]> 19 Dec. 2012 J Sluka, Biocomplexity Insitute, Indiana University 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 1.0 is the initial release of the Cell Behavior Ontology (CBO), Fall 2012. 1.000 hasExtentValueSet1D 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 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 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 A single floating point number. hasFloatValueTarget A single floating point number representing the target value of a quality or function. hasIntValue A single integer number. hasIntValueTarget A single integer number representing the target value of a quality or function. hasLocationValueSet1D 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 2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string. hasLocationValueSet3D 3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string. hasLocationValueSetND 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 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 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 A unit name, for example, "meter", "micrometer*micrometer", "hour". Stored as a text string. hasVTKfieldID 11/9/2012 jps 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 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. JPS 10/25/2012 AcceptanceFunction 24 Aug. 2011 jps 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 24 Aug. 2011 jps An AdhesionEnergy is a CBO:EnergyQuality representing the energy associated with the contact between two physical objects. AdhesionMolecule 24 Aug. 2011 jps urn:miriam:obo.fma:67214 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 24 Aug. 2011 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. jps Advection is a Movement that is caused by a carrying medium (such as blood) that results in a change in location. CellAdvection 29 Oct. 2012 JPS Age 24 Aug. 2011 Age is a CBO:PhysicalObjectQuality class that describes the chronological or generational Age of a physical object. jps Anisotropy 24 Aug. 2011 Anisotropy is a GeometricalProperty describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:Isotropy. jps ApicalPart 24 Aug. 2011 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. jps Apoptosis 24 Aug. 2011 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. jps PATO:0000638 urn:miriam:obo.go:0006915 AreaEnergy 24 Aug. 2011 A AreaEnergy is a CBO:EnergyQuality representing the energy associated with a given area entity. jps AsymmetricCellDivisionOrientedCleavagePlane 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps AutophagicDeath 24 Aug. 2011 urn:miriam:obo.go:0048102 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps urn:miriam:obo.go:0045178 urn:miriam:obo.fma:72558 BasementLaminaChange 24 Aug. 2011 BasementLaminaChange is an BasementLaminaProcess involving a change in the components or characteristics of the basement lamina components. jps BasementLaminaCreation 24 Aug. 2011 jps BasementLaminaCreation is a BasementLaminaProcess involving an increase in the quantity of the basement lamina and its components. BasementLaminaDeletion 24 Aug. 2011 BasementLaminaDeletion is a BasementLaminaProcess involving a decrease in the quantity of the basement lamina and its components. jps BasementLaminaProcess 24 Aug. 2011 BasementLaminaProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of a basement membrane or its components. jps BasementMembrane 24 Aug. 2011 urn:miriam:obo.go:0005605 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. jps BioEntityType 11/8/2012 jps BioEntityType is a CBO class for biological concepts such as Cell and ECM. BodyShape 24 Aug. 2011 jps 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. urn:miriam:opb:'bounded Volume Shape' BoltzmannFactor 24 Aug. 2011 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). jps Boundary 24 Aug. 2011 isA subclass of: BFO:snap:object_Boundary jps Boundary is a CBO:GeometricalEntity that demarks the interface between two bona fide physical objects. BrushBorder 24 Aug. 2011 urn:miriam:obo.fma:70977 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 jps urn:miriam:obo.go:0005903 CBO_Object 24 Aug. 2011 isA subclass of: BFO:snap jps CBO_Process 24 Aug. 2011 isA subclass of: BFO:span jps CHASTEcenter 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 jps 23 Jul. 2012 Cell 24 Aug. 2011 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. urn:miriam:obo.clo:0000000 isA subclass of: BFO:snap:object urn:miriam:obo.fma:68646 jps urn:miriam:obo.go:0005623 CellAdhesion 24 Aug. 2011 urn:miriam:obo.go:0007155 PATO:0001531 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. jps CellAdvection 24 Aug. 2011 jps 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 24 Aug. 2011 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). jps CellBasementMembraneAdhesion 24 Aug. 2011 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. jps CellBorder 24 Aug. 2011 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. jps CellCellAdhesion 24 Aug. 2011 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. PATO:0001531 urn:miriam:obo.go:0016337 jps CellCellContact 24 Aug. 2011 CellCellContact is a CellContact involving the direct physical contact between two cells. Note that contact is distinct from adhesion (see CBO:CellAdhesion). jps CellCellProcess 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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). isA subclass of: BFO:span:fiat_process_part CellDeath 24 Aug. 2011 jps 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. urn:miriam:obo.go:0008219 CellDifferentiation 24 Aug. 2011 CellDifferentiation is an existential_CellProcess in which the type (CBO:Phenotype) of a cell is changed. jps CellDisplacement 24 Aug. 2011 jps 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 24 Aug. 2011 urn:miriam:obo.go:0051301 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 jps urn:miriam:obo.go:0000768 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 24 Aug. 2011 jps urn:miriam:obo.go:0016049 isA subclass of: BFO:span:fiat_process_part PATO:0001489 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 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps CellInterstitialMatrixContact 24 Aug. 2011 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). jps CellMembrane 24 Aug. 2011 urn:miriam:obo.fma:63841 urn:miriam:obo.go:0005886 jps 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 24 Aug. 2011 jps isA subclass of: BFO:snap:specifically_dependent_continuant urn:miriam:obo.go:0042995 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 24 Aug. 2011 jps isA subclass of: BFO:snap:specifically_dependent_continuant urn:miriam:obo.go:0044459 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 24 Aug. 2011 urn:miriam:obo.go:0048870 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. jps CellMovement 24 Aug. 2011 jps 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 24 Aug. 2011 urn:miriam:obo.go:0031589 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. jps CellNonCellContact 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps CellPart 24 Aug. 2011 CellPart is a CBO class including any constituent part of a Cell. jps isA subclass of: BFO:snap:specifically_dependent_continuant urn:miriam:obo.fma:61764 CellProcess 24 Aug. 2011 isA subclass of: BFO:span:process jps CellProcess is a CBO:Process (snap:process) describing a process characteristic of a CBO:Cell. CellRegion 24 Aug. 2011 isA subclass of: BFO:snap:fiat_object_part CellRegion is a CBL:GeometricalEntity class that includes descriptors for various fiat regions. (A fiat region generally does not have clear boundaries.) jps CellRelatedTransport 24 Aug. 2011 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. jps urn:miriam:obo.go:0006810 CellRotation 24 Aug. 2011 urn:miriam:obo.pato:0001599 jps CellRotation is a CellMovement resulting in a Rotation of a cell about it center (center of mass or center of Volume). CellShapeChange 24 Aug. 2011 jps 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 24 Aug. 2011 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. isA subclass of: BFO:snap:quality jps CellVolumeChange 24 Aug. 2011 jps deprecated CellWall 24 Aug. 2011 urn:miriam:obo.go:0005618 jps 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 24 Aug. 2011 jps CellularChemicalProcess is a CellEnvironmentProcess in which an environmental (local) chemical (or chemical gradient) changes a process or quality of a cell. CellularElectricalProcess 24 Aug. 2011 CellularElectricalProcess is a CellEnvironmentProcess that results in a change in an electrical quality of the cell. jps CellularKineticProcess 24 Aug. 2011 jps CellularKineticProcess is a CellularPropertyProcess that changes a kinetic dependence. CellularMechanicalProcess 24 Aug. 2011 CellularMechanicalProcess is a CellularPropertyProcess that results in a change in a mechanical property of a cell. jps CellularPropertyProcess 24 Aug. 2011 jps CellularPropertyProcess is a CellProcess that results in a change in a property of a cell. For example, CellMovement changes the property of location. CenterModelPlatform 23 Jul. 2012 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. jps CenterOfMass 24 Aug. 2011 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. jps CenterOfVolume 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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. urn:miriam:obo:pato:0002193 urn:miriam:opb:'Charge amount' ChemicalAffinity 24 Aug. 2011 jps ChemicalDensity 24 Aug. 2011 jps ChemicalLocalization 24 Aug. 2011 jps ChemicalPattern 24 Aug. 2011 jps ChemicalPatternGradient 24 Aug. 2011 jps ChemicalProperty 24 Aug. 2011 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. jps Chemotaxis 24 Aug. 2011 urn:miriam:obo.go:0006935 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). urn:miriam:obo.go:0060326 jps Compucell3D 23 Jul. 2012 Compucell3D is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.Compucell3D.org jps ComputationalPlatform ComputationalPlatform is a SystemQuality class describing a particular computational platform. jps 23 Jul. 2012 ComputationalPlatformQuality ComputationalPlatformQuality is a CBO class describing qualities of computational platforms for preforming multicell modeling. jps 27 Jul. 2012 ContactSurfaceArea 24 Aug. 2011 ContactSurfaceArea is a CBO:GeometricalProperty describing the scalar value of two objects contact surface area at a particular instant in time. jps DiscreteModelPlatform jps 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 23 Jul. 2012 ContinuousEntity 24 Aug. 2011 jps 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 24 Aug. 2011 ContinousExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionaly sensitive quantity in an infinitely finely grained coordinate System. Compare with DiscreteExtent. jps Contraction 24 Aug. 2011 jps Contraction is a VolumeChange resulting in a decrease in Volume occupied by an object. CorpuscularEntity 24 Aug. 2011 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. jps Creation 24 Aug. 2011 Creation is a FundamentalPhysicalProcess resulting in the Creation of a new object. Often this will involve an increase in count of an object. jps Cytoplasm 24 Aug. 2011 FMA: Cell component which consists of cytosol and Cytoplasmic organelles. jps Deletion 24 Aug. 2011 jps Deletion is a FundamentalPhysicalProcess resulting in the Deletion of an object. Often this will involve a decrease in count of an object. DiffuseEntity 24 Aug. 2011 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. jps Diffusion 24 Aug. 2011 Diffusion is a Movement arising from random motion, either thermal or motive (cf. motility), of an object. jps Dimension1d 24 Aug. 2011 urn:miriam:opb:'One dimensional spatial coordinate System' Dimension1d is a CBO:Dimensionality quality for a System with one spatial dimension. jps Dimension2d 24 Aug. 2011 jps Dimension2d is a CBO:Dimensionality quality for a System with two spatial dimensions. urn:miriam:opb:'Two dimensional spatial coordinate System' Dimension3d 24 Aug. 2011 Dimension3d is a CBO:Dimensionality quality for a System with three spatial dimensions. jps urn:miriam:opb:'Three dimensional spatial coordinate System' Dimensionality 24 Aug. 2011 Dimensionality is a CBO:GeometricalProperty that describes the number of independent spatial axis in a model or System. jps urn:miriam:opb:'Spatial coordinate System' DiscreteExtent 24 Aug. 2011 jps DiscreteExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionally sensitive quantity in a finitely grained coordinate System. Compare with ContinuousExtent. Divisible 24 Aug. 2011 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. jps Dorsal 24 Aug. 2011 urn:miriam:obo.fma:74535 jps 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 24 Aug. 2011 ElectricalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the electrical qualities of objects. ElectricalProperty are intrinsic to the object. jps urn:miriam:opb:'Electrical entity' ElectromechanicalField 1 Dec. 2012 need def jps Energy 24 Aug. 2011 An Energy is a CBO:PhysicalObjectQuality is the Energy of the object for which it is a quality. urn:miriam:opb:'Energy amount' jps EnergyFunction 24 Aug. 2011 isA subclass of: BFO:snap:quality jps 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 24 Aug. 2011 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. jps isA subclass of: BFO:snap:quality ExistentialCellProcesses 24 Aug. 2011 ExistentialCellProcesses is a CellProcess that is assumed, without formal proof, to be a process of a cell. jps Expansion 24 Aug. 2011 jps Expansion is a VolumeChange resulting in an increase in Volume occupied by an object. ExtentGeometrical 24 Aug. 2011 ExtentGeometrical is a CBO:GeometricalProperty that describes the basic granularity of the coordinate System. jps ExtraCellularFluid 24 Aug. 2011 jps 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. isA subclass of: BFO:snap:object ExtraCellularMatrix 24 Aug. 2011 isA subclass of: BFO:snap:object 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. urn:miriam:obo.fma:9672 urn:miriam:obo.go:0031012 jps ExtracellularMatrixProcess 24 Aug. 2011 isA subclass of: BFO:span:process ExtracellularMatrixProcess is a CBO:Process involving a change in the qualities, or quantity of extracellular matrix and its components. jps 19 Jul. 2012 jps 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 jps FieldProcess is a CBO:Process (snap:process) describing a process characteristic of a CBO:Field. 11/8/2012 11/8/2012 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 jps urn:miriam:obo.go:0030175 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 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 A FundamentalPhysicalProcess is a CBO:Process (snap:Process) that changes a quality or characteristic of an object. urn:miriam:dummy:1 urn:miriam:dummy:3 urn:miriam:dummy:2 jps isA subclass of: BFO:span:process GapJunction 24 Aug. 2011 urn:miriam:obo.fma:67423 jps urn:miriam:obo.go:0005921 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 24 Aug. 2011 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. jps urn:miriam:obo.go:0001302 GeometricalCellProcess 24 Aug. 2011 GeometricalCellProcess is a CellularPropertyProcess that results in a change in the geometry of a cell. jps GeometricalEntity 24 Aug. 2011 jps GeometricalEntity is a CBO class for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions. isA subclass of: BFO:snap:independent_continuant GeometricalProperty 24 Aug. 2011 jps 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 24 Aug. 2011 GradientTexture is a CBO:Texture consisting of a Texture description that varies smoothly across one or more dimensions. jps Hamiltonian 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps HarmonicEnergy 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps InterentityImport 24 Aug. 2011 jps 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 24 Aug. 2011 isA subclass of: BFO:span:process jps 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 24 Aug. 2011 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. jps urn:miriam:obo.go:0005614 InterstitialMatrixChange 24 Aug. 2011 InterstitialMatrixChange is an InterstitialMatrixProcess involving a change in the components or characteristics of the interstitial matrix components. jps InterstitialMatrixCreation 24 Aug. 2011 InterstitialMatrixCreation is an InterstitialMatrixProcess involving an increase in the quantity of the interstitial matrix and its components. jps InterstitialMatrixDeletion 24 Aug. 2011 InterstitialMatrixDeletion is an InterstitialMatrixProcess involving a decrease in the quantity of the interstitial matrix and its components. jps InterstitialMatrixProcess 24 Aug. 2011 InterstitialMatrixProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of interstitial matrix and its components. jps IntraentityTransport 24 Aug. 2011 jps 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 24 Aug. 2011 urn:miriam:obo.go:0022831 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps IsHypoxic 24 Aug. 2011 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. jps IsNecrotic 24 Aug. 2011 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. jps IsQuiescent 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 urn:miriam:opb:'Kinetic manifestation' jps KineticProperty is a CBO:PhysicalObjectQuality describing a kinetic characteristic of an object. LJ_6_12Energy 24 Aug. 2011 jps 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 24 Aug. 2011 jps LateralPart is a CBO:CellRegion that is between the CBO:BasalPart and CBO:LateralPart. LinearEnergy 24 Aug. 2011 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. jps Location 24 Aug. 2011 jps 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 24 Aug. 2011 PATO:0000125 jps Mass is a CBO:PhysicalObjectQuality describing the Mass of the object. urn:miriam:opb:'Discrete solid Mass' MechanicalProperty 24 Aug. 2011 jps 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 24 Aug. 2011 MedialPart is a CBO:CellRegion located near the center of the Cell. jps Meiosis 24 Aug. 2011 urn:miriam:obo.go:0007126 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. jps MembraneReceptor 24 Aug. 2011 jps 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 24 Aug. 2011 jps 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 24 Aug. 2011 urn:miriam:obo.go:0007067 jps 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 24 Aug. 2011 isA subclass of: BFO:snap:object 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. jps MolecularTargeting 24 Aug. 2011 MolecularTargeting is an IntraentityTransport in which a molecule is actively directed from one place in a cell to another. jps urn:miriam:obo.go:0006605 Molecule 24 Aug. 2011 Molecule is a CBO:BioEntityType class OPB: ...that is a polyatomic entity. isA subclass of: BFO:snap:object urn:miriam:opb:'Molecule' jps MoleculeBarrierCrossing 24 Aug. 2011 MoleculeBarrierCrossing is a MoleculeProcess describing the transfer of a molecule across a bona fide boundary such as a basement membrane or a cell wall. jps MoleculeChange 24 Aug. 2011 jps MoleculeChange is a MoleculeProcess that results in a phenotypic change in the molecule. For example, changes in the ionization state of an acid. MoleculeCreation 24 Aug. 2011 jps MoleculeCreation is a MoleculeProcess that results in the Creation of a new molecule or an increase in a molecule's concentration. MoleculeDeletion 24 Aug. 2011 MoleculeDeletion is a MoleculeProcess that results in the Deletion of a molecule, or a decrease in a molecule's concentration. jps MoleculeDiffusion 24 Aug. 2011 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. jps isA subclass of: BFO:span:fiat_process_part MoleculeMoleculeAdhesion 24 Aug. 2011 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. jps MoleculeProcess 24 Aug. 2011 MoleculeProcess is a CBO:Process that involves a molecule. jps isA subclass of: BFO:span:process Movement 24 Aug. 2011 Movement is a FundamentalPhysicalProcess resulting in the change in location or Shape of a physical object. isA subclass of: BFO:span:fiat_process_part jps MovementField 24 Aug. 2011 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. jps Necrosis 24 Aug. 2011 jps Necrosis is a CellDeath caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin. PATO:0000647 Nucleus 24 Aug. 2011 urn:miriam:obo.go:0005634 urn:miriam:obo.fma:63840 jps 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 23 Jul. 2012 jps 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 OpenSourceModelPlatform is a CBO:ComputationalPlatformQuality class for compuational platforms which are open source. 23 Jul. 2012 jps OrganismalRegion 24 Aug. 2011 OrganismalRegion is a CBO:GeometricalEntity class for regions of an animal. isA subclass of: BFO:snap:fiat_object_part jps Orientation 24 Aug. 2011 jps 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 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. 23 Jul. 2012 jps OtherPublicationReference jps OtherPublicationReference is a CBO:ComputationalPlatformQuality class for computational platforms referenced only by a literature citation. 23 Jul. 2012 PatternTexture 24 Aug. 2011 jps PatternTexture is a CBO:Texture consisting of a positionally repetitive Texture description. PhenotypicChange 24 Aug. 2011 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. jps PhysicalEntityType 24 Aug. 2011 urn:miriam:dummy:3 A PhysicalEntityType is a CBO:Class (BFO:snap:quality) class of physical objects. For example, a Cell, a basement membrane of a diffusible Molecule. urn:miriam:dummy:2 urn:miriam:dummy:1 jps isA subclass of: BFO:snap:quality PhysicalObjectQuality 24 Aug. 2011 jps isA subclass of: BFO:snap:quality 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 24 Aug. 2011 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). jps PressureMechanical 24 Aug. 2011 jps PressureMechanical is a CBO:MechanicalProperty describing the barometric pressure of an object or Location in space. Protrusion 24 Aug. 2011 Protrusion is a GeometricalProperty describing an extension from an otherwise simpler CBO:BodyShape description. For example, a transient pseudopodia or a persistent neuronal axon. jps Pseudopodium 24 Aug. 2011 urn:miriam:obo.go:0031143 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 jps Pump 24 Aug. 2011 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. MeSH: D12.776.157.530 MeSH:'Membrane Transport Proteins' jps Random 24 Aug. 2011 jps Random is a CBO:StatisticalProperty class that describes a quality of randomness to an object or process. RateFunction 24 Aug. 2011 jps 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. isA subclass of: BFO:snap:quality Rotation 24 Aug. 2011 jps Rotation is a Movement resulting in a change in orientation of an object. SecondOrderRate 24 Aug. 2011 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. jps Shape 24 Aug. 2011 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. PATO:0000052 jps urn:miriam:opb:'bounded Volume Shape' ShapeChange 24 Aug. 2011 ShapeChange is a FundamentalPhysicalProcess resulting in the change in the Shape, including extents, of an object. isA subclass of: BFO:span:fiat_process_part jps SpacialExclusive 24 Aug. 2011 jps 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 24 Aug. 2011 StatisticalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the statistical qualities of objects. StatisticalProperty are intrinsic to the object. jps StiffnessMechanical 24 Aug. 2011 jps StiffnessMechanical is a CBO:MechanicalProperty that describes an elastic object's resistance to deformation by an applied force along a given direction. StructuralProcess 24 Aug. 2011 isA subclass of: BFO:span:process jps 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 24 Aug. 2011 jps SurfaceArea is a CBO:GeometricalProperty describing the scalar value of the object's surface area at a particular instant in time. urn:miriam:opb:'Area of surface region' SymmetricCellDivisionOrientedCleavagePlane 24 Aug. 2011 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. jps SymmetricCellDivisionRandomCleavagePlane 24 Aug. 2011 jps 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 24 Aug. 2011 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. jps isA subclass of: BFO:snap:object SystemBoundary SystemBoundary is a SystemQuality that describes the edges (boundary) of a computational model. jps 25 Jul. 2012 SystemExtent 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. jps 25 Jul. 2012 SystemExtentX 25 Jul. 2012 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. jps SystemExtentY 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. 25 Jul. 2012 jps SystemExtentZ 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. 25 Jul. 2012 jps SystemPeriodic 25 Jul. 2012 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. jps SystemPeriodicX 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. 25 Jul. 2012 jpos SystemPeriodicY 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. 25 Jul. 2012 jps SystemPeriodicZ jps 25 Jul. 2012 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 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. jps 25 Jul. 2012 SystemQuality 24 Jul. 2012 jps 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 jps 25 Jul. 2012 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 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. jps 25 Jul. 2012 SystemWallY 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. jps 25 Jul. 2012 SystemWallZ jps 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. 25 Jul. 2012 TemperatureField 19 Jul. 2012 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.) 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.) jps TemporalAge 24 Aug. 2011 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. urn:miriam:obo.pato:0000011 jps TemporalEntity 24 Aug. 2011 isA subclass of: BFO:span:connected_temporal_region urn:miriam:opb:'temporal entity' jps OPB: ...is a moment or span of time. TemporalInstant 24 Aug. 2011 isA subclass of: BFO:snap:TemporalInstant jps OPB: ...is a point in time. urn:miriam:opb:'temporal instant' TemporalInterval 24 Aug. 2011 jps OPB: ...is a period of time bounded by two temporal moments (that may be the same moment). isA subclass of: BFO:snap:TemporalInterval urn:miriam:opb:'temporal interval' TensionMechanical 24 Aug. 2011 TensionMechanical is a CBO:MechanicalProperty that describes the pulling force exerted on an entity (a stretching or distorting force). jps Texture 24 Aug. 2011 Texture is a CBO:GeometricalProperty describing the characteristics of a surface Texture. jps TightJunction 24 Aug. 2011 jps urn:miriam:obo.go:0005923 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 24 Aug. 2011 jps Translation is a Movement resulting in a change in the spatial location of an object. Transport 24 Aug. 2011 jps 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 24 Aug. 2011 UniformTexture is a CBO:Texture consisting of a positionally independent Texture description. jps VTK_FileName JPS 10/25/2012 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 JPS VTK_FileRoot is a CBO:SystemQuality:VTK_Quality giving the root name for the VTK files associated with the particular model. 10/25/2012 VTK_FileTimeStep 10/25/2012 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). JPS VTK_InitialCondition 10/25/2012 jps 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 VTK_Quality is a CBO:SystemQuality that includes classes for specificying the name, ilneage and time of a VTK snap(shot) of the simulation. 10/29/2012 JPS Ventral 24 Aug. 2011 jps 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 24 Aug. 2011 jps Volume is a GeometricalProperty describing the total Volume of spaced occupied by the object at a particular instant in time. urn:miriam:opb:'Volume of Volume region' PATO:0000918 VolumeChange 24 Aug. 2011 VolumeChange is a FundamentalPhysicalProcess resulting in a change, an increase or decrease, in the Volume occupied by an object. isA subclass of: BFO:span:fiat_process_part jps VolumeEnergy 24 Aug. 2011 jps A VolumeEnergy is a CBO:EnergyQuality representing the energy associated with a given volume entity. YieldingThreshold 24 Aug. 2011 YieldingThreshold (Yield stress threshold, Y) is a CBO:MechanicalProperty describing the rheological yield stress of an object. jps YoungsModulus 24 Aug. 2011 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) jps ZerothOrderRate 24 Aug. 2011 jps 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.