regenbase vocabulary.owl
type: Ontology
license: http://creativecommons.org/licenses/by/3.0
version info: 1.0
creator: Alison Callahan
creator: John Bixby
comment: Revision 114
creator: Saminda Abeyruwan
creator: Ubbo Visser
creator: Vance Lemmon
imports: regenbase metadata.owl
imports: regenbase external.owl

mrna translation
type: ObjectProperty
type: Class
subclass of: biological process
IAO_0000115: The process by which a particular sequence of bases in messenger RNA (mRNA) determines a sequence of amino acids in a polypeptide chain during protein and peptide biosynthesis.

protrudes
type: ObjectProperty
sub property of: topObjectProperty

part of
type: ObjectProperty
type: TransitiveProperty
inverse of: has part

forms
type: ObjectProperty

is steered by
type: ObjectProperty
sub property of: topObjectProperty

repels
type: ObjectProperty
sub property of: topObjectProperty

has level
type: ObjectProperty

extends
type: ObjectProperty

migrates
type: ObjectProperty

attracts
type: ObjectProperty

has part
type: ObjectProperty
type: TransitiveProperty
sub property of: topObjectProperty

has expression
type: ObjectProperty
type: Class
subclass of: transplantation
label: organ transplantation
IAO_0000115: The transfer of an organ from one part of the body to another or from one animal to another.

myelin degeneration
type: ObjectProperty
type: Class
subclass of: degeneration
IAO_0000115: The process of damaging the myelin sheath of a neuron causing it to break down.

has attribute
type: ObjectProperty

has quality
type: ObjectProperty
sub property of: has attribute

has role
type: ObjectProperty
sub property of: has attribute

has member
type: ObjectProperty
sub property of: has attribute

length
type: DatatypeProperty
type: FunctionalProperty
comment: todo: replaced with ulo?
range: float

fetal
type: DatatypeProperty
type: FunctionalProperty

temperature
type: DatatypeProperty
type: FunctionalProperty

adult
type: DatatypeProperty
type: FunctionalProperty
sub property of: topDataProperty

juvenile
type: DatatypeProperty
type: FunctionalProperty

postnatal
type: DatatypeProperty
type: FunctionalProperty

blood brain barrier
type: DatatypeProperty
type: FunctionalProperty
range: boolean

spinal cord section
type: Class
subclass of: histological tissue section
IAO_0000115: A tissue section taken from the spinal cord.

Wallerian degeneration
type: Class
subclass of: degeneration
IAO_0000115: The degeneration of axons and myelin distal to an injury site and subsequent clearing of debris.

brain derived neurotropic factor
type: Class
subclass of: protein
IAO_0000115: A member of the nerve growth factor family. During development, promotes the survival and differentiation of selected neuronal populations of the peripheral and central nervous systems. Participates in axonal growth, pathfinding and in the modulation of dendritic growth and morphology. Major regulator of synaptic transmission and plasticity at adult synapses in many regions of the central nervous system.
IAO_0000118: BDNF

autophagic cell death
type: Class
subclass of: cell death
IAO_0000115: Cell death induced by autophagy.

spinal cord contusion
type: Class
subclass of: contusion
IAO_0000115: An injury to the spinal cord caused by blunt force trauma.

protein tyrosine phosphatase
type: Class
subclass of: enzyme
IAO_0000115: An enzyme that removes phosphate groups from phosphorylated tyrosine residues on proteins, antagonizing the effects of protein tyrosine kinases.

substrate
type: Class
subclass of: role
IAO_0000115: A substance that is acted upon by an enzyme.

myelin basic protein
type: Class
subclass of: protein
IAO_0000115: An 18.5 kDa protein which is one of the most abundant proteins of the myelin sheath of the adult central nervous system.

migration
type: Class
subclass of: biological process
IAO_0000115: The movement of a cell or cell process from one place to another.

focal adhesion complex
type: Class
subclass of: protein complex
IAO_0000115: Focal adhesions are large, dynamic protein complexes through which the cytoskeleton of a cell connects to the extracellular matrix, or ECM. They are limited to clearly defined ranges of the cell, at which the plasma membrane closes to within 15 nm of the ECM substrate. They are studied in cell culture but are thought to represent structures (focal contacts) present in cells in vivo.

glial process
type: Class
subclass of: cell projection
IAO_0000115: A projection extending from a glial cell.

biological mechanism
type: Class
subclass of: function
IAO_0000115: A series of causally interacting parts that produce a biological phenomenon.

axon formation
type: Class
subclass of: biological process
IAO_0000115: The differentiation of a single neurite to form an axon.

medium
type: Class
subclass of: heterogeneous substance
IAO_0000115: A nutrient-rich solution used to grow or maintain cells or organs in vitro.

cell motility
type: Class
subclass of: biological process
IAO_0000115: Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.

inflammatory cell
type: Class
subclass of: immune cell
IAO_0000115: A cell participating in the immune response, generally a macrophage/monocyte or a granulocyte.

stimulation
type: Class
subclass of: process
IAO_0000115: The process of applying energy to a cell or tissue to provoke a specific response.

cell migration
type: Class
subclass of: migration
IAO_0000115: The active movement of a cell from one location to another, particularly the movement of a cell over a surface or through a matrix.

filopodium
type: Class
subclass of: cell projection
IAO_0000115: A long thin spike-like cell projection containing actin filaments.

enzyme activity
type: Class
subclass of: activity
IAO_0000115: An state of an enzyme's capability to convert substrate to product.

nerve regeneration
type: Class
subclass of: regeneration
IAO_0000115: The process of regrowth of a bundle of axons from their damaged proximal ends following injury.

monoclonal antibody
type: Class
subclass of: antibody
IAO_0000115: Antibody that is produced by a single clone of hybridoma cells.

conditioned medium
type: Class
subclass of: medium
IAO_0000115: Cell culture medium in which cells are grown for a period of time to capture agents they secrete, such as growth factors, bioactive lipids,etc. The medium is then used to culture other cells. An example is glial conditioned medium used to culture neurons.

purkinje cell
type: Class
subclass of: neuron
IAO_0000115: Large cerebellar cortical neuron that conveys signals away from the cerebellum.

electrical stimulation
type: Class
subclass of: stimulation
IAO_0000115: The process of producing a reaction in a sensory end organ by an electrical stimulus that initiates a nerve impulse and results in functional activity of an effector.

actin messenger RNA
type: Class
subclass of: messenger RNA
IAO_0000115: Messenger RNA that encodes any of the numerous known actin isoforms.
IAO_0000118: actin mRNA

vehicle control group
type: Class
subclass of: negative treatment control group
IAO_0000115: A control for experimental treatment in which only the vehicle used to dissolve the treatment chemical is delivered at the same concentration and by the same route as in the experimental treatment.

axonal growth cone
type: Class
subclass of: growth cone
IAO_0000115: A growth cone extending from an axon.

phosphorylation
type: Class
subclass of: biological process
IAO_0000115: The addition of phosphate groups to a molecule.

minute
type: Class
subclass of: time interval
IAO_0000115: A period of time lasting 60 seconds.

apoptosis
type: Class
subclass of: cell death
IAO_0000115: A form of programmed cell death that begins when a cell receives internal or external signals that trigger the activity of proteolytic caspases, proceeds through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing (but maintenance of its integrity until the final stages of the process), and ends with the death of the cell.

expression profile
type: Class
subclass of: measurement
IAO_0000115: The expression values of a set of genes under different conditions, e.g. following an environmental insult, following hormonal stimulation, or at a particular developmental stage.

absent
type: Class
subclass of: quality
IAO_0000115: Not present.

myelin
type: Class
subclass of: biological entity
IAO_0000115: A mixture of proteins and phospholipids forming a whitish insulating sheath around many axons, increasing the speed at which action potentials are conducted. In the central nervous system myelin is made by oligodendrocytes. In the periperal nervous system myelin is made by Schwann cells.

macrophage
type: Class
subclass of: cell
IAO_0000115: Long-lived phagocyte derived from blood monocytes and found in tissues.

neuronal process
type: Class
subclass of: cell projection
IAO_0000115: A projection extending from a neuron.

microglial cell
type: Class
subclass of: immune cell
subclass of: glial cell
IAO_0000115: Small glial cell of the monocyte lineage that is found throughout grey and white matter of the brain.
IAO_0000118: microglia

activated microglial cell
type: Class
subclass of: microglial cell
IAO_0000115: Microglial cell that expresses a variety of inflammation-related genes in response to detection of molecular signs of infection or injury.
IAO_0000118: activated microglia

oligodendrocyte
type: Class
subclass of: glial cell
IAO_0000115: Glial cell of the central nervous system responsible for myelinating axons.

antibody
type: Class
subclass of: protein
IAO_0000115: A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.

cortical axon
type: Class
subclass of: axon
IAO_0000115: An axon extending from a neuron in the cerebral cortex.

binding protein
type: Class
subclass of: role
IAO_0000115: Protein that interacts with and binds to a macromolecule.

myelinated axon
type: Class
subclass of: axon
IAO_0000115: An axon covered in an insulating layer of myelin.

tissue culture
type: Class
subclass of: culture
IAO_0000115: Originally the maintenance and growth of pieces of explanted tissue (plant or animal) in culture away from the source organism. Now usually refers to the (much more frequently used) technique of cell culture, using cells dispersed from tissues or distant descendants of such cells.
IAO_0000119: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Tissue_Culture

decrease expression
type: Class
subclass of: biological process
IAO_0000115: Any process that decreases the rate of transcription of a gene into complementary RNA sequences and, for structural genes, subsequent translation of mRNA into polypeptide chains and their assembly into protein products.

retinal explant
type: Class
subclass of: tissue explant
IAO_0000115: A piece of tissue that has been removed from the retina.

fibroblast growth factor
type: Class
subclass of: protein
IAO_0000115: A member of a family of growth factors for mesodermal and neuroectodermal cells and important in developmental signalling.
IAO_0000118: FGF

protein
type: Class
subclass of: macromolecule
IAO_0000115: A linear polymer of amino acids linked by peptide bonds in a sequence specified by mRNA.

histological tissue section
type: Class
subclass of: organ part
IAO_0000115: A histological tissue section is a thin piece of tissue sliced from an organ or piece of tissue. Typically the section is used for some histological study using dyes or antibodies.

neurite
type: Class
subclass of: neuronal process
IAO_0000115: A general term for a neuronal process, especially as isolated in cell or tissue culture.

collapse assay
type: Class
subclass of: assay
IAO_0000115: A cell culture assay often using primary neurons with neurites, in which a protein or peptide is added to the culture medium. Cell protrusions, such as growth cones, are observed to determine if they collapse as a result of the added material.

gene
type: Class
subclass of: biological entity
IAO_0000115: A specific sequence of DNA (RNA in some viruses), corresponding to a unit of inheritance, that has a specific locus on a chromosome, can exist in different allelic forms, and is transcribed.

functional recovery
type: Class
subclass of: biological process
IAO_0000115: A return to a normal state of nervous system function following injury.

epidermal growth factor
type: Class
subclass of: protein
IAO_0000115: A member of the epidermal growth factor superfamily of proteins. The encoded protein is synthesized as a large precursor molecule that is proteolytically cleaved to generate the 53-amino acid epidermal growth factor peptide. Epidermal growth factor is a potent mitogen that plays an important role in the growth, proliferation and differentiation of numerous cell types.
IAO_0000118: EGF

receptor
type: Class
subclass of: role
IAO_0000115: A cell-surface or intracellular molecule, typically a protein, that binds a ligand selectively to yield a cellular response.

culture
type: Class
subclass of: biological entity
IAO_0000115: A cell culture is a material entity consisting of a population of cells that is maintained in vitro

tissue
type: Class
subclass of: biological entity
IAO_0000115: A group or layer of cells that perform a particular function. Tissues represent a level of organization intermediate between cells and organs; organs are made up of more than one tissue.

transplantation
type: Class
subclass of: process
IAO_0000115: The transfer of an organ, tissue, etc. from one part of the body to another or from one animal to another.

conditioning lesion
type: Class
subclass of: nervous system injury
IAO_0000115: An injury to a region of the nervous system that purposely damages axons, performed prior to a second injury, elsewhere, in order to alter the response to the second injury.

complete transection
type: Class
subclass of: spinal cord transection
IAO_0000115: The process of transversely severing the spinal cord.

ciliary neurotrophic factor
type: Class
subclass of: protein
IAO_0000115: A neurotrophin (length 200 aa) that is a trophic factor for various neuronal cell types. It is a member of the interleukin-6 cytokine family since it acts through a receptor containing gp130.
IAO_0000118: CNFTF

endothelial cell
type: Class
subclass of: cell
IAO_0000115: A flattened cell type that forms a sheet (the endothelium) lining all blood vessels.

lesion center
type: Class
subclass of: tissue
IAO_0000115: The volume of tissue characterized by maximal immune cell infiltration and glial scar formation.
IAO_0000118: lesion core

N-methyl-D-aspartate receptor
type: Class
subclass of: protein
IAO_0000115: N-methyl-D-aspartate receptor (also known as the NMDA receptor or NMDAR), is a glutamate receptor. It is implicated in synaptic plasticity and excitotoxicity and neuronal death via apoptosis.
IAO_0000118: NMDA receptor
IAO_0000118: NMDAR

protein complex
type: Class
subclass of: macromolecule
IAO_0000115: A group of two or more associated polypeptide chains.

growth cone guidance
type: Class
subclass of: guidance
IAO_0000115: Any process that influences the direction of growth cone migration.

netrin receptor
type: Class
subclass of: receptor
IAO_0000115: Receptor that binds to and responds to netrin.

molecule
type: Class
subclass of: chemical entity
IAO_0000115: The mereological maximal sum of a collection of covalently bonded atoms.

nerve growth factor
type: Class
subclass of: protein
IAO_0000115: A secreted homodimer THAT can be incorporated into a larger complex; it binds to a receptor tyrosine kinase and other receptors such as p75. This protein has neurotrophic activity and is involved in the regulation of growth, survival and the differentiation of several neuronal types, including sympathetic, sensory, and forebrain cholinergic neurons.
IAO_0000118: NGF

kinase activity
type: Class
subclass of: enzyme activity
IAO_0000115: The state of a kinase's capability to phosphorylate substrate molecules.

cell adhesion molecule
type: Class
subclass of: adhesion molecule
IAO_0000115: A cell surface protein that binds to one or more specific ligands on an adjacent cell, providing specificity in cell-cell binding.

spinal nerve
type: Class
subclass of: nerve
IAO_0000115: Paired peripheral nerve formed by the union of the dorsal and ventral spinal roots from each spinal cord segment.

green fluorescent protein
type: Class
subclass of: protein
IAO_0000115: A protein isolated from the jellyfish Aequorea victoria, excited by blue light and emitting green light. Green fluorescent protein and its derivatives are often used as reporter genes.
IAO_0000118: GFP

receptor activation
type: Class
subclass of: activation
IAO_0000115: The process of inducing a receptor to produce its biological response.

cerebellar granule neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron that coordinates afferent input to and motor output from the cerebellum through excitatory connections with Purkinje neurons.

growth cone attraction
type: Class
subclass of: growth cone guidance
subclass of: attraction
IAO_0000115: Any process involving a signal or cue that draws a growth cone (or axonal tip) to the source of the signal.

guidance
type: Class
subclass of: biological process
IAO_0000115: Any process that influences the direction of growth or extension.

activity
type: Class
subclass of: quality
IAO_0000115: The state of an entity's capability to carry out a given action.

commissural neuron
type: Class
subclass of: role
IAO_0000115: A neuron that projects its axon across the midline to the other side of the central nervous system.

muscle cell
type: Class
subclass of: cell
IAO_0000115: A contractile cell of skeletal muscle, the myocardium, or smooth muscle containing organized contractile filaments of actin and myosin.

thalamocortical axon
type: Class
subclass of: thalamic axon
IAO_0000115: An axon that extends from a neuron in the thalamus to the cerebral cortex.

sensory axon
type: Class
subclass of: axon
IAO_0000115: An axon extending from a sensory neuron.

outgrowth assay
type: Class
subclass of: assay
IAO_0000115: A cell culture assay often using primary neurons with neurites, in which the neurons are perturbed in various ways and the effect on the growth of neurites is determined. Typical perturbagens are compounds, different substrate molecules, proteins and peptides, antibodies, dsRNA, and overexpressed proteins.

immune response
type: Class
subclass of: biological process
IAO_0000115: In the periphery, a state of altered reactivity in the innate and/or adaptive immune system as a result of exposure to antigen. In the central nervous system, this is almost exclusively in the innate immune system as a result of infection, and is associated mainly with resident microglia.

spinal cord tissue
type: Class
subclass of: neural tissue
IAO_0000115: Tissue of the spinal cord.

precursor cell
type: Class
subclass of: cell
IAO_0000115: A cell that gives rise to one or more other cell types.
IAO_0000118: progenitor cell

primary lesion cavity
type: Class
subclass of: cavity
IAO_0000115: A cavity that forms at the primary injury site in a spinal cord injury. It contains macrophages that consume dead cells that are the result of injury.

increase expression
type: Class
subclass of: biological process
IAO_0000115: Any process that increases the amount or local density of an RNA, protein, or specific protein modification in a cell or cell compartment.

negative treatment control group
type: Class
subclass of: treatment control group
IAO_0000115: A control in which a perturbagen that is known to consistently produce no response is used, or in which components of the treatment other than the active perturbagen are used (such as vehicle, vector, inactive compound, etc). This gives the investigators one or more possible baselines to compare to unknowns and can also be used to normalize data across samples as well as experiments done on different days.

glial fibrillary acidic protein
type: Class
subclass of: protein
IAO_0000115: An intermediate filament protein found in mature astrocytes and Schwann cells. It is often used as a marker to distinguish astrocytes from other cells.

mitogen-activated protein kinase
type: Class
subclass of: dual specificity kinase
IAO_0000115: A family of dual-specificity (serine/threonine and tyrosine) kinases (MAP kinases) that regulate cellualr signal transduction as part of a protein kinase cascade.

in vitro
type: Class
subclass of: quality
IAO_0000115: Literally, in glass, but used more generally to describe the state of cell and tissue culture experiments or tests.

primary culture
type: Class
subclass of: culture
IAO_0000115: Cells taken directly from a living organism, which are not immortalized.

nervous system injury
type: Class
subclass of: injury
IAO_0000115: The process of causing damage to the nervous system.
IAO_0000118: neural injury

neurotrophin receptor
type: Class
subclass of: receptor
IAO_0000115: Receptor that binds to and reponds to neurotrophin.

spinal cord repair
type: Class
subclass of: nervous system repair
IAO_0000115: The process of restoring spinal cord tissue to a healthy state after injury or damage.

explant culture
type: Class
subclass of: culture
IAO_0000115: A piece of tissue that has been removed from a cell source and is maintained in vitro without being dissocated to single cells. An example would be a piece of retina, an intact dorsal root ganglion, or a sympathetic ganglion.

membrane potential
type: Class
subclass of: measurement
IAO_0000115: The electrical potential difference across a plasma membrane.

classic protein kinase C
type: Class
subclass of: protein kinase C
IAO_0000115: A subfamily of the protein kinase C (PKC) family that includes PKC alpha, PKC beta1 and beta2, and PKC gamma. cPKC isoforms are activated by calcium, diacylglycerol, and membrane lipids like phosphatidylserine.
IAO_0000118: cPKC

remyelination
type: Class
subclass of: myelination
IAO_0000115: The process by which axons reacquire myelin sheaths following myelin degeneration.

repair
type: Class
subclass of: process
IAO_0000115: The process of restoring tissue to a healthy state after injury or damage.

damage
type: Class
subclass of: condition
IAO_0000115: A state of physical harm that impairs the value, usefulness, or normal function of something.

microRNA
type: Class
subclass of: ribonucleic acid
IAO_0000115: Small noncoding RNA gene products (usually ~22 nt) generated by dicer from precursors with a characteristic hairpin secondary structure.

ischemia
type: Class
subclass of: condition
IAO_0000115: Deficient supply of blood to a body part, due to obstruction of the inflow of arterial blood.

small molecule
type: Class
subclass of: molecule
IAO_0000115: A low molecular weight (<900 Daltons ) organic compound that may help regulate a biological process.

kinase
type: Class
subclass of: enzyme
IAO_0000115: An enzyme that transfers phosphate groups from high-energy donor molecules, such as adenosine triphosphate, to specific substrates, a process referred to as phosphorylation.

male
type: Class
subclass of: gender
IAO_0000115: Denoting the sex that produces gametes, especially spermatozoa, with which a female may be fertilized or inseminated to produce offspring.

siRNA
type: Class
subclass of: ribonucleic acid
IAO_0000115: Small double-stranded RNA molecules (20–25 bp) that interfere with the expression of particular mRNAs (RNA interference) and can also activate innate immune systems that operate to block viral infection. They may also induce gene expression and be termed small activating RNAs (saRNAs).

longitudinal plane
type: Class
subclass of: plane of section
IAO_0000115: A longitudinal plane is any plane perpendicular to the transverse plane. The coronal plane and the sagittal plane are examples of longitudinal planes.

amino acid
type: Class
subclass of: small molecule
IAO_0000115: An organic acid carrying an amino group. Proteins are linear polymers of the l-forms of ~20 common amino acids linked by peptide bonds.

in vivo
type: Class
subclass of: quality
IAO_0000115: Literally, in life, but used generally to describe the state of procedures or tests done on intact organisms.

dendrite growth cone
type: Class
subclass of: growth cone
IAO_0000115: A growth cone extending from a dendrite.

spinal axon
type: Class
subclass of: axon
IAO_0000115: An axon in the spinal cord.

alpha-actin messenger RNA
type: Class
subclass of: actin messenger RNA
IAO_0000118: alpha-actin mRNA
IAO_0000115: mRNA that encodes the alpha-actin isoform of the actin protein.

NG2 cell
type: Class
subclass of: glial cell
IAO_0000115: A cell that expresses the NG2 proteoglycan, has certain precursor cell properties, including the ability to produce oligodendrocytes, and is found throughout the brain and spinal cord parenchyma.

spinal cord neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron with a cell body in the spinal cord.

inhibitor
type: Class
subclass of: role
IAO_0000115: A substance which slows down or prevents a particular chemical reaction or other process or which reduces the activity of a particular reactant, catalyst, or enzyme.

assay
type: Class
subclass of: process
IAO_0000115: A procedure for measuring the biochemical or immunological activity of a sample.

immune cell
type: Class
subclass of: cell
IAO_0000115: A cell of the immune system, including lymphocytes, granulocytes, mast cells, dendritic cells and macrophages/monocytes.

graft
type: Class
subclass of: biological entity
IAO_0000115: A piece of living tissue or collection of cells that is transplanted surgically.

neuroprotection
type: Class
subclass of: biological process
IAO_0000115: The mechanisms and strategies used to protect against neuronal injury or degeneration in the central nervous system following insult, injury, or disease.

dendrite
type: Class
subclass of: neuronal process
IAO_0000115: The process extending from the cell body of a neuron that normally carries information into the cell body. It is normally branched, and tapered so as to be thinner in its more distal portions.

cross section
type: Class
subclass of: histological tissue section
IAO_0000115: A tissue section cut in a transverse plane.
IAO_0000118: transverse section

oligodendrocyte precursor
type: Class
label: resting astrocyte
subclass of: cell
subclass of: astrocyte
IAO_0000115: A lineage-restricted neural precursor cell that expresses PDGFRA and often the proteoglycan NG2. These cells give rise to oligodendrocytes and possibly also to neurons and astrocytes.

branching
type: Class
subclass of: biological process
IAO_0000115: The formation of a new neuronal process from an existing neuronal process (axon or dendrite).

electrical activity
type: Class
subclass of: activity
IAO_0000115: The activity of action potentials in which the inward current is carried by Na ions, Ca ions or neurotransmitters.

signal transduction
type: Class
subclass of: biological process
IAO_0000115: The process by which an extracellular signal (chemical, electrical, or mechanical) is converted into a cellular response

upregulation
type: Class
subclass of: biological process
IAO_0000115: The process of increasing the amount of an RNA or protein species in a cell or tissue.

pain
type: Class
subclass of: condition
IAO_0000115: Unpleasant physical sensation caused by illness or injury.

growth factor
type: Class
subclass of: role
IAO_0000115: A polypeptide that binds to cell surface receptors to stimulate cell division, cell growth and/or cell survival.

cell death
type: Class
subclass of: biological process
IAO_0000115: Any biological process that results in permanent cessation of all vital functions of a cell.

stem cell
type: Class
subclass of: cell
IAO_0000115: A multipotent proliferative progenitor cell that is capable of self-renewal and of giving rise to all cell types of a defined lineage.

axon regeneration
type: Class
subclass of: regeneration
IAO_0000115: The regrowth of axons from their damaged proximal ends following severing.

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
IAO_0000118: DNA
IAO_0000115: The nucleotide polymer that is the genetic material of all cells and many viruses.

tissue damage
type: Class
subclass of: damage
IAO_0000115: A state of injury to tissue.

neuronal migration
type: Class
subclass of: cell migration
IAO_0000115: Migration of immature neurons from their site of origin to some other location. This can occur in the central nervous system or in the periphery. The distance may be short, as in the developing retina, or substantial, as in the case of olfactory precursor cells and cells of the autonomic nervous sytstem.

traumatic brain injury
type: Class
subclass of: nervous system injury
IAO_0000115: Damage to the brain resulting in altered function caused by a blow, jolt, or penetrating wound.

olfactory ensheathing cell
type: Class
subclass of: cell
IAO_0000115: A specialized glial cell that guides olfactory receptor axons from the nasal mucosa into the brain where it makes synaptic contacts in the olfactory bulb.

retinal ganglion cell axon
type: Class
subclass of: axon
IAO_0000115: An axon extending from a retinal ganglion cell.

projection neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron with a long axon that carries information from its anatomical region (area, nucleus or ganglion) to another region.

receptor subunit
type: Class
subclass of: subunit
IAO_0000115: A protein that, when combined with one or more other proteins, forms a receptor for some signaling molecule.

cell polarity
type: Class
subclass of: quality
IAO_0000115: In motile cells, the internal polarity that defines ‘front’ and ‘back’ and allows locomotion.

leading process
type: Class
subclass of: role
IAO_0000115: For a motile cell, a cytoplasmic extension from the cell in the direction of movement.

cell line
type: Class
subclass of: biological entity
IAO_0000115: An established population of cells that can be maintained indefinitely in culture provided the medium is replenished.

autophagy
type: Class
subclass of: biological process
IAO_0000115: The digestion of cellular components by the cell's own lysosomes. This can proceed by formation of intracellular membrane compartments that fuse with lysosomes or by direct import of the cell's components into lysosomes.

nucleus
type: Class
subclass of: organelle
IAO_0000115: The large organelle of eukaryotic cells, bounded by the nuclear envelope, in which the chromosomes are located.

messenger RNA
type: Class
subclass of: ribonucleic acid
IAO_0000115: The single-stranded RNA molecule that is transcribed from DNA and processed before being released to the cytoplasm, where it is translated into a polypeptide.
IAO_0000118: mRNA

inflammation
type: Class
subclass of: biological process
IAO_0000115: A response to injury or infection involving the migration and activation of inflammatory cells, such as neutrophils, macrophages/microglia, and lymphocytes.
IAO_0000118: Inflammatory response

axonal protein
type: Class
subclass of: role
IAO_0000115: Neuronal protein found in and normally concentrated in axons.

nogo receptor
type: Class
subclass of: receptor
IAO_0000115: Receptor that binds to and responds to the class of neurite outgrowth inhibitor called nogo.

membrane
type: Class
subclass of: biological entity
IAO_0000115: Generally, a sheet or skin. In cell biology it almost invariably means a modified phospholipid bilayer with integral and peripheral proteins, the standard compartmentalizing barrier in and around cells.

mutant
type: Class
subclass of: genotype
IAO_0000115: A strain, gene or characteristic which is rare among individuals in natural conditions, as distinct from a wild type.

netrin-1
type: Class
subclass of: protein
IAO_0000115: A member of the netrin family of proteins that mediates axonal growth cone guidance through both chemoattractive and chemorepulsive signaling.

axon degeneration
type: Class
subclass of: degeneration
IAO_0000115: The death and subsequent loss of axons following disease, insult, or injury.

cell proliferation
type: Class
subclass of: proliferation
IAO_0000115: The multiplication or reproduction of cells, resulting in the expansion of a cell population.

extracellular matrix
type: Class
subclass of: biological entity
IAO_0000115: Material produced and secreted by cells, either in culture or in tissues, that self-assembles to take up space between the cells.

axotomy
type: Class
subclass of: nervous system injury
IAO_0000115: The severing of an axon.

cell body
type: Class
subclass of: biological entity
IAO_0000115: The main portion of a neuron around the nucleus and excluding long processes such as axons.
IAO_0000118: soma

growth cone area
type: Class
subclass of: measurement
IAO_0000115: The two dimensional area covered by a growth cone, normally on a tissue culture plate.

cortical neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron in the cerebral cortex.

spinal cord ischemia
type: Class
subclass of: ischemia
IAO_0000115: Deficient supply of blood to the spinal cord that is due to obstruction of the inflow of arterial blood.

dorsal horn neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron in the dorsal horn.

morphology
type: Class
subclass of: quality
IAO_0000115: A set of defining structural features.

dynamic microtubule
type: Class
subclass of: microtubule
IAO_0000115: A microtubule with a relatively short lifetime in the cell, and characterized by tyrosinated tubulin dimers.

spared tissue
type: Class
subclass of: tissue
IAO_0000115: Area of intact tissue surrounding a lesion.

transverse plane
type: Class
subclass of: plane of section
IAO_0000115: A transverse plane, also known as cross-section, divides the body into cranial and caudal (head and tail) portions.

positive treatment control group
type: Class
subclass of: treatment control group
IAO_0000115: A control in which a perturbagen that is known to produce a consistent response is used. This gives the investigators confidence that the assay is performing as expected.

focal cerebral ischemia
type: Class
subclass of: ischemia
IAO_0000115: Transient ischemia to a region of the brain cause by occlusion of a blood vessel, normally the middle cerebral artery.

growth cone
type: Class
subclass of: neuronal process part
IAO_0000115: The motile tip of a growing neurite that receives cues from the environment and transduces those cues into movement.

neuronal activity
type: Class
subclass of: activity
IAO_0000115: The state of a neuron's ability to transduce signals, generate electrical impulses or change the rate of firing of impulses.

axon guidance
type: Class
subclass of: guidance
IAO_0000115: Any process that influences the direction of axon growth.
IAO_0000118: axonal guidance

attraction
type: Class
subclass of: guidance
IAO_0000115: Orientation, growth, or movement toward a source of a positive cue.

axon growth
type: Class
subclass of: growth
IAO_0000115: A process following axon formation, in which the axon extends from the cell body (soma).
IAO_0000118: axon elongation
IAO_0000118: axon extension
IAO_0000118: axonal growth

molecular mechanism
type: Class
subclass of: biological mechanism
IAO_0000115: A series of causally interacting molecular processes that produce a biological phenomenon.

microtubule
type: Class
subclass of: cytoskeleton
IAO_0000115: A component of the cytoskeleton, a tubule of 25 nm outside diameter with a wall 5 nm thick, assembled from heterodimers of tubulin packed in a regular fashion and associated with various other proteins (including microtubule associated proteins (MAPs), dynein, and kinesin).

border
type: Class
subclass of: material entity
IAO_0000115: An edge or boundary.

tissue explant
type: Class
subclass of: tissue
IAO_0000115: A tissue or organ that has been removed from its source.

actin cytoskeleton
type: Class
subclass of: cytoskeleton
IAO_0000115: Polymers of actin that confer mechanical properties and motility in a cell.

cell cycle
type: Class
subclass of: biological process
IAO_0000115: The period between the formation of a cell by division of its mother cell and the time when the cell itself divides to form two daughter cells.

wild-type
type: Class
subclass of: genotype
IAO_0000115: A strain, gene, or characteristic which prevails among individuals in natural conditions, as distinct from an atypical mutant type.

turning assay
type: Class
subclass of: assay
IAO_0000115: A cell culture assay often using primary neurons with neurites, in which the neurons are perturbed using a gradient of a perturbagen administered via a micropipette near a growth cone. The assay evaluates whether the agent can influence turning of the growth cone by attraction or repulsion.

sympathetic neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron with a cell body in one of the sympathetic autonomic ganglia.

survival
type: Class
subclass of: biological process
IAO_0000115: The process of remaining alive or in existence.

coronal plane
type: Class
subclass of: plane of section
IAO_0000115: A coronal or frontal plane divides the body into dorsal and ventral (back and front, or posterior and anterior) portions.

proliferation
type: Class
subclass of: biological process
IAO_0000115: The multiplication or reproduction of entities, resulting in the expansion of a population.

gender
type: Class
subclass of: quality
IAO_0000115: The state of being male or female.

HEK293 cell line
type: Class
subclass of: cell line
IAO_0000115: A cell line derived from human embryo renal cortical cells (HEK293).

thalamic axon
type: Class
subclass of: axon
IAO_0000115: An axon extending from a neuron in the thalamus.

beta-actin messenger RNA
type: Class
subclass of: actin messenger RNA
IAO_0000118: beta-actin mRNA
IAO_0000115: mRNA that encodes the beta-actin isoform of the actin protein.

spinal cord segment
type: Class
subclass of: organ part
IAO_0000115: One of 31 divisions of the spinal cord, formed in relation to the embryonic myotomes, each of which gives rise to a spinal nerve.

nogo-66 receptor
type: Class
subclass of: nogo receptor
IAO_0000115: Receptor that binds to and responds to neurite outgrowth inhibitor nogo-66.

nerve growth
type: Class
subclass of: growth
IAO_0000115: The process of nerve tissue undergoing development by increasing in size and changing physically; maturation.

repulsive guidance
type: Class
subclass of: guidance
IAO_0000115: Any process that influences growth or extension by causing movement away from the source of the cue.
IAO_0000118: repulsion

motor neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron that synapses on muscle cells and stimulates contraction.
IAO_0000118: motoneuron

microglial activation
type: Class
subclass of: glial activation
IAO_0000115: The proliferation, change in functional state, and/or hypertrophy of microglia. In its most extreme form activation of microglia/macrophages leads to severe inflammation.

glutamate receptor
type: Class
subclass of: receptor
IAO_0000115: Receptor that binds to and responds to glutamate.

spinal cord transection
type: Class
subclass of: transection
subclass of: spinal cord injury
IAO_0000115: The process of cutting the spinal cord in half transversely.

schwann cell
type: Class
subclass of: glial cell
IAO_0000115: The principal glial cell of the peripheral nervous system. Functions include producing peripheral myelin, guiding axons during development and regeneration, and providing support and synaptic regulation. Schwann cells are derived from neural crest cells.

sagittal plane
type: Class
subclass of: plane of section
IAO_0000115: A sagittal plane, being a plane parallel to the sagittal suture, divides the body into sinister and dexter (left and right) portions.

nucleic acid
type: Class
subclass of: macromolecule
IAO_0000115: A linear nucleotide polymer with 3′,5′-phosphodiester linkages.

local protein synthesis
type: Class
subclass of: protein synthesis
IAO_0000115: The translation of mRNA into polypeptides occurring in a specific cell compartment; especially in axons, dendrites, or growth cones of neurons.

protein kinase
type: Class
subclass of: kinase
IAO_0000115: Kinase that acts on proteins, phosphorylating them on their serine, threonine, tyrosine, or histidine residues.

glial cell
type: Class
subclass of: cell
IAO_0000115: The most numerous cell type in the nervous system, comprising most non-neuronal cells. Glia are generally divided into macroglia (astrocytes, Schwann cells, oligodendrocytes) and microglia.

Rho-associated protein kinase
type: Class
subclass of: serine-threonine kinase
IAO_0000115: A protein serine/threonine kinase that is activated when bound to the GTP-bound form of Rho.
IAO_0000118: ROCK

bone marrow stromal cell
type: Class
subclass of: stromal cell
IAO_0000115: Cell that provides the structural and physiological support for hematopoetic cells.

mesenchymal stem cell
type: Class
subclass of: stem cell
IAO_0000115: A pluripotent cell with the capacity for induced in vitro differentiation into bone, fat or cartilage cells.

neurotransmitter
type: Class
subclass of: role
IAO_0000115: A chemical released from the presynaptic terminal of a neuron in response to depolarization, which diffuses across the synaptic cleft and binds a post synaptic receptor, normally a ligand-gated ion channel or a 7-transmembrane G protein-coupled receptor.

axon branch
type: Class
subclass of: branch
IAO_0000115: A segment of an axon that splits off from the main projection.

hippocampal neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron in the hippocampus.

neuropathic pain
type: Class
subclass of: pain
IAO_0000115: Pain arising as a direct consequence of a lesion or disease affecting the somatosensory system.

actin filament
type: Class
subclass of: actin cytoskeleton
IAO_0000115: A polymer of actin protein in the form of a thin, flexible fiber approximately 7 nm in diameter and up to several micrometers in length.

transection
type: Class
subclass of: nervous system injury
IAO_0000115: Dividing by cutting with a sharp edge. In the case of spinal cord injury research, a transection can be complete or partial, and is typically transverse, but may be longitudinal.

pathfinding
type: Class
subclass of: biological process
IAO_0000115: Growth or extension of axons guided by cues outside the neuron.

mitochondria
type: Class
subclass of: organelle
IAO_0000115: The organelles that generate ATP by oxidative phosphorylation. Morphologically variable and may be short and rod-like or long and branched. Contain non-chromosomal DNA and ribosomes and are surrounded by double membranes-- the inner one, which contains the components of the electron transport chain, is often infolded to form cristae.

neurobasal medium
type: Class
subclass of: medium
IAO_0000115: A serum-free medium developed to grow embryonic hippocampal neurons.

cell graft
type: Class
subclass of: graft
IAO_0000115: Cells that have been transplanted into a tissue, typically in an attempt to restore function to a damaged area.

demyelination
type: Class
subclass of: biological process
IAO_0000115: The removal of an existing myelin sheath in the peripheral or central nervous system.

control group
type: Class
subclass of: study group
IAO_0000115: A group separated from the rest of the experiment where the independent variable(s) being tested cannot influence the results. This isolates the independent variable's effects on the experiment and can help rule out alternate explanations of the experimental results.

protein synthesis
type: Class
subclass of: biological process
IAO_0000115: The process through which activated amino acids are polymerized to form polypeptides through association with mRNA and transfer RNAs on ribosomes.

nerve injury
type: Class
subclass of: nervous system injury
IAO_0000115: The process of causing damage to nerve(s) or nerve tissue.

cell adhesion
type: Class
subclass of: biological adhesion
IAO_0000115: Attachment of a cell to another cell, plasma membrane structure, or the extracellular matrix.

glial activation
type: Class
subclass of: activation
IAO_0000115: The proliferation, change in functional state, and/or hypertrophy of different types of glial cells, including astrocytes and microglia. In its most extreme form, activation associated with astrogliosis leads to the formation of a glial scar, and activation of microglia/macrophages leads to severe inflammation.

regrowth
type: Class
subclass of: growth
IAO_0000115: The process of increasing in size or length and changing physically after damage or injury.

cytokine
type: Class
subclass of: role
IAO_0000115: Small protein (~5-20 kDa) that is released by cells and that affects the behavior of other cells.

contusion
type: Class
subclass of: tissue damage
IAO_0000115: A state in which blood vessels and surrounding tissue are damaged or broken as the result of an injury.

cytoskeleton
type: Class
subclass of: biological entity
IAO_0000115: The cytoplasmic elements that confer mechanical properties and motility to a cell. The main components are long polymers of actin (microfilaments) that form a meshwork, polymers of tubulin (microtubules), and the intermediate filaments(polymers of various proteins), together with a range of anchoring, crosslinking, and motor proteins.

biological adhesion
type: Class
subclass of: biological process
IAO_0000115: (in pathology) The abnormal union of surfaces or parts, usually due to the formation of fibrous tissue following inflammation.

nerve
type: Class
subclass of: neural tissue
IAO_0000115: Bundle of axons traveling outside the central nervous system (exception is the optic nerve, which travels from the retina to the optic chiasm).

retraction
type: Class
subclass of: biological process
IAO_0000115: A process in which an axon experiences backward or inward movement of its terminal ending and the branch that gives rise to it.

laminectomy
type: Class
subclass of: injury
IAO_0000115: The process of surgically removing the posterior arch of a vertebra.

degeneration
type: Class
subclass of: biological process
IAO_0000115: The process whereby a cell, tissue, or organ changes to a less specialized or functionally less active form.

endocytosis
type: Class
subclass of: biological process
IAO_0000115: The uptake of external materials by cells through the invagination of the plasma membrane to form a vesicle or vacuole.

macromolecule
type: Class
subclass of: molecule
IAO_0000115: A molecule containing a very large number of atoms, such as a protein, nucleic acid, or synthetic polymer.

sciatic nerve
type: Class
subclass of: nerve
IAO_0000115: Nerve that originates from the motor neurons and spinal ganglia of the lower lumbar and upper sacral region, and travels from lower back through the hips and buttocks and down the leg.

optic nerve
type: Class
subclass of: nerve
IAO_0000115: Nerve that travels between the retina and the optic chiasm.

compound
type: Class
subclass of: small molecule
IAO_0000115: A chemical compound is a pure chemical substance consisting of two or more different chemical elements that can be separated into simpler substances by chemical reactions
IAO_0000118: chemical compound

dorsal root ganglion neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron in the dorsal root ganglion.
IAO_0000118: DRG sensory neuron

nervous system repair
type: Class
subclass of: repair
IAO_0000115: The process of restoring neural tissue to a healthy state after injury or damage.
IAO_0000118: neural repair

secondary antibody
type: Class
subclass of: role
IAO_0000115: A labeled antibody added to recognize a primary antibody.

pro-inflammatory cytokine
type: Class
subclass of: cytokine
IAO_0000115: Cytokine that activates all or part of the systemic inflammatory cascade.

protein kinase C
type: Class
subclass of: serine-threonine kinase
IAO_0000118: PKC
IAO_0000115: The protein kinase C family of serine/threonine protein kinases comprises 15 members divided into 3 subfamilies (conventional, novel, and atypical). These are differentially expressed and differentially regulated by intracellular mediators.

axon pathfinding
type: Class
subclass of: pathfinding
IAO_0000115: The process of axons growing in appropriate directions to reach their target cells.

axon shaft
type: Class
subclass of: shaft
IAO_0000115: The part of an axon proximal to the growth cone, normally delineated from the tip by differing cytoskeletal features.

motor axon
type: Class
subclass of: axon
IAO_0000115: An axon extending from a motor neuron.

sham surgery control group
type: Class
subclass of: injury control group
IAO_0000115: A control for a surgical procedure in which aspects of the procedure other than the injury intended to induce the neurological effect itself are mimicked, including anaesthesia, surgical preparation (e.g., dissection, nerve exposure, laminectomy, durotomy) and post-operative treatments.

polyclonal antibody
type: Class
subclass of: antibody
IAO_0000115: Antibody produced by one of several clones of B lymphocytes and potentially directed at multiple epitopes.

signaling mechanism
type: Class
subclass of: biological mechanism
IAO_0000115: A series of causally interacting signals that produce a biological phenomenon.

dorsal hemisection
type: Class
subclass of: incomplete transection
IAO_0000115: The process of partially severing the dorsal region of the spinal cord.

incomplete transection
type: Class
subclass of: spinal cord transection
IAO_0000115: The process of transversely partially severing the spinal cord.

rat
type: Class
subclass of: animal
IAO_0000115: Animal of the genus Rattus.

necrotic cell death
type: Class
subclass of: cell death
IAO_0000115: Cell death induced by necrosis.
IAO_0000118: necrosis

injury
type: Class
subclass of: process
IAO_0000115: The process of causing damage to an entity or tissue.

mouse
type: Class
subclass of: animal
IAO_0000115: Animal of the genus Mus.

pyramidal neuron
type: Class
subclass of: neuron
IAO_0000115: CNS neuron with a characteristic pyramidal shape to its cell body.

protein kinase inhibitor
type: Class
subclass of: kinase inhibitor
IAO_0000115: A chemical that inhibits protein kinase activity.

radial glial cell
type: Class
subclass of: glial cell
IAO_0000115: A member of a population of precursor cells with processes spanning the width of the developing CNS, from the ventricular surface to the pial surface. These cells give rise to neurons and glia.

slice culture
type: Class
subclass of: culture
IAO_0000115: A culture containing a thin flat piece cut from a tissue, such as a brain or spinal cord.

kinase inhibitor
type: Class
subclass of: inhibitor
IAO_0000115: A chemical that inhibits kinase activity.

adhesion molecule
type: Class
subclass of: protein
IAO_0000115: A cell surface protein that binds to one or more specific ligands on an adjacent cell or matrix, providing specificity in cell binding.

neurite growth inhibitor
type: Class
subclass of: growth inhibitor
IAO_0000115: A chemical compound, or cell surface or secreted protein that inhibits neurite growth and/or maintenance.

reactive astrocyte
type: Class
subclass of: astrocyte
IAO_0000115: Astrocyte that exhibits a graded response to injury, including changes in gene expression, hypertrophy and process extension, and in some cases cell division.

expression vector
type: Class
subclass of: role
IAO_0000115: A vector that will allow the gene that it is carrying to be expressed in the host cell into which it has been transfected. The vector usually contains a strong promoter, often inducible (e.g. under the control of the lac repressor and inducible with IPTG) and optimized for the host cell.

cell
type: Class
subclass of: biological entity
IAO_0000115: A self-replicating biological unit enclosed by a plasma membrane and containing cytoplasm, ribosomes, and DNA.

axon tract
type: Class
subclass of: biological entity
IAO_0000115: A bundle of axons in the central nervous system.

PC12 cell line
type: Class
subclass of: cell line
IAO_0000115: A single cell clonal line that responds reversibly to nerve growth factor (NGF) established from a transplantable rat adrenal pheochromocytoma. There are multiple sublines of PC12 cells with distinct morphological and growth properties.

experimental group
type: Class
subclass of: study group
IAO_0000115: A group of samples/individals that is exposed to (one of) the independent variable (s) being tested.
IAO_0000118: treatment group

fusion protein
type: Class
subclass of: protein
IAO_0000115: A protein encoded by an mRNA produced through the joining of two or more genes that originally coded for separate proteins.

stromal cell
type: Class
subclass of: cell
IAO_0000115: A connective tissue cell that makes up supportive structures for other, functional cells of the tissue.

quiescent microglial cell
type: Class
subclass of: microglial cell
IAO_0000115: Microglial cell with a specific ramified morphological phenotype, in a resting, unactivated state.
IAO_0000115: quiescent microglia
IAO_0000115: resting microglia
IAO_0000118: resting microglial cell

substrate adhesion molecule
type: Class
subclass of: adhesion molecule
IAO_0000115: A cell surface protein that binds to one or more specific ligands in the extracellular matrix adjacent to the cell, providing specfiity in cell-substrate binding.

dendrite regeneration
type: Class
subclass of: regeneration
IAO_0000115: The process of dendrite regrowth following injury.

primary antibody
type: Class
subclass of: role
IAO_0000115: Antibody added to recognize an antigen of interest.

myelination
type: Class
subclass of: biological process
IAO_0000115: The process by which a nerve axon acquires a myelin sheath.

neuronal culture
type: Class
subclass of: culture
IAO_0000115: Culture containing neuronal cells. The culture may be relatively pure neurons or may be a combination of neurons and support cells, such as astrocytes.

neurite growth
type: Class
subclass of: growth
IAO_0000115: The process of neurite(s) undergoing development by increasing in size and changing physically; maturation.
IAO_0000118: neurite extension
IAO_0000118: neurite outgrowth

neural development
type: Class
subclass of: development
IAO_0000115: The process of growth and differentiation of the neural system.

sprouting
type: Class
subclass of: biological process
IAO_0000115: The process by which nerve processes grow out either from the sides of intact axons or from intact nerve terminals, or from injured axons at regions other than from the cut ending.

retraction bulb
type: Class
subclass of: neuronal process part
IAO_0000115: The rounded swollen tip of a neurite that shows no net forward movement.

cell transplant
type: Class
subclass of: biological entity
IAO_0000115: A cell or collection of cells transferred from one part of the body to another or from one animal to another.

atrophy
type: Class
subclass of: biological process
IAO_0000115: Wasting or decrease in size of a cell, tissue, or organ as a result of disuse, injury, or nutritional deficiency.

neural tissue
type: Class
subclass of: tissue
IAO_0000115: Tissue of the nervous system, including the brain, retina, spinal cord and peripheral nervous system (peripheral nerves and sympathetic, parasympathetic, and enteric nervous systems).
IAO_0000118: nervous tissue

regenerative sprouting
type: Class
subclass of: sprouting
IAO_0000115: The process of sprouting following damage or injury.

nerve crush
type: Class
subclass of: nerve injury
IAO_0000115: The process of causing damage to nerve(s) or nerve tissue by compression.

nerve graft
type: Class
subclass of: graft
IAO_0000115: A section of a healthy nerve that has been removed from another part of the body or from another animal and is used to replace a damaged nerve.

tyrosine kinase
type: Class
subclass of: protein kinase
IAO_0000115: A kinase that phosphorylates the hydroxyl group of tyrosine residues on its substrate proteins. Tyrosine kinases are critical signal transduction elements in numerous cell biological pathways.

cell transplantation
type: Class
subclass of: transplantation
IAO_0000115: The transfer of cells within an individual, between individuals of the same species, or between individuals of different species into a tissue.

tyrosine phosphorylation
type: Class
subclass of: phosphorylation
IAO_0000115: The addition of phosphates to a protein on hydroxyl groups of tyrosine residues. A common method for regulating activity, the effect being reversed by protein phosphatases.

development
type: Class
subclass of: biological process
IAO_0000115: The process of growth and differentiation.

embryonic stem cell
type: Class
subclass of: stem cell
IAO_0000115: A pluripotent stem cell derived from the inner cell mass of an embryo.

brain
type: Class
subclass of: organ part
IAO_0000115: The brain is a soft, spongy mass of nerve cells and supportive cells. It has three major parts: the cerebrum, the cerebellum, and the brain stem.

astrocyte
type: Class
subclass of: glial cell
IAO_0000115: A type of macroglial cell, expressing the intermediate filament protein GFAP and with numerous sheet-like processes extending from its cell body. Astrocytes are found throughout the central nervous system. There are multiple developmental and region-specific subtypes of astrocytes, and they have a wide array of functions from blood-brain barrier formation to synaptic plasticity.
IAO_0000118: astroglial cell

female
type: Class
subclass of: gender
IAO_0000115: Denoting the sex that can bear offspring or produce eggs, distinguished biologically by the production of gametes (ova) which can be fertilized by male gametes.

regeneration
type: Class
subclass of: biological process
IAO_0000115: The process of tissue regrowth following damage or injury.

treatment
type: Class
subclass of: role
IAO_0000115: A chemical or biological substance administered to induce a specific therapeutic or experimental effect.

commissural axon
type: Class
subclass of: axon
IAO_0000115: An axon that crosses the midline to the other side of the central nervous system.

serine-threonine kinase
type: Class
subclass of: protein kinase
IAO_0000115: A kinase that phosphorylates the hydroxyl group of serine or threonine or both on its substrate proteins.

injury control group
type: Class
subclass of: control group
IAO_0000115: A control for experimental injury in which the animal is not injured.

plasma membrane
type: Class
subclass of: membrane
IAO_0000115: A membrane bilayer, 5-10 nm thick, of lipids and proteins that forms the external boundary of the cytoplasm of a cell.
IAO_0000118: cell membrane
IAO_0000118: cell surface

study group
type: Class
subclass of: role
IAO_0000115: A group of samples/individuals used in a biological study.

activation
type: Class
subclass of: biological process
IAO_0000115: An increase in the frequency, rate or extent of a biological process.

neuronal development
type: Class
subclass of: neural development
IAO_0000115: The process of growth and differentiation of neurons.

chronic pain
type: Class
subclass of: pain
IAO_0000115: Pain lasting longer than 3-6 months, or beyond the "normal" period of healing.

secondary damage
type: Class
subclass of: tissue damage
IAO_0000115: Secondary damage is a state that is an indirect result of an insult. It results from processes initiated by trauma. It occurs in the hours and days following a primary injury and may play a large role in the damage and death that results from spinal cord injury or traumatic brain injury. Factors that contribute to secondary damage include excitotoxicity, breakdown of the blood–brain barrier, edema, ischemia hypoxia, and immune system reaction.

biological process
type: Class
subclass of: process
IAO_0000115: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

neuronal cell death
type: Class
subclass of: cell death
IAO_0000115: Any biological process that results in permanent cessation of all vital functions of a neuronal cell.

growth cone filopodium
type: Class
subclass of: filopodium
IAO_0000115: A long thin spike-like cell projection containing actin filaments that extends from a growth cone.

axon
type: Class
subclass of: neuronal process
IAO_0000115: The process extending from the cell body of a neuron that normally carries outgoing action potentials towards the target cell. These are generally of a constant radius and may be very long (millimeters to centimeters).
IAO_0000118: nerve fiber

stable microtubule
type: Class
subclass of: microtubule
IAO_0000115: A microtubule with a relatively long lifetime in the cell (in contrast to a dynamic microtubule), and characterized by the presence of detyrosinated and acetylated tubulin dimers

Vascular endothelial growth factor
type: Class
subclass of: protein
IAO_0000115: A member of VEGF subfamily of the PDGF growth factor family; the mature form is a disulfide linked homodimer. This protein is a glycosylated mitogen that acts through receptor tyrosine kinases and other receptors on endothelial cells and numerous other cell types.
IAO_0000118: Endothelial cell growth factor
IAO_0000118: VEGF

neuron
type: Class
subclass of: cell
IAO_0000115: An excitable cell that transmits electrical signals to recipient cells through synapses.

dual specificity kinase
type: Class
subclass of: protein kinase
IAO_0000115: A protein kinase that phosphorylates its substrate proteins both on serine or threonine and on tyrosine residues.

cavity
type: Class
subclass of: material entity
IAO_0000115: A hollow place or space, or a potential space, within the body or one of its organs. The thoracic cavity is an example. An abnormal cavity can also occur in a tissue, like the spinal cord, as a result of some injury followed by an inflammatory reaction.

growth
type: Class
subclass of: biological process
IAO_0000115: The process of undergoing development by increasing in size and changing physically; maturation.
IAO_0000118: extension
IAO_0000118: outgrowth

sensory neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron with a peripheral axon or specialized terminal that is activated by sensory input, and transmits a signal to the CNS.

neuron projection guidance
type: Class
subclass of: guidance
IAO_0000115: Any process that influences the direction of neuron projection migration.

propriospinal neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron with both cell body and axonal projections confined to the spinal cord.

dendrite guidance
type: Class
subclass of: guidance
IAO_0000115: Any process that influences the direction of dendrite growth.

spinal cord injury
type: Class
subclass of: nervous system injury
IAO_0000115: The process of causing damage to the spinal cord.

serine-threonine phosphorylation
type: Class
subclass of: phosphorylation
IAO_0000115: The addition of phosphates to a protein on hydroxyl groups either of serine or threonine residues or both. A common method for regulating activity, the effect being reversed by protein phosphatases.

subunit
type: Class
subclass of: role
IAO_0000115: A distinct component of something.

spinal cord
type: Class
subclass of: organ part
subclass of: Restriction
  on property: has part
  some values from: spinal cord segment
IAO_0000115: The part of the central nervous system lodged in the spinal canal, extending from the medulla oblongata down through the spinal column and from which the spinal nerves branch off to various parts of the body. It is composed of an inner core of gray substance in which nerve cells predominate and an outer layer of white substance in which myelinated nerve fibers predominate.

neuron regeneration
type: Class
subclass of: regeneration
IAO_0000115: The process of neuron regrowth following injury.

mechanical stimulation
type: Class
subclass of: stimulation
IAO_0000115: The process of producing a reaction in a sensory end organ by a mechanical agent or stimulus that initiates a nerve impulse and results in functional activity of an effector.

lesion
type: Class
subclass of: tissue
IAO_0000115: An area of damaged tissue that is the result of an injury.

neuron degeneration
type: Class
subclass of: degeneration
IAO_0000115: The death and subsequent loss of neurons following disease, insult, or injury.

animal
type: Class
subclass of: biological entity
IAO_0000115: An organism of the kingdom Animalia.

corticospinal tract axon
type: Class
subclass of: cortical axon
IAO_0000115: An axon extending from a neuron in the primary motor cortex, supplementary motor area, the premotor cortex, or the somatosensory cortex.

growth inhibitor
type: Class
subclass of: inhibitor
IAO_0000115: A chemical (typically a polypeptide) that binds to cell surface receptors to inhibit cell division, cell growth and/or cell survival.

transcription factor
type: Class
subclass of: role
IAO_0000115: A protein that binds to a specific DNA sequence upstream of a coding region and triggers the assembly of an RNA polymerase complex and the production of mRNA or other RNA species.

sagittal section
type: Class
subclass of: histological tissue section
IAO_0000115: A tissue section cut in a sagittal plane.

coronal section
type: Class
subclass of: histological tissue section
IAO_0000115: A tissue section cut in a coronal plane.

longitudinal section
type: Class
subclass of: histological tissue section
IAO_0000115: A tissue section cut in a longitudinal plane.

plane of section
type: Class
subclass of: information content entity
IAO_0000115: A body plane of section is an imaginary flat surface that is used to define a particular area of anatomy.

measurement
type: Class
subclass of: information content entity
IAO_0000115: A quantitative description that reflects the magnitude of some attribute.

dependence receptor
type: Class
subclass of: receptor
IAO_0000115: Receptor that induces apoptosis in the absence of the required stimulus (when occupied by a trophic ligand, or possibly when bound by a competing, nontrophic ligand), but blocks apoptosis following binding to its ligand.

long non-coding rna
type: Class
subclass of: ribonucleic acid
IAO_0000115: Any RNA longer than 200 nucleotides that does not encode a protein.

ribonucleic acid
type: Class
subclass of: nucleic acid
IAO_0000115: A linear polymer of ribose units linked through 3′ and 5′ positions by a phosphodiester bond and with a purine or pyrimidine base attached in the 1′ position.
IAO_0000118: RNA

neuronal process part
type: Class
subclass of: cell projection
IAO_0000115: A substructure of a neuronal process.

branch
type: Class
subclass of: neuronal process part
IAO_0000115: A segment of a neuronal process that splits off from the main projection.

shaft
type: Class
subclass of: neuronal process part
IAO_0000115: The part of a neurite proximal to the tip or growth cone, normally delineated from the tip by differing cytoskeletal features.

dendrite shaft
type: Class
subclass of: shaft
IAO_0000115: The part of a dendrite proximal to the tip or growth cone, normally delineated from the tip by differing cytoskeletal features.

dendrite branch
type: Class
subclass of: branch
IAO_0000115: A segment of a dendrite that splits off from the main projection.

collapsed morphology
type: Class
subclass of: morphology
IAO_0000115: Morphology of a growth cone in which filopodia and lamellipodia have retracted, leaving a smooth convex tip.

filopodial
type: Class
subclass of: morphology
IAO_0000115: Morphological feature involving slender elongated cytoplasmic projections containing actin filaments.

lamellipodial
type: Class
subclass of: morphology
IAO_0000115: Morphological feature involving sheet-like cytoplasmic protrusions containing actin meshwork.

chemical stimulation
type: Class
subclass of: stimulation
IAO_0000115: The process of exposing a cell or tissue to a chemical to provoke a specific response.

neurotransmitter stimulation
type: Class
subclass of: chemical stimulation
IAO_0000115: The process of exposing a cell or tissue to a neurotransmitter to provoke a specific response.

growth factor stimulation
type: Class
subclass of: chemical stimulation
IAO_0000115: The process of exposing a cell or tissue to a growth factor to provoke a specific response.

embryo
type: Class
subclass of: biological entity
IAO_0000115: The developmental stage of an animal while it is isolated from the external environment by egg membranes, fetal membranes, etc.

tissue transplantation
type: Class
subclass of: transplantation
IAO_0000115: The transfer of a tissue from one part of the body to another or from one animal to another.

glial development
type: Class
subclass of: neural development
IAO_0000115: The process of growth and differentiation of glial cells.

PNS Wallerian degeneration
type: Class
subclass of: Wallerian degeneration
IAO_0000115: In peripheral nervous system Wallerian degeneration, the myelin sheaths separate from the degenerating axons at the Schmidt-Lanterman incisures first and then rapidly deteriorate and shorten to form bead-like structures. Schwann cells continue to clear up the myelin debris by degrading their own myelin, phagocytose extracellular myelin and attract macrophages to myelin debris for further phagocytosis.
IAO_0000118: peripheral nervous system Wallerian degeneration

CNS Wallerian degeneration
type: Class
subclass of: Wallerian degeneration
IAO_0000115: In central nervous system Wallerian degeneration, oligodendrocytes either undergo programmed cell death or enter a state of rest. Therefore, unlike Schwann cells, oligodendrocytes fail to clean up the myelin sheaths and their debris. Myelin debris can persist for months to years.
IAO_0000118: central nervous system Wallerian degeneration

astrocyte activation
type: Class
subclass of: glial activation
IAO_0000115: The proliferation, change in functional state, and/or hypertrophy of astrocytes. In its most extreme form, activation associated with astrogliosis leads to the formation of a glial scar.

GTPase
type: Class
subclass of: enzyme
IAO_0000115: A GTPase is a hydrolase enzyme that can bind and hydrolyze guanosine triphosphate (GTP). The GTP binding and hydrolysis takes place in the highly conserved G domain common to all GTPases.

Ras homolog family member A
type: Class
subclass of: GTPase
IAO_0000115: Ras homolog gene family, member A (RhoA) is a small GTPase protein known to regulate the actin cytoskeleton.
IAO_0000118: RhoA

glial cell death
type: Class
subclass of: cell death
IAO_0000115: A biological process that results in permanent cessation of all vital functions of a glial cell.

growth cone migration
type: Class
subclass of: migration
IAO_0000115: The movement of a growth cone that accompanies the extension of an axon, dendrite or neurite.

growth cone repulsion
type: Class
subclass of: growth cone guidance
subclass of: repulsive guidance
IAO_0000115: Any process involving a signal or cue that repels a growth cone (or axonal tip) from the source of the signal.

contusive injury
type: Class
subclass of: nervous system injury
IAO_0000115: The process of causing a contusion.

weight drop injury
type: Class
subclass of: spinal cord contusive injury
IAO_0000115: The process of causing a contusion by dropping a weight onto the spinal cord.

impactor injury
type: Class
subclass of: spinal cord contusive injury
IAO_0000115: The process of causing a contusion by applying an impactor to the spinal cord.

NYU impactor injury
type: Class
subclass of: impactor injury
IAO_0000115: The process of causing a contusion by applying an NYU impactor to the spinal cord.

Ohio State University impactor injury
type: Class
subclass of: impactor injury
IAO_0000115: The process of causing a contusion by applying an Ohio State University impactor to the spinal cord.

Infinite Horizon impactor injury
type: Class
subclass of: impactor injury
IAO_0000115: The process of causing a contusion by applying an Infinite Horizon impactor to the spinal cord.

clip compression injury
type: Class
subclass of: spinal cord contusive injury
IAO_0000115: The process of causing a contusion by applying clip compression to the spinal cord.

spinal cord contusive injury
type: Class
subclass of: spinal cord injury
subclass of: contusive injury
IAO_0000115: The process of causing a contusion to the spinal cord.

M1 microglial cell
type: Class
subclass of: microglial cell
IAO_0000118: M1 microglia
IAO_0000115: Microglial cell activated by either LPS or INF-gamma, and that leads to tissue damage.

material entity
type: Class
IAO_0000115: A physical entity that is spatially extended, exists as a whole at any point in time and has mass.

cell projection
type: Class
subclass of: biological entity
IAO_0000115: A prolongation or process extending from a cell.

attribute
type: Class
IAO_0000115: A characteristic of some entity.

quality
type: Class
subclass of: attribute
IAO_0000115: An attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary.

role
type: Class
subclass of: attribute
IAO_0000115: A realizable entity that describes behaviors, rights and obligations of an entity in some particular circumstance.

information content entity
type: Class
IAO_0000115: An object that requires some background knowledge or procedure to correctly interpret.

genotype
type: Class
subclass of: quality
IAO_0000115: The genetic constitution of an organism.

lesion epicenter
type: Class
subclass of: tissue
IAO_0000115: Region containing the least amount of spared peripheral rim white matter.

organelle
type: Class
subclass of: biological entity
IAO_0000115: Any structurally discrete component of a cell.

time interval
type: Class
subclass of: information content entity
IAO_0000115: A contiguous temporal region having some duration.

function
type: Class
subclass of: attribute
IAO_0000115: A capability that satisfies some agentive objective, or (evolutionary) optimization.

M2 microglial cell
type: Class
subclass of: microglial cell
IAO_0000118: M2 microglia
IAO_0000115: Microglial cell activated by IL-4, IL-10 or IL-13 and exhibiting an anti-inflammatory response, leading to tissue repair.

collection
type: Class
subclass of: information content entity
IAO_0000115: A set for which there exists at least one member, although any member need not to exist at any point in the collection's existence.

chemical entity
type: Class
subclass of: material entity
IAO_0000115: A material entity composed of chemical(s).

heterogeneous substance
type: Class
subclass of: chemical entity
IAO_0000115: A material entity that is composed of more than one different kind of chemical component.

biological entity
type: Class
subclass of: heterogeneous substance
IAO_0000115: A heterogeneous substance that contains genomic material or is the product of a biological process.

organ
type: Class
subclass of: biological entity
IAO_0000115: A part of the body, composed of more than one tissue, that forms a structural unit responsible for a particular function (or functions).

organ part
type: Class
subclass of: biological entity
IAO_0000115: A subsection of an organ.

neuraxis
type: Class
subclass of: organ
IAO_0000115: The axis of the central nervous system formed by the embryonic spinal cord, rhombencephalon, mesencephalon, and diencephalon.

brain stem
type: Class
subclass of: organ part
IAO_0000115: The brainstem is the region of the brain that connects the cerebrum with the spinal cord. It consists of the midbrain, pons and medulla oblongata.

protein synthesis inhibitor
type: Class
subclass of: inhibitor
IAO_0000115: A chemical that inhibits protein synthesis.

process
type: Class
IAO_0000115: An entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.

enzyme
type: Class
subclass of: protein
IAO_0000115: Macromolecules that are selective catalysts, accelerating both the rate and specificity of metabolic reactions. Most known enzymes are proteins, although catalytic RNA molecules have been identified. Enzymes adopt a specific three-dimensional structure, and may employ organic (e.g. biotin) and inorganic (e.g. magnesium ion) cofactors to assist in catalysis.

pyramidal tract neuron
type: Class
subclass of: neuron
IAO_0000115: A neuron in layer V of the primary motor cortex that projects to the spinal cord and is involved in controlling movement.

condition
type: Class
subclass of: quality
IAO_0000115: The state of something with regard to its appearance, quality, or working order.

propiospinal axon
type: Class
subclass of: axon
IAO_0000115: An axon originating in the spinal cord and terminating in the spinal cord.

spinal cord lesion
type: Class
subclass of: lesion
IAO_0000115: An area of damaged tissue that is the result of a spinal cord injury.

secondary lesion cavity
type: Class
subclass of: cavity
IAO_0000115: A cavity that forms at distant sites from the primary injury site after a spinal cord injury. A secondary lesion cavity appears later compared to the primary lesion cavity, and lacks the macrophages found in the primary lesion cavity.

laminectomy control group
type: Class
subclass of: sham surgery control group
IAO_0000115: A control for a surgical procedure in which all aspects of a surgical procedure including the laminectomy are mimicked, including anaesthesia, surgical preparation and post-operative treatment.

treatment control group
type: Class
subclass of: control group
IAO_0000115: A control in which a treatment/perturbagen with a known response effect is used (positive control) or different aspects of the treatment delivery, other than the perturbagen per se, are used (negative control). This gives the investigators confidence that the assay measuring the effect is performing as expected, and that the treatment effect is due to the perturbagen itself.

no treatment control group
type: Class
subclass of: negative treatment control group
IAO_0000115: A control for experimental treatment in which neither the perturbagen nor its vehicle is added.

inactive treatment control group
type: Class
subclass of: negative treatment control group
IAO_0000115: A control for experimental treatment in which an inactive form of the treatment is substituted for the active form, such as a scrambled siRNA, a plasmid/virus with inactive insert, or an inactive but related chemical compound.

dura intact control group
type: Class
subclass of: laminectomy control group
IAO_0000115: A control for a surgical procedure in which all aspects of the surgical procedure including the laminectomy are mimicked, including anaesthesia, surgical preparation and post-operative treatment, but dura remains intact.

dura open control group
type: Class
subclass of: laminectomy control group
IAO_0000115: A control for a surgical procedure in which all aspects of the surgical procedure including the laminectomy are mimicked, including anaesthesia, surgical preparation and post-operative treatment and the dura is opened.

naive control group
type: Class
subclass of: injury control group
IAO_0000115: A control for experimental injury in which the animal is not injured, and does not receive anaesthesia or post-operative treatments such as antibiotics, analgesics or injected fluids.

NeuN
type: Class
subclass of: protein
IAO_0000118: Neuronal Nuclei

behavioral assessment
type: Class
subclass of: outcome measure
IAO_0000115: A quantitative or qualitative assessment of the behavioral outcome of an experiment.

BBB score
type: Class
subclass of: behavioral assessment
IAO_0000115: A behavioral assessment (the Basso, Beattie and Bresnahan open field locomotion score) that quantifies the recovery of locomotion following a spinal cord injury in rats on a scale of 0-21.
IAO_0000118: Basso, Beattie, and Bresnahan open field locomotion score

BBB subscore
type: Class
subclass of: BBB score
IAO_0000115: A sub-evaluation of the BBB score that measures paw rotation and toe clearance of the hindlimb on a scale of 0-5.

BMS score
type: Class
subclass of: behavioral assessment
IAO_0000115: A behavioral assessment (the Basso mouse scale) that quantifies the recovery of locomotion following a spinal cord injury in mice on a scale of 0-9.

BMS subscore
type: Class
subclass of: BMS score
IAO_0000115: A sub-evaluation of the BMS scale that measures stepping frequency, coordination, paw position, trunk stability and tail position on a scale of 0-11.

gridwalk performance
type: Class
subclass of: behavioral assessment
IAO_0000115: A quantitative assessment of the ability of a rat or mouse to traverse a series of irregularly spaced rungs in a horizontal walkway, aimed to quantify deficits in motor control.

nociception assay
type: Class
subclass of: behavioral assessment
IAO_0000115: A quantitative assessment of responsiveness to putatively painful stimuli.

paw withdrawal frequency
type: Class
subclass of: nociception assay
IAO_0000115: The frequency with which a rat or mouse withdraws its paw from a source of painful stimulus.

paw withdrawal latency
type: Class
subclass of: nociception assay
IAO_0000115: The amount of time it takes for a rat or mouse to withdraw its paw from a source of painful stimulus.

tail flick latency
type: Class
subclass of: nociception assay
IAO_0000115: The amount of time it takes for a rat or mouse to flick its tail in response to a painful heat stimulus.

paw grasping frequency
type: Class
subclass of: behavioral assessment
IAO_0000115: The frequency with which a rat or mouse successfully grasps a food pellet with a paw.

injured paw grasping frequency
type: Class
subclass of: paw grasping frequency
IAO_0000115: The frequency with which a rat or mouse successfully grasps a food pellet with an paw innervated from the injured side of the spinal cord.

neuroanatomical assessment
type: Class
subclass of: outcome measure
IAO_0000115: A quantitative or qualitative assessment of a neuroanatomical property of an experimental subject.

lesion volume
type: Class
subclass of: neuroanatomical assessment
IAO_0000115: A quantitative assessment of the volume of a lesion created by a central nervous system injury.

central nervous system tissue sparing
type: Class
subclass of: neuroanatomical assessment
IAO_0000115: A quantitative assessment of the amount of central nervous system tissue that is left undamaged by a central nervous system injury.

tissue sparing of white matter
type: Class
subclass of: central nervous system tissue sparing
IAO_0000115: A quantitative assessment of the amount of white matter that is left undamaged by a central nervous system injury.

tissue sparing of gray matter
type: Class
subclass of: central nervous system tissue sparing
IAO_0000115: A quantitative assessment of the amount of gray matter that is left undamaged by a central nervous system injury.

number of axons
type: Class
subclass of: neuroanatomical assessment
IAO_0000115: A count of the axons present in a defined region.

number of tyrosine hydrolase positive axons
type: Class
subclass of: number of axons
IAO_0000115: A quantitative assessment of the number of discrete fibers present in a region that stain positive for tyrosine hydroxylase.

physiological assessment
type: Class
subclass of: outcome measure
IAO_0000115: A quantitative assessment of a physiological property of an experimental subject.

neuron responsiveness
type: Class
subclass of: physiological assessment
IAO_0000115: A quantitative assessment of evoked action potential frequency in a neuron or neuronal population.

dorsal horn neuron responsiveness
type: Class
subclass of: neuron responsiveness
IAO_0000115: A quantitative assessment of evoked action potential frequency in a dorsal horn neuron or dorsal horn neuronal population.

neuronal hyperactivity
type: Class
subclass of: neuron responsiveness
IAO_0000115: A quantitative assessment of higher-than-normal activity of neurons caused by an experimental intervention.

phrenic nerve activity
type: Class
subclass of: neuron responsiveness
IAO_0000115: A quantitative assessment of action potential frequency in the phrenic nerve.

outcome measure
type: Class
subclass of: measurement
IAO_0000115: A quantitative or qualitative description of the result of an experiment.

number of corticospinal tract axons
type: Class
subclass of: number of axons
IAO_0000115: A quantitative assessment of the number of corticospinal tract axons present in a region.

gene expression
type: Class
subclass of: biological process
IAO_0000115: The conversion of genetic information in DNA to RNA, through transcription, and/or, in the case of protein coding genes, of mRNA into protein, through translation.

TUNEL positive cell
type: Class
subclass of: cell
IAO_0000115: A cell that has been identified by TUNEL assay as containing fragmented DNA

NeuN positive cell
type: Class
subclass of: cell
IAO_0000115: A cell that is positive for neuronal nuclei markers.

cell loss
type: Class
subclass of: biological process
IAO_0000115: A decrease in the number of cells or cell density in a specific area.

arborization
type: Class
subclass of: branching
IAO_0000115: The terminal branching of a neuronal process in treelike pattern.

cavity formation
type: Class
subclass of: degeneration
IAO_0000115: the process of formation of a cavity in tissue following spinal cord injury

cavity size
type: Class
subclass of: neuroanatomical assessment
IAO_0000115: A quantitative assessment of the size of a cavity created by a central nervous system injury

neuronal debris
type: Class
subclass of: heterogeneous substance
IAO_0000115: protein, filaments and other molecules generated by neuraxonal degradation

vimentin positive cell
type: Class
subclass of: cell
IAO_0000115: A cell that stains positively for the presence of vimentin, an intermediate filament for mesenchymal tissue.