CBO 1 0.owl
type: Ontology
date: 19 Dec. 2012
creator: J Sluka, Biocomplexity Insitute, Indiana University
comment: The cell Behavior Ontology (CBO) is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.
version info: Version 1.0 is the initial release of the Cell Behavior Ontology (CBO), Fall 2012.
version info: 1.000
imports: ro
imports: http://www.ifomis.org/bfo/1.1

hasExtentValueSet1D
type: DatatypeProperty
type: FunctionalProperty
definition: 1 value (included for completeness, probably best to just use hasFloatValue or hasIntValue). For example, the 1D length of an object of "3.2". Stored as a text string. Value is assumed to be X in a square coordinate system.

hasExtentValueSet2D
type: DatatypeProperty
type: FunctionalProperty
definition: 2 Comma separated values (CSV). For example, the extent of a 2D region (area) "5,10". Stored as a text string. Values are assumed to be X,Y in a square coordinate system.

hasExtentValueSet3D
type: DatatypeProperty
type: FunctionalProperty
definition: 3 Comma separated values (CSV). For example, the extent of a 3D region (volume) "5,5,10". Stored as a text string. Values are assumed to be X,Y,Z in a square coordinate system.

hasFloatValue
type: DatatypeProperty
type: FunctionalProperty
definition: A single floating point number.

hasFloatValueTarget
type: DatatypeProperty
type: FunctionalProperty
definition: A single floating point number representing the target value of a quality or function.

hasIntValue
type: DatatypeProperty
type: FunctionalProperty
definition: A single integer number.

hasIntValueTarget
type: DatatypeProperty
type: FunctionalProperty
definition: A single integer number representing the target value of a quality or function.

hasLocationValueSet1D
type: DatatypeProperty
type: FunctionalProperty
definition: 1 value (included for completeness, probably best to just use hasFloatValue or hasIntValue). For example, the location of a point "3.2". Stored as a text string.

hasLocationValueSet2D
type: DatatypeProperty
type: FunctionalProperty
definition: 2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string.

hasLocationValueSet3D
type: DatatypeProperty
type: FunctionalProperty
definition: 3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string.

hasLocationValueSetND
type: DatatypeProperty
type: FunctionalProperty
definition: Comma separated values (CSV) with [CR] end of row markers. Dimension (rows and column counts) not explicitly stated. Assumed that all units are the same. Stored as a text string.

hasParameterValueSetND
type: DatatypeProperty
type: FunctionalProperty
definition: Data is a list of n-tupes (one n-tuple/line) listing values of various kinds. For example, the list of interaction energies between a set of cell types. Comma separated values (CSV) with [CR] end of row markers. The dimensions (number of rows and columns) is not explicitly stated. Stored as a text string.

hasPointsValueSetND
type: DatatypeProperty
type: FunctionalProperty
definition: Data is a list of n-tupes (one n-tuple/line) listing the coordinates of the elements within a set. For example, the list of x,y,z coordinates of a cell in a grid-based coordinate system. Comma separated values (CSV) with [CR] end of row markers. The dimensions (number of rows and columns) is not explicitly stated. Stored as a text string.

hasUnit
type: DatatypeProperty
type: FunctionalProperty
definition: A unit name, for example, "meter", "micrometer*micrometer", "hour". Stored as a text string.

hasVTKfieldID
type: DatatypeProperty
date: 11/9/2012
creator: jps
definition: hasVTKfieldID is a CBO data property that links a field prototype to the character string name used in the VTK files. For example, an oxygen field in the simulaitno will probably be named described inthe VTK file as a field called "oxygen".

hasVTKtypeID
type: DatatypeProperty
type: FunctionalProperty
definition: hasVTKtypeID is a CBO data property that links a cell prototype (or other physical entitiy prototype) to the integer ID used in the VTK files. Often, in models that include medium as a CBO:Fill, the value of hasVTKtypeID will be 0 (zero). Note that a VTK "cell" has both a type ID (hasVTKtypeID) and an ID. The type ID identifies the class of cell, the ID identifies the individual cell. Many cells can have the same type ID, no two cells can have the same ID. Both types of IDs are unsigned integers.
creator: JPS
date: 10/25/2012
range: int

AcceptanceFunction
type: Class
subclass of: EnergyFunction
date: 24 Aug. 2011
creator: jps
definition: An AcceptanceFunction is a CBO:EnergyFunction describing the acceptance and rejection criteria for a change in the system. A simple AcceptanceFunction might state that all changes to the system which result in a lowering of the systems energy are accepted but all other changes are rejected.

AdhesionEnergy
type: Class
subclass of: EnergyQuality
date: 24 Aug. 2011
creator: jps
definition: An AdhesionEnergy is a CBO:EnergyQuality representing the energy associated with the contact between two physical objects.

AdhesionMolecule
type: Class
subclass of: CellMembranePart
date: 24 Aug. 2011
creator: jps
definition: AdhesionMolecule is a CBO:CellMembranePart that is a protein that mediates the adhesion between the Cell and other Cells or components of the extracellular space. MeSH: Surface ligands, usually glycoproteins, that mediate Cell-to-Cell adhesion. Their functions include the assembly and interconnection of various vertebrate Systems, as well as maintenance of tissue integration, wound healing, morphogenic movements, cellular migrations, and metastasis.

AdhesiveProperty
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
definition: AdhesiveProperty is a CBO:MechanicalProperty that describes an aspect of one of the objects involved in an adhesive force between two entities. For example, the adhesion properties of one Cell in the adhesion between a pair of Cells in contact, or between a Cell and a basement membrane.
creator: jps

Advection
type: Class
subclass of: Movement
definition: Advection is a Movement that is caused by a carrying medium (such as blood) that results in a change in location.
date: 29 Oct. 2012
creator: JPS

Age
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: Age is a CBO:PhysicalObjectQuality class that describes the chronological or generational Age of a physical object.
creator: jps

Anisotropy
type: Class
subclass of: BodyShape
disjoint with: Isotropy
date: 24 Aug. 2011
definition: Anisotropy is a GeometricalProperty describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:Isotropy.
creator: jps

ApicalPart
type: Class
subclass of: CellRegion
date: 24 Aug. 2011
definition: ApicalPart is a CBO:CellRegion of a polarized Cell is the region that is closest to the lumen. (Wikipedia)This is particularly evident in epithelial and endothelial cells, but also describes other polarized cells, such as neurons.
creator: jps

Apoptosis
type: Class
subclass of: CellDeath
date: 24 Aug. 2011
definition: Apoptosis is a CellDeath characterized by an orderly, and triggered process of cell death. GO: 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 pseudopods, 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.
creator: jps

AreaEnergy
type: Class
subclass of: EnergyQuality
date: 24 Aug. 2011
definition: A AreaEnergy is a CBO:EnergyQuality representing the energy associated with a given area entity.
creator: jps

AsymmetricCellDivisionOrientedCleavagePlane
type: Class
subclass of: Mitosis
date: 24 Aug. 2011
creator: jps
definition: AsymmetricCellDivisionOrientedCleavagePlane is a Mitosis characterized by the Creation of two non-identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is oriented with respect to either the environment or the characteristics of the parent cell. GO: The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity.

AsymmetricCellDivisionRandomCleavagePlane
type: Class
subclass of: Mitosis
date: 24 Aug. 2011
definition: AsymmetricCellDivisionRandomCleavagePlane is a Mitosis characterized by the Creation of two non-identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is oriented randomly with respect to both the environment and the characteristics of the parent cell. GO: The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity.
creator: jps

AutophagicDeath
type: Class
subclass of: CellDeath
date: 24 Aug. 2011
creator: jps
definition: AutophagicDeath is a CellDeath characterized by the auto degradation of cellular components. GO: A form of programmed cell death that is accompanied by macroautophagy, which is characterized by the sequestration of cytoplasmic material within autophagosomes for bulk degradation by lysosomes. Autophagic cell death is characterized by lack of chromatin condensation, massive vacuolization of the cytoplasm, and accumulation of (double-membrane) autophagic vacuoles, with little or no uptake by phagocytic cells.

BarrierCrossing
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
creator: jps
definition: BarrierCrossing is a FundamentalPhysicalProcess involving the transfer of an object across a bona fide boundary. For example, diiffusive transfer of a small molecule, such as molecular oxygen, across a cell membrane. For active Transport see CBO:CellImport and CBO:CellExport.

BasalPart
type: Class
subclass of: CellRegion
date: 24 Aug. 2011
definition: BasalPart is a CBO:CellRegion that includes the base of the Cell where the base is generally defined relative to an extraCellular membrane. GO: The region of a Cell situated near the base. For example, in a polarized epithelial Cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
creator: jps

BasementLaminaChange
type: Class
subclass of: BasementLaminaProcess
date: 24 Aug. 2011
definition: BasementLaminaChange is an BasementLaminaProcess involving a change in the components or characteristics of the basement lamina components.
creator: jps

BasementLaminaCreation
type: Class
subclass of: BasementLaminaProcess
date: 24 Aug. 2011
creator: jps
definition: BasementLaminaCreation is a BasementLaminaProcess involving an increase in the quantity of the basement lamina and its components.

BasementLaminaDeletion
type: Class
subclass of: BasementLaminaProcess
date: 24 Aug. 2011
definition: BasementLaminaDeletion is a BasementLaminaProcess involving a decrease in the quantity of the basement lamina and its components.
creator: jps

BasementLaminaProcess
type: Class
subclass of: ExtracellularMatrixProcess
disjoint with: InterstitialMatrixProcess
date: 24 Aug. 2011
definition: BasementLaminaProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of a basement membrane or its components.
creator: jps

BasementMembrane
type: Class
subclass of: ExtraCellularMatrix
disjoint with: InterstitialMatrix
date: 24 Aug. 2011
definition: GO: A thin layer of dense material found in various animal tissues interposed between the Cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
creator: jps

BioEntityType
type: Class
subclass of: CBO_Object
date: 11/8/2012
creator: jps
definition: BioEntityType is a CBO class for biological concepts such as Cell and ECM.

BodyShape
type: Class
subclass of: Shape
disjoint with: Protrusion
date: 24 Aug. 2011
creator: jps
definition: BodyShape is a GeometricalProperty describing the spatial (2 or 3 dimensions) Shape of a region of spaced occupied by an object at a particular instant in time. BodyShape may be defined as a locus of point in 3 (or 2) dimensional space, or as a predefined common Shape such as a sphere or cube.
is defined by: urn:miriam:opb:'bounded Volume Shape'

BoltzmannFactor
type: Class
subclass of: AcceptanceFunction
disjoint with: MinimizationAcceptanceFunction
date: 24 Aug. 2011
definition: A BoltzmannFactor is a CBO:EnergyFunction:AcceptanceFunction describing an acceptance criteria that uses a Boltzmann factor. A Boltzmann function accepts all system changes that result in a lowering of the systems total energy. In addition, changes that result in an increase in the systems energy are accepted based on a probability function. The probability function is generally described as being based on the temperature of the system (though the temperature may not be directly related to a physical temepertature.) The form of the Boltzmann factor is: Accept if deltaE is less than zero, where deltaE is the change in energy of the system calculated as the new energy minus the previous energy. If deltaE is greater than zero then accept the change if e^(-1/(k*T*deltaE)) is greater than a randomly choosen number between zero and one. k is Boltzmann's constant (in MKS units 1.38x10^-23 m^2 kg/(s^2 K) ) and T is the Boltzmann temperature (T is greater than zero).
creator: jps

Boundary
type: Class
subclass of: GeometricalEntity
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap:object_Boundary
creator: jps
definition: Boundary is a CBO:GeometricalEntity that demarks the interface between two bona fide physical objects.

BrushBorder
type: Class
subclass of: CellMembraneLocalStructure
date: 24 Aug. 2011
definition: A BrushBorder is a CBO:CellMembraneLocalStructure characterized by a highly convoluted Cell surface. GO: Dense covering of microvilli on the apical surface of epithelial Cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the Cell. MeSH: Minute projections of Cell membranes which greatly increase the surface area of the Cell. AKA: Microvilli, Striated Border
creator: jps

CBO_Object
type: Class
disjoint with: CBO_Process
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap
creator: jps

CBO_Process
type: Class
date: 24 Aug. 2011
see also: isA subclass of: BFO:span
creator: jps

CHASTEcenter
type: Class
subclass of: ComputationalPlatform
definition: CHASTERcenter is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.cs.ox.ac.uk/chaste/sysbio_index.html
creator: jps
date: 23 Jul. 2012

Cell
type: Class
subclass of: BioEntityType
disjoint with: Molecule
date: 24 Aug. 2011
definition: Cell is a CBO:BioEntityType class for the basic unit of an organism. A Cell includes at least the plasma membrane and the cytosol. GO: The basic structural and functional unit of all organisms.
see also: isA subclass of: BFO:snap:object
creator: jps

CellAdhesion
type: Class
subclass of: CellEnvironmentProcess
date: 24 Aug. 2011
definition: CellAdhesion is a CellEnvironmentProcess involving the adhesive interaction between a cell and some other physical object (another cell, basement membrane etc.). Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact.
creator: jps

CellAdvection
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
creator: jps
definition: CellAdvection is a CellMovement that is caused by a carrying medium (such as blood) that results in a change in location, defined by the center of mass or center of Volume, of a cell.

CellBasementLaminaContact
type: Class
subclass of: CellNonCellContact
disjoint with: CellInterstitialMatrixContact
date: 24 Aug. 2011
definition: CellBasementLaminaContact is a CellNonCellContact involving the direct contact between a cell and a basement membrane. Note that contact is a distinct process from adhesion (see CBO:CellAdhesion).
creator: jps

CellBasementMembraneAdhesion
type: Class
subclass of: CellNonCellAdhesion
disjoint with: CellInterstitialMatrixAdhesion
date: 24 Aug. 2011
definition: CellBasementMembraneAdhesion is a CellNonCellAdhesion involving the adhesive interaction between a cell and a basement membrane. Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact.
creator: jps

CellBorder
type: Class
subclass of: CellPart
date: 24 Aug. 2011
definition: CellBorder is a CBO:CellPart consisting of the outer Boundary of the Cell, that is, the surface that delineates the Cell from the surroundings. Depending on the species and phyla the CellBorder may be either a CBO:CellMembrane or a CBO: CellWall.
creator: jps

CellCellAdhesion
type: Class
subclass of: CellAdhesion
disjoint with: CellNonCellAdhesion
date: 24 Aug. 2011
definition: CellCellAdhesion is a CellAdhesion involving the adhesive interaction between two cells. Note that adhesion is a distinct process from contact (see CBO:CellContact) but that adhesion requires contact.
creator: jps

CellCellContact
type: Class
subclass of: CellContact
disjoint with: CellNonCellContact
date: 24 Aug. 2011
definition: CellCellContact is a CellContact involving the direct physical contact between two cells. Note that contact is distinct from adhesion (see CBO:CellAdhesion).
creator: jps

CellCellProcess
type: Class
subclass of: CellProcess
date: 24 Aug. 2011
creator: jps
definition: CellCellProcess is a CellProcess in which the interaction between two cells leads to a change in characteristic or behavior of one or both of the cells.

CellContact
type: Class
subclass of: CellEnvironmentProcess
date: 24 Aug. 2011
creator: jps
definition: CellContact is a CellEnvironmentProcess involving the direct physical contact between a cell and some other physical object (another cell, basement membrane etc.). Note that contact is distinct from adhesion (see CBO:CellAdhesion).
see also: isA subclass of: BFO:span:fiat_process_part

CellDeath
type: Class
subclass of: ExistentialCellProcesses
date: 24 Aug. 2011
creator: jps
definition: CellDeath is an existential_CellProcess in involving the death of a cell. The cell count in the system is decreased by one and there may or may not be cellular fragments left behind.

CellDifferentiation
type: Class
subclass of: ExistentialCellProcesses
date: 24 Aug. 2011
definition: CellDifferentiation is an existential_CellProcess in which the type (CBO:Phenotype) of a cell is changed.
creator: jps

CellDisplacement
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
creator: jps
definition: CellDisplacement is a CellMovement that results in a change in the location, defined by the center of mass or center of Volume, of a cell.

CellDivision
type: Class
subclass of: ExistentialCellProcesses
date: 24 Aug. 2011
creator: jps
definition: CellDivision is an ExistentialCellProcess involving the Creation of two new cells (daughters) from a single parent cell. GO: The process resulting in the physical partitioning and separation of a cell into daughter cells.

CellEnvironmentProcess
type: Class
subclass of: CellProcess
date: 24 Aug. 2011
creator: jps
definition: CellEnvironmentProcess is an ExistentialCellProcess involving the interaction between a cell and a component of the environment, where the environment includes other cells. For example, adhesion of a cell to a basement membrane.

CellExport
type: Class
subclass of: CellRelatedTransport
disjoint with: CellImport
date: 24 Aug. 2011
creator: jps
definition: CellExport is a CellRelatedTransport involving Movement of an entity across the cell membrane from the inside of the cell to the outside of the cell. For passive (e.g., diffusive) Transport see CBO:BarrierCrossing.

CellFusion
type: Class
subclass of: ExistentialCellProcesses
date: 24 Aug. 2011
creator: jps
definition: CellFusion is an existential_CellProcess involving the merging of two or more cells into a single giant cell containing multiple nuclei. GO: The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.

CellGrowth
type: Class
subclass of: ExistentialCellProcesses
date: 24 Aug. 2011
creator: jps
see also: isA subclass of: BFO:span:fiat_process_part
definition: CellGrowth is a CellProcess that changes the Volume of a cell. CellGrowth includes both an increase and a decrease in the cell's Volume. (Similar to, but here specific to a CBO:Cell) to CBO:VolumeChange. This definition differs from that in GO:0016049 The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.

CellImport
type: Class
subclass of: CellRelatedTransport
date: 24 Aug. 2011
creator: jps
definition: CellImport is a CellRelatedTransport involving Movement of an entity across the cell membrane from the outside of the cell to the inside of the cell. For passive (e.g., diffusive) Transport see CBO:BarrierCrossing.

CellInterstitialMatrixAdhesion
type: Class
subclass of: CellNonCellAdhesion
date: 24 Aug. 2011
definition: CellInterstitialMatrixAdhesion is a CellNonCellAdhesion involving the adhesive interaction between a cell and the interstitial matrix. Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact.
creator: jps

CellInterstitialMatrixContact
type: Class
subclass of: CellNonCellContact
date: 24 Aug. 2011
definition: CellInterstitialMatrixContact is a CellNonCellContact involving the direct contact between a cell and a component of the interstitial matrix. Note that contact is a distinct process from adhesion (see CBO:CellAdhesion).
creator: jps

CellMembrane
type: Class
subclass of: CellBorder
disjoint with: CellWall
date: 24 Aug. 2011
creator: jps
definition: CellMembrane is a CBO:CellBorder consisting of (MeSH) the lipid- and protein-containing, selectively permeable membrane that surrounds the Cytoplasm in prokaryotic and eukaryotic Cells.

CellMembraneLocalStructure
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
creator: jps
see also: isA subclass of: BFO:snap:specifically_dependent_continuant
definition: A CellMembraneLocalStructure is a CBO class that includes the various topological patterns found, often transiently, on Cell walls. For example, filopodia. MeSH: Specialized structures of the Cell that extend the Cell membrane and project out from the Cell surface. GO: A prolongation or process extending from a Cell, e.g. a flagellum or axon.

CellMembranePart
type: Class
subclass of: CellPart
date: 24 Aug. 2011
creator: jps
see also: isA subclass of: BFO:snap:specifically_dependent_continuant
definition: CellMembranePart is a CBO:CellPart class that includes the various proteinaceous parts commonly found on a Cell membrane. Note that this class does not include topological features such as axons or filopodia. GO: plasma membrane part; Any constituent part of the plasma membrane, the membrane surrounding a Cell that separates the Cell from its external environment.

CellMotility
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
definition: CellMotility is a CellMovement involving an Energy dependent self-propelled displacement of a cell's center of mass or center of volume. GO: Any process involved in the controlled self-propelled Movement of a cell that results in translocation of the cell from one place to another.
creator: jps

CellMovement
type: Class
subclass of: GeometricalCellProcess
date: 24 Aug. 2011
creator: jps
definition: CellMovement is a GeometricalCellProcess that results in a change in the location or orientation of a cell. Note that this definition is incompatible with GO:0006928 cell Movement.

CellNonCellAdhesion
type: Class
subclass of: CellAdhesion
date: 24 Aug. 2011
definition: CellNonCellAdhesion is a CellAdhesion involving the adhesive interaction between a cell and another physical object where the second object is not itself a cell. Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact.
creator: jps

CellNonCellContact
type: Class
subclass of: CellContact
date: 24 Aug. 2011
creator: jps
definition: CellNonCellContact is a CellContact involving direct physical contact between a cell and another physical object where the second object is not itself a cell. Note that contact is a distinct process from adhesion (see CBO:CellAdhesion).

CellOrientationChange
type: Class
subclass of: GeometricalCellProcess
date: 24 Aug. 2011
definition: CellOrientationChange is a GeometricalCellProcess that changes the relationship between the cell's internal axis and the environments axis. For example, a change in the alignment between a cell's apical-basal axis and the organismal animal-vegetal axis.
creator: jps

CellPart
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
definition: CellPart is a CBO class including any constituent part of a Cell.
creator: jps
see also: isA subclass of: BFO:snap:specifically_dependent_continuant

CellProcess
type: Class
subclass of: CBO_Process
date: 24 Aug. 2011
see also: isA subclass of: BFO:span:process
creator: jps
definition: CellProcess is a CBO:Process (snap:process) describing a process characteristic of a CBO:Cell.

CellRegion
type: Class
subclass of: GeometricalEntity
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap:fiat_object_part
definition: CellRegion is a CBL:GeometricalEntity class that includes descriptors for various fiat regions. (A fiat region generally does not have clear boundaries.)
creator: jps

CellRelatedTransport
type: Class
subclass of: CellEnvironmentProcess
date: 24 Aug. 2011
definition: CellRelatedTransport is a CellEnvironmentProcess involving Movement of an entity across the cell's membrane. The moving entity becomes contained in the cell but is not partOf the cell. CellRelatedTransport includes active and selective processes. For passive (e.g., diffusive) Transport see CBO:BarrierCrossing.
creator: jps

CellRotation
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
creator: jps
definition: CellRotation is a CellMovement resulting in a Rotation of a cell about it center (center of mass or center of Volume).

CellShapeChange
type: Class
subclass of: GeometricalCellProcess
date: 24 Aug. 2011
creator: jps
definition: CellShapeChange is a GeometricalCellProcess that results in a change in Shape of the bounding surface of the cell defined by the cell wall or cell membrane.

CellState
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
definition: An CellState is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the biological state of a cell at a particular time. CellState includes concepts such as "quiescent", "growing", "necrotic" (dying) etc.
see also: isA subclass of: BFO:snap:quality
creator: jps

CellVolumeChange
type: Class
subclass of: GeometricalCellProcess
date: 24 Aug. 2011
creator: jps
definition: deprecated

CellWall
type: Class
subclass of: CellBorder
date: 24 Aug. 2011
creator: jps
definition: CellWall is a CBO:CellBorder consisting of (MeSH) the outermost layer of a Cell in most PLANTS; BACTERIA; FUNGI; and ALGAE. The Cell wall is usually a rigid structure that lies external to the Cell MEMBRANE, and provides a protective barrier against physical or chemical agents. (GO) The rigid or semi-rigid envelope lying outside the Cell membrane of plant, fungal, and most prokaryotic Cells, maintaining their Shape and protecting them from osmotic lysis. In plants it is made of Cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan. It is unclear if CellWall is a CellPart of if CellWall should be classified as a type of extracellular matrix. Is a particular portion of CellWall "owned" by a single cell or is it "owned" and maintained by the two or more cells on either side?

CellularChemicalProcess
type: Class
subclass of: CellEnvironmentProcess
date: 24 Aug. 2011
creator: jps
definition: CellularChemicalProcess is a CellEnvironmentProcess in which an environmental (local) chemical (or chemical gradient) changes a process or quality of a cell.

CellularElectricalProcess
type: Class
subclass of: CellEnvironmentProcess
date: 24 Aug. 2011
definition: CellularElectricalProcess is a CellEnvironmentProcess that results in a change in an electrical quality of the cell.
creator: jps

CellularKineticProcess
type: Class
subclass of: CellularPropertyProcess
date: 24 Aug. 2011
creator: jps
definition: CellularKineticProcess is a CellularPropertyProcess that changes a kinetic dependence.

CellularMechanicalProcess
type: Class
subclass of: CellularPropertyProcess
date: 24 Aug. 2011
definition: CellularMechanicalProcess is a CellularPropertyProcess that results in a change in a mechanical property of a cell.
creator: jps

CellularPropertyProcess
type: Class
subclass of: CellProcess
date: 24 Aug. 2011
creator: jps
definition: CellularPropertyProcess is a CellProcess that results in a change in a property of a cell. For example, CellMovement changes the property of location.

CenterModelPlatform
type: Class
subclass of: ComputationalPlatformQuality
date: 23 Jul. 2012
definition: CenterModelPlatform is a CBO:ComputationalPlatformQuality class for computational platforms which describe a cell (or other CBO:CorpuscularEntity) primarily as the center point of an object. The extent of the object are described by other characteristics and often the complete extent of an object can only be described by reference to other (adjacent) objects. Unlike DiscreteModelPlatform a CenterModelPlatform does not impose a regular grid on the location of objects and does not contain pixels/voxels.
creator: jps

CenterOfMass
type: Class
subclass of: Location
disjoint with: CenterOfVolume
date: 24 Aug. 2011
definition: The CenterOfMass is a CBO:position that describes the center of Mass of a spatially extended object at a particular time. The CenterOfMass inherits the CBO:Dimensionality of the particular object or CBO:Dimensionality of the CBO:System object. See also CenterOfVolume which may be, for practical purposes, identical.
creator: jps

CenterOfVolume
type: Class
subclass of: Location
date: 24 Aug. 2011
creator: jps
definition: The CenterOfVolume is a CBO:position that describes the center of Volume of a spatially extended object at a particular time. The CenterOfVolume inherits the CBO:Dimensionality of the particular object or CBO:Dimensionality of the CBO:System object. See also CenterOfMass which may be, for practical purposes, identical.

Charge
type: Class
subclass of: ElectricalProperty
date: 24 Aug. 2011
creator: jps
definition: Charge is a CBO:ElectricalProperty describing the overall electrical charge of an entitiy. PATO: A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons.
is defined by: urn:miriam:opb:'Charge amount'

ChemicalAffinity
type: Class
subclass of: ChemicalProperty
date: 24 Aug. 2011
creator: jps

ChemicalDensity
type: Class
subclass of: ChemicalProperty
date: 24 Aug. 2011
creator: jps

ChemicalLocalization
type: Class
subclass of: ChemicalProperty
date: 24 Aug. 2011
creator: jps

ChemicalPattern
type: Class
subclass of: ChemicalProperty
date: 24 Aug. 2011
creator: jps

ChemicalPatternGradient
type: Class
subclass of: ChemicalPattern
date: 24 Aug. 2011
creator: jps

ChemicalProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: ChemicalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the physical behavior of chemicals ChemicalProperty(ies) are intrinsic to the object.
creator: jps

Chemotaxis
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
definition: Chemotaxis is a CellMovement in which an Energy dependent process gives a directed Movement of the cell relative to an external gradient. GO: The directed Movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive Chemotaxis) or towards a lower concentration (negative Chemotaxis).
creator: jps

Compucell3D
type: Class
subclass of: ComputationalPlatform
date: 23 Jul. 2012
definition: Compucell3D is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.Compucell3D.org
creator: jps

ComputationalPlatform
type: Class
subclass of: SystemQuality
definition: ComputationalPlatform is a SystemQuality class describing a particular computational platform.
creator: jps
date: 23 Jul. 2012

ComputationalPlatformQuality
type: Class
subclass of: CBO_Object
definition: ComputationalPlatformQuality is a CBO class describing qualities of computational platforms for preforming multicell modeling.
creator: jps
date: 27 Jul. 2012

ContactSurfaceArea
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
definition: ContactSurfaceArea is a CBO:GeometricalProperty describing the scalar value of two objects contact surface area at a particular instant in time.
creator: jps

DiscreteModelPlatform
type: Class
subclass of: ComputationalPlatformQuality
creator: jps
definition: DiscreteModelPlatform is a CBO:ComputationalPlatformQuality class for computational platforms which describe a cell (or other CBO:CorpuscularEntity) in a discretized coordinate system (a regular grid) of voxels or pixels. Unlike DiscreteModelPlatform a
date: 23 Jul. 2012

ContinuousEntity
type: Class
subclass of: PhysicalEntityType
date: 24 Aug. 2011
creator: jps
definition: A ContinuousEntity is a PhysicalEntityType (BFO:snap:object) that has a particular extent at a particular time but which also may extend beyond the limits of the view or model. ContinuousEntities are spatially exclusive and do not overlap. Unlike a CorpuscularEntity, a ContinuousEntity is geometrically divisible without a fundamental change in characteristics, qualities or identity. For example, a portion of a basement membrane, Cell wall, or medium (e.g., water).

ContinuousExtent
type: Class
subclass of: ExtentGeometrical
disjoint with: DiscreteExtent
date: 24 Aug. 2011
definition: ContinousExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionaly sensitive quantity in an infinitely finely grained coordinate System. Compare with DiscreteExtent.
creator: jps

Contraction
type: Class
subclass of: VolumeChange
disjoint with: Expansion
date: 24 Aug. 2011
creator: jps
definition: Contraction is a VolumeChange resulting in a decrease in Volume occupied by an object.

CorpuscularEntity
type: Class
subclass of: PhysicalEntityType
date: 24 Aug. 2011
definition: A CorpuscularEntity is a PhysicalEntityType (BFO:snap:object) that has a particular Location and Volume at a particular time. Corpuscular_entities are spatially exclusive and do not overlap. Furthermore, a CorpuscularEntity is not divisible without a fundamental change in characteristics, qualities or identity. For example, an individual Cell.
creator: jps

Creation
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
definition: Creation is a FundamentalPhysicalProcess resulting in the Creation of a new object. Often this will involve an increase in count of an object.
creator: jps

Cytoplasm
type: Class
subclass of: CellPart
date: 24 Aug. 2011
definition: FMA: Cell component which consists of cytosol and Cytoplasmic organelles.
creator: jps

Deletion
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
creator: jps
definition: Deletion is a FundamentalPhysicalProcess resulting in the Deletion of an object. Often this will involve a decrease in count of an object.

DiffuseEntity
type: Class
subclass of: PhysicalEntityType
date: 24 Aug. 2011
definition: A DiffuseEntity is a PhysicalEntityType (BFO:snap:object) that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a DiffuseEntity may be described as having a position dependent concentration or density function. Unlike a CorpuscularEntity, a ContinuousEntity is geometrically divisible without a fundamental change in characteristics or identity. A DiffuseEntity may be restricted to exist along with another PhysicalEntityType, such as the case of a cell membrane bound receptor (DiffuseEntity) distributed on the cell membrane of a particular cell (a CorpuscularEntity). For example, a portion of a chemical field distributed across the interstitial space of a region.
creator: jps

Diffusion
type: Class
subclass of: Movement
date: 24 Aug. 2011
definition: Diffusion is a Movement arising from random motion, either thermal or motive (cf. motility), of an object.
creator: jps

Dimension1d
type: Class
subclass of: Dimensionality
date: 24 Aug. 2011
is defined by: urn:miriam:opb:'One dimensional spatial coordinate System'
definition: Dimension1d is a CBO:Dimensionality quality for a System with one spatial dimension.
creator: jps

Dimension2d
type: Class
subclass of: Dimensionality
date: 24 Aug. 2011
creator: jps
definition: Dimension2d is a CBO:Dimensionality quality for a System with two spatial dimensions.
is defined by: urn:miriam:opb:'Two dimensional spatial coordinate System'

Dimension3d
type: Class
subclass of: Dimensionality
date: 24 Aug. 2011
definition: Dimension3d is a CBO:Dimensionality quality for a System with three spatial dimensions.
creator: jps
is defined by: urn:miriam:opb:'Three dimensional spatial coordinate System'

Dimensionality
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
definition: Dimensionality is a CBO:GeometricalProperty that describes the number of independent spatial axis in a model or System.
creator: jps
is defined by: urn:miriam:opb:'Spatial coordinate System'

DiscreteExtent
type: Class
subclass of: ExtentGeometrical
date: 24 Aug. 2011
creator: jps
definition: DiscreteExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionally sensitive quantity in a finitely grained coordinate System. Compare with ContinuousExtent.

Divisible
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: A Divisible quality is a CBO:PhysicalObjectQuality for objects which can be divided, conceptually or for ease of representation, without a fundamental change in the character or qualites of the object. For example, the fluid (medium, CBO:ExtraCellularFluid) surronding a cell. Physical objects with the Divisible quality can often be treated as portionsOf, the individual protions behave as does the bulk object with only changes in, for example, the location, extent and identifier for the portionOfs.
creator: jps

Dorsal
type: Class
subclass of: OrganismalRegion
disjoint with: Ventral
date: 24 Aug. 2011
creator: jps
definition: Dorsal is a CBO:OrganismalRegion characteristic of the back of an object relative to the body it is contained in. For example Dorsal fin.

ElectricalProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: ElectricalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the electrical qualities of objects. ElectricalProperty are intrinsic to the object.
creator: jps
is defined by: urn:miriam:opb:'Electrical entity'

ElectromechanicalField
type: Class
subclass of: Field
date: 1 Dec. 2012
definition: need def
creator: jps

Energy
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: An Energy is a CBO:PhysicalObjectQuality is the Energy of the object for which it is a quality.
is defined by: urn:miriam:opb:'Energy amount'
creator: jps

EnergyFunction
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap:quality
creator: jps
definition: An EnergyFunction is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the mathematical form used to define a particular EnergyQuality.

EnergyQuality
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
definition: A EnergyQuality is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the energy qualities of physical objects. For example, the energy of a particular cell, at a particular cell in a particular environment.
creator: jps
see also: isA subclass of: BFO:snap:quality

ExistentialCellProcesses
type: Class
subclass of: CellProcess
date: 24 Aug. 2011
definition: ExistentialCellProcesses is a CellProcess that is assumed, without formal proof, to be a process of a cell.
creator: jps

Expansion
type: Class
subclass of: VolumeChange
date: 24 Aug. 2011
creator: jps
definition: Expansion is a VolumeChange resulting in an increase in Volume occupied by an object.

ExtentGeometrical
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
definition: ExtentGeometrical is a CBO:GeometricalProperty that describes the basic granularity of the coordinate System.
creator: jps

ExtraCellularFluid
type: Class
subclass of: BioEntityType
date: 24 Aug. 2011
creator: jps
definition: ExtracellularFluid is a CBO:BioEntityType for the fluids that exist outsides of cells. MeSH: The fluid of the body that is outside of Cells. It is the external environment for the Cells.
see also: isA subclass of: BFO:snap:object

ExtraCellularMatrix
type: Class
subclass of: BioEntityType
disjoint with: Molecule
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap:object
definition: ExtraCellularMatrix is a CBO:BioEntityType that includes all physical entities that are discrete (though possible of considerable extent) that are distinct from Cell and media. The ExtraCellularMatrix provides support and restricts movement of objects.
creator: jps

ExtracellularMatrixProcess
type: Class
subclass of: CBO_Process
date: 24 Aug. 2011
see also: isA subclass of: BFO:span:process
definition: ExtracellularMatrixProcess is a CBO:Process involving a change in the qualities, or quantity of extracellular matrix and its components.
creator: jps

Field
type: Class
subclass of: CBO_Object
date: 19 Jul. 2012
creator: jps
definition: A Field is a CBO class for the description of entities that span a particular extent at a particular time but are not spatially exclusive and may, and generally do, overlap with other PhysicalEntityTypes at a particular time. In addition, a Field may be described as having a position dependent concentration, density or value function. Unlike a CBO:Cell, a Field is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) A Field may be restricted to a particular region or part of a physical object (CBO:PhysicalEntityType:CorpuscularEntity or CBO:PhysicalEntityType:ContinousEntity), such as the case of an electromagnetic field. Or, a portion of a chemical field distributed across the interstitial space of a region.

FieldProcess
type: Class
subclass of: CBO_Process
creator: jps
definition: FieldProcess is a CBO:Process (snap:process) describing a process characteristic of a CBO:Field.
date: 11/8/2012

FieldQuality
type: Class
subclass of: CBO_Object
date: 11/8/2012
definition: jps
definition: A FieldQuality is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the qualities of field objects. BFO uses QUALITY, OPB uses PROPERTY. For example, quality is a characteristic of a physical object such as Location, Volume, Energy, type etc.

Fill
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
creator: jps
definition: A Fill quality is a CBO:PhysicalObjectQuality for objects that can be understood to fill all available space. An object with the Fill quality also has the SpatialExclusive quality. Examples include the medium (CBO:ExtraCellularFluid) or the air inside the lungs.

Filopodium
type: Class
subclass of: CellMembraneLocalStructure
date: 24 Aug. 2011
creator: jps
definition: A Filopodium is a CBO:CellMembraneLocalStructure and is a thin, stiff Protrusion extended by the leading edge of a motile Cell such as a crawling fibroblast or amoeba, or an axonal growth cone. GO: 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. MeSH: A dynamic actin-rich extension of the surface of an animal Cell used for locomotion or prehension of food. AKA: Axopodia, Filopodia, Lamellipodia, Lobopodia, Pseudopodium, Reticulopodia

FirstOrderRate
type: Class
subclass of: RateFunction
date: 24 Aug. 2011
creator: jps
definition: A FirstOrderRate is a CBO:RateFunction describing the mathematical form used to define a first order rate of change of a quality with respect to time. For quality n; dn/dt=k*n, where k is the rate constant.

Fission
type: Class
subclass of: CellDivision
date: 24 Aug. 2011
creator: jps
definition: Fission is an ExistentialCellProcess of bacterial cells resulting in the Creation of two daughter cells from a single parent cell. Fission is specific to bacterial cells.

FundamentalPhysicalProcess
type: Class
subclass of: CBO_Process
date: 24 Aug. 2011
definition: A FundamentalPhysicalProcess is a CBO:Process (snap:Process) that changes a quality or characteristic of an object.
creator: jps
see also: isA subclass of: BFO:span:process

GapJunction
type: Class
subclass of: CellMembranePart
date: 24 Aug. 2011
creator: jps
definition: GapJunction is a CBO:CellMembranePart that acts as a connection between, and adhesion mediator, between two Cells. In addition, the gap allows for the transfer of small Molecules (hence information) between two adjacent Cells. MeSH: Connections between Cells which allow passage of small Molecules and electric current. Gap junctions were first described anatomically as regions of close apposition between Cells with a narrow (1-2 nm) gap between Cell membranes. The variety in the properties of gap junctions is reflected in the number of CONNEXINS, the family of proteins which form the junctions.

GenerationalAge
type: Class
subclass of: Age
disjoint with: TemporalAge
date: 24 Aug. 2011
definition: GenerationalAge is a CBO:Age that describes the number of generations that have passed for a particular Cell within its lineage. For example, a mesenchymal Cell derived from a stem cell would have GenerationalAge equal to one. When that mesenchymal cell divides both daughter cells would have GenerationalAge of 2. GO:0001302 replicative cell aging, namespace: biological_process def: The process associated with progression of the Cell from its inception to the end of its lifespan that occurs as the Cell continues cycles of growth and division.
creator: jps

GeometricalCellProcess
type: Class
subclass of: CellularPropertyProcess
date: 24 Aug. 2011
definition: GeometricalCellProcess is a CellularPropertyProcess that results in a change in the geometry of a cell.
creator: jps

GeometricalEntity
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
creator: jps
definition: GeometricalEntity is a CBO class for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions.
see also: isA subclass of: BFO:snap:independent_continuant

GeometricalProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
creator: jps
definition: GeometricalProperty are CBO:physical_object_qualities that define the geometrical qualities of an object at a particular time. This includes the Shape, extents, position etc. of an abject.

GradientTexture
type: Class
subclass of: Texture
date: 24 Aug. 2011
definition: GradientTexture is a CBO:Texture consisting of a Texture description that varies smoothly across one or more dimensions.
creator: jps

Hamiltonian
type: Class
subclass of: EnergyQuality
date: 24 Aug. 2011
creator: jps
definition: A Hamiltonian is a CBO:PhysicalObjectQuality is the total energy associated with a physical object. The Hamiltonian is the algebraic sum of the energies associated with the physical object.

Haptotaxis
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
definition: Haptotaxis is a CellMovement in which an Energy dependent process gives a directed Movement of the cell relative to an external matrix such as interstitial fibrils or a basement membrane.
creator: jps

HarmonicEnergy
type: Class
subclass of: EnergyFunction
date: 24 Aug. 2011
creator: jps
definition: A HarmonicEnergy function is a CBO:EnergyFunction describing the mathematical form used to define a harmonic relationship used to calculate a particular energyQuality. The equation is of the form E = k(target value - current value)^2, where k is a scaling canstant and target value and current value are qualities of a particular physical object. This HarmonicEnergy function is Hooke's Law in the energy domain.

InterentityExport
type: Class
subclass of: InterentityTransport
disjoint with: InterentityImport
date: 24 Aug. 2011
definition: InterentityExport is an InterentityTransport of an object across a bona fide boundary in which the Transporting entity is moving out of another object. For example, from inside of a bone to the outside of the bone.
creator: jps

InterentityImport
type: Class
subclass of: InterentityTransport
date: 24 Aug. 2011
creator: jps
definition: InterentityImport is an InterentityTransport of an object across a bona fide boundary in which the Transporting entity is moving into (containedIn) another object. For example, from the space outside of a bone to within the bone.

InterentityTransport
type: Class
subclass of: Transport
disjoint with: IntraentityTransport
date: 24 Aug. 2011
see also: isA subclass of: BFO:span:process
creator: jps
definition: InterentityTransport is a Transport of an object across a bona fide boundary. For example, from within a bone to the space outside the bone.

InterstitialMatrix
type: Class
subclass of: ExtraCellularMatrix
date: 24 Aug. 2011
definition: GO: A type of extracellular matrix found in interstitial connective tissue, characterized by the presence of fibronectins, proteoglycans, and types I, III, V, VI, VII and XII collagens.
creator: jps

InterstitialMatrixChange
type: Class
subclass of: InterstitialMatrixProcess
date: 24 Aug. 2011
definition: InterstitialMatrixChange is an InterstitialMatrixProcess involving a change in the components or characteristics of the interstitial matrix components.
creator: jps

InterstitialMatrixCreation
type: Class
subclass of: InterstitialMatrixProcess
date: 24 Aug. 2011
definition: InterstitialMatrixCreation is an InterstitialMatrixProcess involving an increase in the quantity of the interstitial matrix and its components.
creator: jps

InterstitialMatrixDeletion
type: Class
subclass of: InterstitialMatrixProcess
date: 24 Aug. 2011
definition: InterstitialMatrixDeletion is an InterstitialMatrixProcess involving a decrease in the quantity of the interstitial matrix and its components.
creator: jps

InterstitialMatrixProcess
type: Class
subclass of: ExtracellularMatrixProcess
date: 24 Aug. 2011
definition: InterstitialMatrixProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of interstitial matrix and its components.
creator: jps

IntraentityTransport
type: Class
subclass of: Transport
date: 24 Aug. 2011
creator: jps
definition: IntraentityTransport is a Transport of an entity from one place within a containing object to another place within the same object. For example, Movement of an mRNA from the nucleus to the cytosol.

IonChannel
type: Class
subclass of: CellMembranePart
date: 24 Aug. 2011
creator: jps
definition: An IonChannel is a CBO:CellMembranePart that is a membrane bound protein that transfers ions across the Cell membrane against the natural diffusion gradient direction or transfers an ion across a membrane that would normally be impervious to the ion. MeSH: Membrane proteins whose primary function is to facilitate the transport of Molecules across a biological membrane. Included in this broad category are proteins involved in active transport ( BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS. GO: Enables the transport of a solute across a membrane via a narrow pore channel that opens in response to a particular stimulus.

IsApoptotic
type: Class
subclass of: CellState
date: 24 Aug. 2011
creator: jps
definition: IsApoptotic is a CBO:CellState describing a biological state of apoptotic (programmed) dying of a cell at a particular time. This is a boolean (true/false) concept.

IsDebris
type: Class
subclass of: CellState
date: 24 Aug. 2011
creator: jps
definition: IsDebris is a CBO:CellState describing a biologicaly dead cell at a particular time. IsDebris is used to represent the material left over after a cell dies. This is a boolean (true/false) concept.

IsGrowing
type: Class
subclass of: CellState
date: 24 Aug. 2011
definition: IsGrowing is a CBO:CellState describing a biological state of a cell that is growing at a particular time. This is a boolean (true/false) concept.
creator: jps

IsHypoxic
type: Class
subclass of: CellState
date: 24 Aug. 2011
definition: IsHypoxic is a CBO:CellState describing a biological state of oxygen deprivation of a cell at a particular time. This is a boolean (true/false) concept. Also known as anoxic or anoxia.
creator: jps

IsNecrotic
type: Class
subclass of: CellState
date: 24 Aug. 2011
definition: IsNerotic is a CBO:CellState describing a biological state of dying of a cell at a particular time. This is a boolean (true/false) concept. See also IsApoptotic.
creator: jps

IsQuiescent
type: Class
subclass of: CellState
date: 24 Aug. 2011
creator: jps
definition: IsQuiescent is a CBO:CellState describing a biological state of resting (minimal growth or other characteristic cellular processing) of a cell at a particular time. This is a boolean (true/false) concept.

Isotropy
type: Class
subclass of: BodyShape
date: 24 Aug. 2011
creator: jps
definition: Isotropy is a GeometricalProperty describing the lack of a directionality of a directionally dependent quality of the object. This is the opposite of CBO:Anisotropy.

KineticProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
is defined by: urn:miriam:opb:'Kinetic manifestation'
creator: jps
definition: KineticProperty is a CBO:PhysicalObjectQuality describing a kinetic characteristic of an object.

LJ_6_12Energy
type: Class
subclass of: EnergyFunction
date: 24 Aug. 2011
creator: jps
definition: A LJ_6_12Energy function is a CBO:EnergyFunction describing the mathematical form used to define a Leonard-Jones energy potential used to calculate a particular energyQuality. The equation is of the form E = e((rm/r)^12 - 2(rm/r)^6), where e is the depth of the potential well, rm is the value of the quality at which the potential is a mimimum and r is the current value of the quality.

LateralPart
type: Class
subclass of: CellRegion
date: 24 Aug. 2011
creator: jps
definition: LateralPart is a CBO:CellRegion that is between the CBO:BasalPart and CBO:LateralPart.

LinearEnergy
type: Class
subclass of: EnergyFunction
date: 24 Aug. 2011
definition: A LinearEnergy function is a CBO:EnergyFunction describing the mathematical form used to define a linear relationship used to calculate a particular energyQuality. The equation is of the form E = mX + b, where m is a scaling constant, X is the value quality of a particular physical object and b is an offset. A LinearEnergy fucntion is often used to describe the energy of adhesions between, for example, two cells. For cell-cell adhesion m might represent the cell type(s) specific adhesion energy and X the contact area between the two cells.
creator: jps

Location
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
creator: jps
definition: Location is a GeometricalProperty of a mathematical point. Depending on the CBO:Dimensionality of the System this may have one, two or three dataProperty values. AKA: position

Mass
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
creator: jps
definition: Mass is a CBO:PhysicalObjectQuality describing the Mass of the object.
is defined by: urn:miriam:opb:'Discrete solid Mass'

MechanicalProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
creator: jps
definition: MechanicalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the physical behavior of objects. MechanicalProperty(ies) are intrinsic to the object.

MedialPart
type: Class
subclass of: CellRegion
date: 24 Aug. 2011
definition: MedialPart is a CBO:CellRegion located near the center of the Cell.
creator: jps

Meiosis
type: Class
subclass of: CellDivision
date: 24 Aug. 2011
definition: Meiosis is a CellDivision specific to meiotic cells. GO: A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations.
creator: jps

MembraneReceptor
type: Class
subclass of: CellMembranePart
date: 24 Aug. 2011
creator: jps
definition: MembraneReceptor is a CBO:CellMembranePart that is a protein embedded in the CellMembrane that interacts with extracellular Molecules. Binding (or occupancy) of the receptor results in a signal to the Cell. A protein Molecule (or assembly of proteins) that is permanently attached or firmly anchored in the plasma membrane via its hydrophobic domains interacting with the membrane phospholipids which can transfer information from the Cell exterior to its interior.

MinimizationAcceptanceFunction
type: Class
subclass of: AcceptanceFunction
date: 24 Aug. 2011
creator: jps
definition: A MinimizationAcceptanceFunction is a CBO:EnergyFunction:AcceptanceFunction describing an acceptance criteria that requires that the energy of the new state is less than the energy of the previous state.

Mitosis
type: Class
subclass of: CellDivision
date: 24 Aug. 2011
creator: jps
definition: Mitosis is a CellDivision resulting in the Creation of two daughter cells from a single parent cell. Mitosis is specific to eukaryotic cells. GO: A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, Mitosis produces two daughter nuclei whose chromosome complement is identical to that of the parent cell.

MolecularField
type: Class
subclass of: Field
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap:object
definition: A MolecularField is a CBO:Field class for the description of moleules (or sets of molecules) that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a MolecularField may be described as having a position dependent concentration or density function. Unlike a CBO:Cell, a MolecularField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) A MolecularField may be restricted to a particular region or part of a physical object (CBO:PhysicalEntityType:CorpuscularEntity or CBO:PhysicalEntityType:ContinousEntity), such as the case of a cell membrane bound receptor molecule distributed on the cell membrane of a particular cell (a CorpuscularEntity). Or, a portion of a chemical field distributed across the interstitial space of a region.
creator: jps

MolecularTargeting
type: Class
subclass of: IntraentityTransport
date: 24 Aug. 2011
definition: MolecularTargeting is an IntraentityTransport in which a molecule is actively directed from one place in a cell to another.
creator: jps

Molecule
type: Class
subclass of: BioEntityType
date: 24 Aug. 2011
definition: Molecule is a CBO:BioEntityType class OPB: ...that is a polyatomic entity.
see also: isA subclass of: BFO:snap:object
creator: jps

MoleculeBarrierCrossing
type: Class
subclass of: MoleculeProcess
date: 24 Aug. 2011
definition: MoleculeBarrierCrossing is a MoleculeProcess describing the transfer of a molecule across a bona fide boundary such as a basement membrane or a cell wall.
creator: jps

MoleculeChange
type: Class
subclass of: MoleculeProcess
date: 24 Aug. 2011
creator: jps
definition: MoleculeChange is a MoleculeProcess that results in a phenotypic change in the molecule. For example, changes in the ionization state of an acid.

MoleculeCreation
type: Class
subclass of: MoleculeProcess
date: 24 Aug. 2011
creator: jps
definition: MoleculeCreation is a MoleculeProcess that results in the Creation of a new molecule or an increase in a molecule's concentration.

MoleculeDeletion
type: Class
subclass of: MoleculeProcess
date: 24 Aug. 2011
definition: MoleculeDeletion is a MoleculeProcess that results in the Deletion of a molecule, or a decrease in a molecule's concentration.
creator: jps

MoleculeDiffusion
type: Class
subclass of: MoleculeProcess
date: 24 Aug. 2011
definition: MoleculeDiffusion is a MoleculeProcess in which a molecule passively diffuses through the medium, a cell cytosol of the interstitial space. For Diffusion across a bone fide boundary see CBO:MoleculeBarrierCrossing.
creator: jps
see also: isA subclass of: BFO:span:fiat_process_part

MoleculeMoleculeAdhesion
type: Class
subclass of: MoleculeProcess
date: 24 Aug. 2011
definition: MoleculeMoleculeAdhesion is a MoleculeProcess that describes the interaction Energy (or interaction equilibrium) between a pair of molecules. The molecules may be of the same or different types. One or both of the molecules may be associated with another object. For example, the adhesive interaction between a pair of cellular adhesion molecules each located (embedded, bound) to the cell membranes of different cells.
creator: jps

MoleculeProcess
type: Class
subclass of: CBO_Process
date: 24 Aug. 2011
definition: MoleculeProcess is a CBO:Process that involves a molecule.
creator: jps
see also: isA subclass of: BFO:span:process

Movement
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
definition: Movement is a FundamentalPhysicalProcess resulting in the change in location or Shape of a physical object.
see also: isA subclass of: BFO:span:fiat_process_part
creator: jps

MovementField
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: MovementField is a CBO:PhysicalObjectProperty describing the movement of a physical object or aggregate of physical objects. For example, blood flow through a blood vessel is a MovementField capable of carrying physical objects such as cells.
creator: jps

Necrosis
type: Class
subclass of: CellDeath
date: 24 Aug. 2011
creator: jps
definition: Necrosis is a CellDeath caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin.

Nucleus
type: Class
subclass of: CellPart
date: 24 Aug. 2011
creator: jps
definition: GO: A membrane-bounded organelle of eukaryotic Cells in which chromosomes are housed and replicated. In most Cells, the Nucleus contains all of the Cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized Cell types, RNA metabolism or DNA replication may be absent.

OpenAlea
type: Class
subclass of: ComputationalPlatform
date: 23 Jul. 2012
creator: jps
definition: OpenAlea is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. OpenALea is targeted to plant modeling. See http://openalea.gforge.inria.fr/dokuwiki/doku.php?id=openalea

OpenSourceModelPlatform
type: Class
subclass of: ComputationalPlatformQuality
definition: OpenSourceModelPlatform is a CBO:ComputationalPlatformQuality class for compuational platforms which are open source.
date: 23 Jul. 2012
creator: jps

OrganismalRegion
type: Class
subclass of: GeometricalEntity
date: 24 Aug. 2011
definition: OrganismalRegion is a CBO:GeometricalEntity class for regions of an animal.
see also: isA subclass of: BFO:snap:fiat_object_part
creator: jps

Orientation
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
creator: jps
definition: Orientation is a CBO:GeometricalProperty describing the directionality of a quality of an object. The directionality of the Orientation may be described in terms of the CBO:System axis or Isotropy of the objects local environment or by the Isotropy of the object itself.

OtherComputationalPlatform
type: Class
subclass of: ComputationalPlatform
definition: OtherComputationalPlatform is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. This is a "cover-all" class for platforms which do not have a specific name.
date: 23 Jul. 2012
creator: jps

OtherPublicationReference
type: Class
subclass of: ComputationalPlatformQuality
creator: jps
definition: OtherPublicationReference is a CBO:ComputationalPlatformQuality class for computational platforms referenced only by a literature citation.
date: 23 Jul. 2012

PatternTexture
type: Class
subclass of: Texture
date: 24 Aug. 2011
creator: jps
definition: PatternTexture is a CBO:Texture consisting of a positionally repetitive Texture description.

PhenotypicChange
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
definition: PhenotypicChange is a FundamentalPhysicalProcess resulting in the change of type of an object. PhenotypicChange applies to both the normally defined phenotypic change of a cell and also includes molecular changes such as ionization.
creator: jps

PhysicalEntityType
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
definition: A PhysicalEntityType is a CBO:Class (BFO:snap:quality) class of physical objects. For example, a Cell, a basement membrane of a diffusible Molecule.
creator: jps
see also: isA subclass of: BFO:snap:quality

PhysicalObjectQuality
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
creator: jps
see also: isA subclass of: BFO:snap:quality
definition: A PhysicalObjectQuality is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the qualities of physical objects. BFO uses QUALITY, OPB uses PROPERTY. For example, quality is a characteristic of a physical object such as Location, Volume, Energy, type etc.

PoissonRatio
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
definition: PoissonRatio is a CBO:MechanicalProperty that describes the ratio, when an object is stretched, of the contraction or transverse strain (perpendicular to the applied load), to the extension or axial strain (in the direction of the applied load).
creator: jps

PressureMechanical
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
creator: jps
definition: PressureMechanical is a CBO:MechanicalProperty describing the barometric pressure of an object or Location in space.

Protrusion
type: Class
subclass of: Shape
date: 24 Aug. 2011
definition: Protrusion is a GeometricalProperty describing an extension from an otherwise simpler CBO:BodyShape description. For example, a transient pseudopodia or a persistent neuronal axon.
creator: jps

Pseudopodium
type: Class
subclass of: CellMembraneLocalStructure
date: 24 Aug. 2011
definition: A Pseudopodium is a CBO:CellMembraneLocalStructure characterized by a transient extension of the Cell wall. MeSH: A dynamic actin-rich extension of the surface of an animal Cell used for locomotion or prehension of food. GO: A temporary Protrusion or retractile process of a Cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding. AKA: pseudopodia
creator: jps

Pump
type: Class
subclass of: CellMembranePart
date: 24 Aug. 2011
definition: A Pump is a CBO:CellMembranePart that is a membrane bound protein that transfers ions and Molecules across the Cell membrane against the natural diffusion gradient direction. MeSH: Membrane proteins whose primary function is to facilitate the transport of Molecules across a biological membrane. Included in this broad category are proteins involved in active transport ( BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS.
is defined by: MeSH: D12.776.157.530
is defined by: MeSH:'Membrane Transport Proteins'
creator: jps

Random
type: Class
subclass of: StatisticalProperty
date: 24 Aug. 2011
creator: jps
definition: Random is a CBO:StatisticalProperty class that describes a quality of randomness to an object or process.

RateFunction
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
creator: jps
definition: An RateFunction is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the mathematical form used to define a changes in a particular Quality as a function of time.
see also: isA subclass of: BFO:snap:quality

Rotation
type: Class
subclass of: Movement
date: 24 Aug. 2011
creator: jps
definition: Rotation is a Movement resulting in a change in orientation of an object.

SecondOrderRate
type: Class
subclass of: RateFunction
date: 24 Aug. 2011
definition: A SecondOrderRate is a CBO:RateFunction describing the mathematical form used to define a second order rate of change of a quality with respect to time. For quality n (and m); dn/dt=k*n^2, or dn/dt=k*n*m, where k is the rate constant.
creator: jps

Shape
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
definition: Shape is a GeometricalProperty describing the spatial (2 or 3 dimensions) of a region of spaced occupied by an object at a particular instant in time.
creator: jps
is defined by: urn:miriam:opb:'bounded Volume Shape'

ShapeChange
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
definition: ShapeChange is a FundamentalPhysicalProcess resulting in the change in the Shape, including extents, of an object.
see also: isA subclass of: BFO:span:fiat_process_part
creator: jps

SpacialExclusive
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
creator: jps
definition: A SpatialExclusive quality is a CBO:PhysicalObjectQuality for objects that can be the only occupier of a particular point or region of space for the set of all objects with the SpatialExclusive quality. For example, CBO:Cell and medium (CBO:ExtracellularFluid) generally will individually have the SpatialExclusive quality and hence individual cells and medium cannot occupy the same region of space at the same time. Objects without the SpatialExclusive quality, for example a chemical field (CBO:DiffuseEntity, CBO:SoluteMaterialType), can overlay objects with the SpatialExclusive quality. That is fields and solutes do not generally have the SpatialExclusive quality.

StatisticalProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
definition: StatisticalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the statistical qualities of objects. StatisticalProperty are intrinsic to the object.
creator: jps

StiffnessMechanical
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
creator: jps
definition: StiffnessMechanical is a CBO:MechanicalProperty that describes an elastic object's resistance to deformation by an applied force along a given direction.

StructuralProcess
type: Class
subclass of: CBO_Process
date: 24 Aug. 2011
see also: isA subclass of: BFO:span:process
creator: jps
definition: StructuralProcess is a CBO:Process (snap:process) that results does not result in a change in the identity of the Object, but the Object does change in its DATA structure.

SurfaceArea
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
creator: jps
definition: SurfaceArea is a CBO:GeometricalProperty describing the scalar value of the object's surface area at a particular instant in time.
is defined by: urn:miriam:opb:'Area of surface region'

SymmetricCellDivisionOrientedCleavagePlane
type: Class
subclass of: Mitosis
date: 24 Aug. 2011
definition: SymmetricCellDivisionOrientedCleavagePlane is a Mitosis characterized by the Creation of two identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is oriented with respect to either the environment or the characteristics of the parent cell.
creator: jps

SymmetricCellDivisionRandomCleavagePlane
type: Class
subclass of: Mitosis
date: 24 Aug. 2011
creator: jps
definition: SymmetricCellDivisionRandomCleavagePlane is a Mitosis characterized by the Creation of two identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is randomly oriented with respect to both the environment and the characteristics of the parent cell.

System
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
definition: System is a CBO class that describes and includes the universe described by the model or experiment. In general cell instances and fields are "contained_In" (inverse of "contains") a CBO:System as opposed to "part_Of" a CBO:System since cells, fields, etc. may come and go during a simulation.
creator: jps
see also: isA subclass of: BFO:snap:object

SystemBoundary
type: Class
subclass of: SystemQuality
definition: SystemBoundary is a SystemQuality that describes the edges (boundary) of a computational model.
creator: jps
date: 25 Jul. 2012

SystemExtent
type: Class
subclass of: SystemQuality
definition: SystemExtent classes are SystemQualties the describe the extent of the model in two or three dimensions. SystemExtent can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
creator: jps
date: 25 Jul. 2012

SystemExtentX
type: Class
subclass of: SystemExtent
date: 25 Jul. 2012
definition: SystemExtentX is a are SystemExtent the describe the extent of the model in the X dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
creator: jps

SystemExtentY
type: Class
subclass of: SystemExtent
definition: SystemExtentY is a are SystemExtent the describe the extent of the model in the Y dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
date: 25 Jul. 2012
creator: jps

SystemExtentZ
type: Class
subclass of: SystemExtent
definition: SystemExtentZ is a are SystemExtent the describe the extent of the model in the Y dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
date: 25 Jul. 2012
creator: jps

SystemPeriodic
type: Class
subclass of: SystemBoundary
disjoint with: SystemWall
date: 25 Jul. 2012
definition: SystemPeriodic is a SystemBoundary that describes the edges (boundary) of a computational model as being a periodic edge. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side.
creator: jps

SystemPeriodicX
type: Class
subclass of: SystemPeriodic
definition: SystemPeriodicX is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the X-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side.
date: 25 Jul. 2012
creator: jpos

SystemPeriodicY
type: Class
subclass of: SystemPeriodic
definition: SystemPeriodicY is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the Y-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side.
date: 25 Jul. 2012
creator: jps

SystemPeriodicZ
type: Class
subclass of: SystemPeriodic
creator: jps
date: 25 Jul. 2012
definition: SystemPeriodicZ is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the Z-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side.

SystemPixel2DistanceScale
type: Class
subclass of: SystemQuality
definition: SystemPixel2DistanceScale is a SystemQualties that describes the relationship between the size of a voxel (or pixel) and a length measurement. In general, SystemPixel2Distance will point to a floating point number that, when multiplied by a number of pixels will return a distance. For example, a SystemPixel2DistanceScale=2um/pix indicates that each pixel is 2 micrometers wide.
creator: jps
date: 25 Jul. 2012

SystemQuality
type: Class
subclass of: CBO_Object
date: 24 Jul. 2012
creator: jps
definition: SystemQualities is CBO_Object class that describes the computational platform (suite of code or a standalone computational tool) and instantiation of a particular model.

SystemWall
type: Class
subclass of: SystemBoundary
creator: jps
date: 25 Jul. 2012
definition: SystemWall is a SystemBoundary that describes the edges (boundary) of a computational model as being an impenetrable wall. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall.

SystemWallX
type: Class
subclass of: SystemWall
definition: SystemWallX is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the X-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall.
creator: jps
date: 25 Jul. 2012

SystemWallY
type: Class
subclass of: SystemWall
definition: SystemWallY is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the Y-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall.
creator: jps
date: 25 Jul. 2012

SystemWallZ
type: Class
subclass of: SystemWall
creator: jps
definition: SystemWallZ is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the Z-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall.
date: 25 Jul. 2012

TemperatureField
type: Class
subclass of: Field
date: 19 Jul. 2012
comment: A TemperatureField is a CBO:Field class for the description of the temperature that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a TemperatureField may be described as having a position dependent intensity function. Unlike a CBO:Cell, a TemperatureField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.)
definition: A TemperatureField is a CBO:Field class for the description of the temperature that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a TemperatureField may be described as having a position dependent intensity function. Unlike a CBO:Cell, a TemperatureField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.)
creator: jps

TemporalAge
type: Class
subclass of: Age
date: 24 Aug. 2011
definition: TemporalAge is a CBO:Age that describes the time interval between the time of the objects creation and the current time. PATO: A time quality inhering in a bearer by virtue of how long the bearer has existed.
creator: jps

TemporalEntity
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
see also: isA subclass of: BFO:span:connected_temporal_region
is defined by: urn:miriam:opb:'temporal entity'
creator: jps
definition: OPB: ...is a moment or span of time.

TemporalInstant
type: Class
subclass of: TemporalEntity
disjoint with: TemporalInterval
date: 24 Aug. 2011
see also: isA subclass of: BFO:snap:TemporalInstant
creator: jps
definition: OPB: ...is a point in time.
is defined by: urn:miriam:opb:'temporal instant'

TemporalInterval
type: Class
subclass of: TemporalEntity
date: 24 Aug. 2011
creator: jps
definition: OPB: ...is a period of time bounded by two temporal moments (that may be the same moment).
see also: isA subclass of: BFO:snap:TemporalInterval
is defined by: urn:miriam:opb:'temporal interval'

TensionMechanical
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
definition: TensionMechanical is a CBO:MechanicalProperty that describes the pulling force exerted on an entity (a stretching or distorting force).
creator: jps

Texture
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
definition: Texture is a CBO:GeometricalProperty describing the characteristics of a surface Texture.
creator: jps

TightJunction
type: Class
subclass of: CellMembranePart
date: 24 Aug. 2011
creator: jps
definition: GO: An occluding Cell-Cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each Cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes. Cell-Cell junctions that seal adjacent epithelial Cells together, preventing the passage of most dissolved Molecules from one side of the epithelial sheet to the other. (Alberts et al., Molecular Biology of the Cell, 2nd ed, p22)

Translation
type: Class
subclass of: Movement
date: 24 Aug. 2011
creator: jps
definition: Translation is a Movement resulting in a change in the spatial location of an object.

Transport
type: Class
subclass of: CBO_Process
date: 24 Aug. 2011
creator: jps
definition: Transport is a CBO:Process describing the general case of Movement of an object across space, a fiat boundary or a bona fide boundary. For example, Transport of oxygen from the outside of an animal to the inside of the animal. Note that there are specific terms elsewhere for Transport across cell boundaries (CBO:CellImport and CBO:CellExport) and for molecules (CBO:MoleculeBarrierCrossing).

UniformTexture
type: Class
subclass of: Texture
date: 24 Aug. 2011
definition: UniformTexture is a CBO:Texture consisting of a positionally independent Texture description.
creator: jps

VTK_FileName
type: Class
subclass of: VTK_Quality
creator: JPS
date: 10/25/2012
definition: VTK_FileName is a CBO:SystemQuality:VTK_Quality giving a full file name (which may or may not by a URI, IRI, or fully qualified path+filename to the local file system) for a snapshot VTK file giving the cells, cell extents, cell types, fields etc of the model at a particular point in simulated time. Recommended file name structure: ModelName_TimeStamp_runID_time.vtk where; "ModelName" is the same string used for the CBO_System instant that encompasses the entire model. This should also be the name of the OWL ontology for the model. "TimeStamp" is the wall clock time that the simulation that created the VTK was started. Resommended format of YYYYMMDDhhmmss. "runID" is an additional qualifier to differentiate multiple runs of the same model that may have been started at the same wall clock time. Often this may be assumed to be "1". "time" is the simulated time for this particular snapshot of the system. It is recomended that the "time" be a zero filled string, for example 000000010, for the file created after the simulated time of 10*VTK_FileTimeStep in the simulation.

VTK_FileRoot
type: Class
subclass of: VTK_Quality
creator: JPS
definition: VTK_FileRoot is a CBO:SystemQuality:VTK_Quality giving the root name for the VTK files associated with the particular model.
date: 10/25/2012

VTK_FileTimeStep
type: Class
subclass of: VTK_Quality
date: 10/25/2012
definition: VTK_FileTimeStep is a CBO:SystemQuality:VTK_Quality that carries the time scale for the VTK files. The value of the VTK_FileTimeStep instance, when multiplied by it's units and then by the numeric part of the VTK_FileName gives the simulated time offset from the start of the simulated time. For example; VTK_fts instanceOf VTK_FileTimeStep VTK_fts hasFloatValue 100 VTK_fts hasUnit UO:milliseconds and the VTK file name "MySim_20121024112233_1_000250.vtk is understood to represent the simulated time of (100)(250)milliseconds = 25 seconds Often the instance of VTK_FileTimeStep will have a numeric value of 1 and most of the time information will be carried by the units (seconds, minutes, days, ...) and the numeric part of the VTK file name (000250 in the example above).
creator: JPS

VTK_InitialCondition
type: Class
subclass of: VTK_Quality
date: 10/25/2012
creator: jps
definition: VTK_InitialCondition is a CBO:SystemQuality:VTK_Quality that points at a VTK file giving the initial configuration of the model. Typically this configuration represents time=0 in the model.

VTK_Quality
type: Class
subclass of: SystemQuality
definition: VTK_Quality is a CBO:SystemQuality that includes classes for specificying the name, ilneage and time of a VTK snap(shot) of the simulation.
date: 10/29/2012
creator: JPS

Ventral
type: Class
subclass of: OrganismalRegion
date: 24 Aug. 2011
creator: jps
definition: Ventral is a CBO:OrganismalRegion characteristic of the front of an object relative to the body it is contained in. EFO: Ventral is a geometric modifier describing parts pertaining to the front or anterior of any structure for example Ventral striatum.

Volume
type: Class
subclass of: GeometricalProperty
date: 24 Aug. 2011
creator: jps
definition: Volume is a GeometricalProperty describing the total Volume of spaced occupied by the object at a particular instant in time.
is defined by: urn:miriam:opb:'Volume of Volume region'

VolumeChange
type: Class
subclass of: FundamentalPhysicalProcess
date: 24 Aug. 2011
definition: VolumeChange is a FundamentalPhysicalProcess resulting in a change, an increase or decrease, in the Volume occupied by an object.
see also: isA subclass of: BFO:span:fiat_process_part
creator: jps

VolumeEnergy
type: Class
subclass of: EnergyQuality
date: 24 Aug. 2011
creator: jps
definition: A VolumeEnergy is a CBO:EnergyQuality representing the energy associated with a given volume entity.

YieldingThreshold
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
definition: YieldingThreshold (Yield stress threshold, Y) is a CBO:MechanicalProperty describing the rheological yield stress of an object.
creator: jps

YoungsModulus
type: Class
subclass of: MechanicalProperty
date: 24 Aug. 2011
definition: YoungsModulus (Young's modulus, tensile modulus) is a numerical CBO:PhysicalObjectQuality indicating the measure of stiffness in a material. It is defined by the ratio of stress in a unit area of substance to the resulting deformation (strain). This allows the behavior of a material under load (such as bone) to be calculated. (From Mesh)
creator: jps

ZerothOrderRate
type: Class
subclass of: RateFunction
date: 24 Aug. 2011
creator: jps
definition: A ZerothOrderRate is a CBO:RateFunction describing the mathematical form used to define a constant rate of change of a quality with respect to time. For quality n; dn/dt=k, where k is a constant.