modified date: 2006-09-28
subclass of: birnlex 3
externally sourced definition: Supracellular structure consisting of 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.
has external source: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#UMLS
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#pending_final_vetting
created date: 2006-07-15
umls cui: C0228081
has definition source: http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#MeSH_defSource

Functional role of nerve cell
type: Class
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
subclass of: Functional role of cell
modified date: 2007-08-25
created date: 2007-08-25

Functional role of cell
type: Class
modified date: 2007-08-25
subclass of: Role
created date: 2007-08-25
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated

Intrinsic neuron role
type: Class
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
temp definition: An interneuron participating in aneuronal circuit where all the neurons are bounded within a defined and limited region of the nervous system.(BB).
subclass of: Functional role of nerve cell
created date: 2007-08-26
modified date: 2007-08-26
disjoint with: Principal neuron role
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug

Principal neuron role
type: Class
disjoint with: Intrinsic neuron role
subclass of: Functional role of nerve cell
created date: 2007-08-26
has curation status: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated
example: CA3 Pyramidal neurons are principal neurons projecting out of the CA3 cytoarchitectural part of the hippocampus of vertebrates.
has birnlex curator: http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug
modified date: 2007-08-26
temp definition: A principal projection neuron in a neuronal circuit whose axon extends beyond the region where its soma is located to synapse on the dendrites of cells in other regions of the nervous system (BB).
example: Cerebellar Purkinje neurons are principal neurons projecting out from the cerebellar cortex of vertebrates.