Annotation
literal: jps

Annotation
literal: J Sluka, Biocomplexity Insitute, Indiana University

Annotation
literal: 1.0.3

Annotation
literal: 1.3

Annotation
literal: 1.0.3

Annotation
literal: 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.

Annotation
literal: Version 1.1.0 added classes for OMERO-Tiff files similar to those for VTK files Version 1.0.0 is the initial release of the Cell Behavior Ontology (CBO). Version 1.0.1 added Journal citation for the Cell Behavior Ontology (CBO). Version 1.0.2 corrected a few annotations that had "snap:process" that should be "span:process". Version 1.0.3 corrected/changed class "SpacialExclusive" to "SpatialExclusive" and property "has_Quality" to "has_quality".

Annotation
literal: OBO_REL http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry"

Annotation
literal: 10 Oct 2017

Annotation
literal: release version 1.1.0

Annotation
literal: 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. Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA. The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinformatics. 2014 Apr 22. pii: btu210. [Epub ahead of print] PubMed PMID: 24755304. http://bioinformatics.oxfordjournals.org/content/early/2014/05/18/bioinformatics.btu210.long

AnnotationAssertion
IRI: #OMEtiff_FileName
literal: JPS

AnnotationAssertion
IRI: #OMEtiff_FileName
literal: 10/10/2017

AnnotationAssertion
IRI: #OMEtiff_FileName
literal: OMEtiff_FileName is a CBO:SystemQuality:OMEtiff_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 OMERO Tiff 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.tiff 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*OMEtiff_FileTimeStep in the simulation.

AnnotationAssertion
IRI: #OMEtiff_FileRoot
literal: JPS

AnnotationAssertion
IRI: #OMEtiff_FileRoot
literal: 10/10/2017

AnnotationAssertion
IRI: #OMEtiff_FileRoot
literal: OMEtiff_FileRoot is a CBO:SystemQuality:OMEtiff_Quality giving the root name for the OMERO-Tiff files associated with the particular model.

AnnotationAssertion
IRI: #OMEtiff_FileTimeStep
literal: JPS

AnnotationAssertion
IRI: #OMEtiff_FileTimeStep
literal: 10/10/2017

AnnotationAssertion
IRI: #OMEtiff_FileTimeStep
literal: OMEtiff_FileTimeStep is a CBO:SystemQuality:OMEtiff_Quality that carries the time scale for the OMERO-Tiff files. The value of the OMEtiff_FileTimeStep instance, when multiplied by it's units and then by the numeric part of the OMEtiff_FileName gives the simulated time offset from the start of the simulated time. For example; OMEtiff_fts instanceOf OMEtiff_FileTimeStep OMEtiff_fts hasFloatValue 100 OMEtiff_fts hasUnit UO:milliseconds and the OMEtiff file name "MySim_20121024112233_1_000250.tiff is understood to represent the simulated time of (100)(250)milliseconds = 25 seconds Often the instance of OMEtiff_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 OMEtiff file name (000250 in the example above).

AnnotationAssertion
IRI: #OMEtiff_InitialCondition
literal: jps

AnnotationAssertion
IRI: #OMEtiff_InitialCondition
literal: 10/10/2017

AnnotationAssertion
IRI: #OMEtiff_InitialCondition
literal: OMEtiff_InitialCondition is a CBO:SystemQuality:OMEtiff_Quality that points at a OMERO Tiff file giving the initial configuration of the model. Typically this configuration represents time=0 in the model.

AnnotationAssertion
IRI: #OMEtiff_Quality
literal: JPS

AnnotationAssertion
IRI: #OMEtiff_Quality
literal: 10/10/2017

AnnotationAssertion
IRI: #OMEtiff_Quality
literal: OMEtiff_Quality is a CBO:SystemQuality that includes classes for specificying the name, image and time of an OMERO-Tiff snap(shot) of the simulation.

AnnotationAssertion
IRI: #has_Quality
literal: jps

AnnotationAssertion
IRI: #has_Quality
literal: 1/24/2012

AnnotationAssertion
IRI: #has_Quality
literal: has_Quality links an instance of a CBO quality to a class or individual.

AnnotationAssertion
IRI: #has_Quality
literal: has_Quality links an instance of a CBO quality to a class or individual.

AnnotationAssertion
IRI: #has_Quality
literal: has_Quality

AnnotationAssertion
IRI: .owl#AcceptanceFunction
literal: jps

AnnotationAssertion
IRI: .owl#AcceptanceFunction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AcceptanceFunction
literal: 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.

AnnotationAssertion
IRI: .owl#AcceptanceFunction
literal: AcceptanceFunction

AnnotationAssertion
IRI: .owl#AdhesionEnergy
literal: jps

AnnotationAssertion
IRI: .owl#AdhesionEnergy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AdhesionEnergy
literal: An AdhesionEnergy is a CBO:EnergyQuality representing the energy associated with the contact between two physical objects.

AnnotationAssertion
IRI: .owl#AdhesionEnergy
literal: AdhesionEnergy

AnnotationAssertion
IRI: .owl#AdhesionMolecule
literal: jps

AnnotationAssertion
IRI: .owl#AdhesionMolecule
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AdhesionMolecule
literal: 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.

AnnotationAssertion
IRI: .owl#AdhesionMolecule
literal: urn:miriam:obo.fma:67214

AnnotationAssertion
IRI: .owl#AdhesionMolecule
literal: AdhesionMolecule

AnnotationAssertion
IRI: .owl#AdhesiveProperty
literal: jps

AnnotationAssertion
IRI: .owl#AdhesiveProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AdhesiveProperty
literal: 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.

AnnotationAssertion
IRI: .owl#AdhesiveProperty
literal: AdhesiveProperty

AnnotationAssertion
IRI: .owl#Advection
literal: jps

AnnotationAssertion
IRI: .owl#Advection
literal: 29 Oct. 2012

AnnotationAssertion
IRI: .owl#Advection
literal: Advection is a Movement that is caused by a carrying medium (such as blood) that results in a change in location.

AnnotationAssertion
IRI: .owl#Advection
literal: Advection

AnnotationAssertion
IRI: .owl#Advection
literal: CellAdvection

AnnotationAssertion
IRI: .owl#Age
literal: jps

AnnotationAssertion
IRI: .owl#Age
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Age
literal: Age is a CBO:PhysicalObjectQuality class that describes the chronological or generational Age of a physical object.

AnnotationAssertion
IRI: .owl#Age
literal: Age

AnnotationAssertion
IRI: .owl#Anisotropy
literal: jps

AnnotationAssertion
IRI: .owl#Anisotropy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Anisotropy
literal: Anisotropy is a GeometricalProperty describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:Isotropy.

AnnotationAssertion
IRI: .owl#Anisotropy
literal: Anisotropy

AnnotationAssertion
IRI: .owl#ApicalPart
literal: jps

AnnotationAssertion
IRI: .owl#ApicalPart
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ApicalPart
literal: 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.

AnnotationAssertion
IRI: .owl#ApicalPart
literal: ApicalPart

AnnotationAssertion
IRI: .owl#Apoptosis
literal: jps

AnnotationAssertion
IRI: .owl#Apoptosis
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Apoptosis
literal: 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.

AnnotationAssertion
IRI: .owl#Apoptosis
literal: PATO:0000638

AnnotationAssertion
IRI: .owl#Apoptosis
literal: urn:miriam:obo.go:0006915

AnnotationAssertion
IRI: .owl#Apoptosis
literal: Apoptosis

AnnotationAssertion
IRI: .owl#AreaEnergy
literal: jps

AnnotationAssertion
IRI: .owl#AreaEnergy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AreaEnergy
literal: A AreaEnergy is a CBO:EnergyQuality representing the energy associated with a given area entity.

AnnotationAssertion
IRI: .owl#AreaEnergy
literal: AreaEnergy

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionOrientedCleavagePlane
literal: jps

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionOrientedCleavagePlane
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionOrientedCleavagePlane
literal: 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.

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionOrientedCleavagePlane
literal: AsymmetricCellDivisionOrientedCleavagePlane

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionRandomCleavagePlane
literal: jps

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionRandomCleavagePlane
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionRandomCleavagePlane
literal: 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.

AnnotationAssertion
IRI: .owl#AsymmetricCellDivisionRandomCleavagePlane
literal: AsymmetricCellDivisionRandomCleavagePlane

AnnotationAssertion
IRI: .owl#AutophagicDeath
literal: jps

AnnotationAssertion
IRI: .owl#AutophagicDeath
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#AutophagicDeath
literal: 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.

AnnotationAssertion
IRI: .owl#AutophagicDeath
literal: urn:miriam:obo.go:0048102

AnnotationAssertion
IRI: .owl#AutophagicDeath
literal: AutophagicDeath

AnnotationAssertion
IRI: .owl#BarrierCrossing
literal: jps

AnnotationAssertion
IRI: .owl#BarrierCrossing
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BarrierCrossing
literal: 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.

AnnotationAssertion
IRI: .owl#BarrierCrossing
literal: BarrierCrossing

AnnotationAssertion
IRI: .owl#BasalPart
literal: jps

AnnotationAssertion
IRI: .owl#BasalPart
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BasalPart
literal: 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.

AnnotationAssertion
IRI: .owl#BasalPart
literal: urn:miriam:obo.fma:72558

AnnotationAssertion
IRI: .owl#BasalPart
literal: urn:miriam:obo.go:0045178

AnnotationAssertion
IRI: .owl#BasalPart
literal: BasalPart

AnnotationAssertion
IRI: .owl#BasementLaminaChange
literal: jps

AnnotationAssertion
IRI: .owl#BasementLaminaChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BasementLaminaChange
literal: BasementLaminaChange is an BasementLaminaProcess involving a change in the components or characteristics of the basement lamina components.

AnnotationAssertion
IRI: .owl#BasementLaminaChange
literal: BasementLaminaChange

AnnotationAssertion
IRI: .owl#BasementLaminaCreation
literal: jps

AnnotationAssertion
IRI: .owl#BasementLaminaCreation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BasementLaminaCreation
literal: BasementLaminaCreation is a BasementLaminaProcess involving an increase in the quantity of the basement lamina and its components.

AnnotationAssertion
IRI: .owl#BasementLaminaCreation
literal: BasementLaminaCreation

AnnotationAssertion
IRI: .owl#BasementLaminaDeletion
literal: jps

AnnotationAssertion
IRI: .owl#BasementLaminaDeletion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BasementLaminaDeletion
literal: BasementLaminaDeletion is a BasementLaminaProcess involving a decrease in the quantity of the basement lamina and its components.

AnnotationAssertion
IRI: .owl#BasementLaminaDeletion
literal: BasementLaminaDeletion

AnnotationAssertion
IRI: .owl#BasementLaminaProcess
literal: jps

AnnotationAssertion
IRI: .owl#BasementLaminaProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BasementLaminaProcess
literal: BasementLaminaProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of a basement membrane or its components.

AnnotationAssertion
IRI: .owl#BasementLaminaProcess
literal: BasementLaminaProcess

AnnotationAssertion
IRI: .owl#BasementMembrane
literal: jps

AnnotationAssertion
IRI: .owl#BasementMembrane
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BasementMembrane
literal: 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.

AnnotationAssertion
IRI: .owl#BasementMembrane
literal: urn:miriam:obo.go:0005605

AnnotationAssertion
IRI: .owl#BasementMembrane
literal: BasementMembrane

AnnotationAssertion
IRI: .owl#BioEntityType
literal: jps

AnnotationAssertion
IRI: .owl#BioEntityType
literal: 11/8/2012

AnnotationAssertion
IRI: .owl#BioEntityType
literal: BioEntityType is a CBO_Object for biological concepts such as Cell and ECM.

AnnotationAssertion
IRI: .owl#BioEntityType
literal: BioEntityType

AnnotationAssertion
IRI: .owl#BioEntityType
literal: subclass of: BFO:snap:object

AnnotationAssertion
IRI: .owl#BodyShape
literal: jps

AnnotationAssertion
IRI: .owl#BodyShape
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BodyShape
literal: 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.

AnnotationAssertion
IRI: .owl#BodyShape
literal: urn:miriam:opb:'bounded Volume Shape'

AnnotationAssertion
IRI: .owl#BodyShape
literal: BodyShape

AnnotationAssertion
IRI: .owl#BoltzmannFactor
literal: jps

AnnotationAssertion
IRI: .owl#BoltzmannFactor
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BoltzmannFactor
literal: 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).

AnnotationAssertion
IRI: .owl#BoltzmannFactor
literal: BoltzmannFactor

AnnotationAssertion
IRI: .owl#Boundary
literal: jps

AnnotationAssertion
IRI: .owl#Boundary
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Boundary
literal: Boundary is a CBO:GeometricalEntity that demarks the interface between two bona fide physical objects.

AnnotationAssertion
IRI: .owl#Boundary
literal: Boundary

AnnotationAssertion
IRI: .owl#Boundary
literal: subclass of: BFO:snap:object_Boundary

AnnotationAssertion
IRI: .owl#BrushBorder
literal: jps

AnnotationAssertion
IRI: .owl#BrushBorder
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#BrushBorder
literal: 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

AnnotationAssertion
IRI: .owl#BrushBorder
literal: urn:miriam:obo.fma:70977

AnnotationAssertion
IRI: .owl#BrushBorder
literal: urn:miriam:obo.go:0005903

AnnotationAssertion
IRI: .owl#BrushBorder
literal: BrushBorder

AnnotationAssertion
IRI: .owl#CBO_Object
literal: jps

AnnotationAssertion
IRI: .owl#CBO_Object
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CBO_Object
literal: CBO_Object is the top level CBO class for physical objects and object qualities. CBO_Object is BFO:continuant (endurant).

AnnotationAssertion
IRI: .owl#CBO_Object
literal: CBO_Object

AnnotationAssertion
IRI: .owl#CBO_Object
literal: subclass of: BFO:continuant

AnnotationAssertion
IRI: .owl#CBO_Process
literal: jps

AnnotationAssertion
IRI: .owl#CBO_Process
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CBO_Process
literal: CBO_Process is the top level CBO class for processes. CBO_Process is BFO:occurant (processual).

AnnotationAssertion
IRI: .owl#CBO_Process
literal: CBO_Process

AnnotationAssertion
IRI: .owl#CBO_Process
literal: subclass of: BFO:occurrent

AnnotationAssertion
IRI: .owl#CHASTEcenter
literal: jps

AnnotationAssertion
IRI: .owl#CHASTEcenter
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#CHASTEcenter
literal: 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

AnnotationAssertion
IRI: .owl#CHASTEcenter
literal: CHASTEcenter

AnnotationAssertion
IRI: .owl#Cell
literal: jps

AnnotationAssertion
IRI: .owl#Cell
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Cell
literal: 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.

AnnotationAssertion
IRI: .owl#Cell
literal: urn:miriam:obo.clo:0000000

AnnotationAssertion
IRI: .owl#Cell
literal: urn:miriam:obo.fma:68646

AnnotationAssertion
IRI: .owl#Cell
literal: urn:miriam:obo.go:0005623

AnnotationAssertion
IRI: .owl#Cell
literal: Cell

AnnotationAssertion
IRI: .owl#CellAdhesion
literal: jps

AnnotationAssertion
IRI: .owl#CellAdhesion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellAdhesion
literal: 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.

AnnotationAssertion
IRI: .owl#CellAdhesion
literal: PATO:0001531

AnnotationAssertion
IRI: .owl#CellAdhesion
literal: urn:miriam:obo.go:0007155

AnnotationAssertion
IRI: .owl#CellAdhesion
literal: CellAdhesion

AnnotationAssertion
IRI: .owl#CellAdvection
literal: jps

AnnotationAssertion
IRI: .owl#CellAdvection
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellAdvection
literal: 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.

AnnotationAssertion
IRI: .owl#CellAdvection
literal: CellAdvection

AnnotationAssertion
IRI: .owl#CellBasementLaminaContact
literal: jps

AnnotationAssertion
IRI: .owl#CellBasementLaminaContact
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellBasementLaminaContact
literal: 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).

AnnotationAssertion
IRI: .owl#CellBasementLaminaContact
literal: CellBasementLaminaContact

AnnotationAssertion
IRI: .owl#CellBasementMembraneAdhesion
literal: jps

AnnotationAssertion
IRI: .owl#CellBasementMembraneAdhesion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellBasementMembraneAdhesion
literal: 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.

AnnotationAssertion
IRI: .owl#CellBasementMembraneAdhesion
literal: CellBasementMembraneAdhesion

AnnotationAssertion
IRI: .owl#CellBorder
literal: jps

AnnotationAssertion
IRI: .owl#CellBorder
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellBorder
literal: 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.

AnnotationAssertion
IRI: .owl#CellBorder
literal: CellBorder

AnnotationAssertion
IRI: .owl#CellCellAdhesion
literal: jps

AnnotationAssertion
IRI: .owl#CellCellAdhesion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellCellAdhesion
literal: 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.

AnnotationAssertion
IRI: .owl#CellCellAdhesion
literal: PATO:0001531

AnnotationAssertion
IRI: .owl#CellCellAdhesion
literal: urn:miriam:obo.go:0016337

AnnotationAssertion
IRI: .owl#CellCellAdhesion
literal: CellCellAdhesion

AnnotationAssertion
IRI: .owl#CellCellContact
literal: jps

AnnotationAssertion
IRI: .owl#CellCellContact
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellCellContact
literal: CellCellContact is a CellContact involving the direct physical contact between two cells. Note that contact is distinct from adhesion (see CBO:CellAdhesion).

AnnotationAssertion
IRI: .owl#CellCellContact
literal: CellCellContact

AnnotationAssertion
IRI: .owl#CellCellProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellCellProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellCellProcess
literal: 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.

AnnotationAssertion
IRI: .owl#CellCellProcess
literal: CellCellProcess

AnnotationAssertion
IRI: .owl#CellContact
literal: jps

AnnotationAssertion
IRI: .owl#CellContact
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellContact
literal: 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).

AnnotationAssertion
IRI: .owl#CellContact
literal: CellContact

AnnotationAssertion
IRI: .owl#CellContact
literal: subclass of: BFO:span:fiat_process_part

AnnotationAssertion
IRI: .owl#CellDeath
literal: jps

AnnotationAssertion
IRI: .owl#CellDeath
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellDeath
literal: 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.

AnnotationAssertion
IRI: .owl#CellDeath
literal: urn:miriam:obo.go:0008219

AnnotationAssertion
IRI: .owl#CellDeath
literal: CellDeath

AnnotationAssertion
IRI: .owl#CellDifferentiation
literal: jps

AnnotationAssertion
IRI: .owl#CellDifferentiation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellDifferentiation
literal: CellDifferentiation is an existential_CellProcess in which the type (CBO:Phenotype) of a cell is changed.

AnnotationAssertion
IRI: .owl#CellDifferentiation
literal: CellDifferentiation

AnnotationAssertion
IRI: .owl#CellDisplacement
literal: jps

AnnotationAssertion
IRI: .owl#CellDisplacement
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellDisplacement
literal: 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.

AnnotationAssertion
IRI: .owl#CellDisplacement
literal: CellDisplacement

AnnotationAssertion
IRI: .owl#CellDivision
literal: jps

AnnotationAssertion
IRI: .owl#CellDivision
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellDivision
literal: 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.

AnnotationAssertion
IRI: .owl#CellDivision
literal: urn:miriam:obo.go:0051301

AnnotationAssertion
IRI: .owl#CellDivision
literal: CellDivision

AnnotationAssertion
IRI: .owl#CellEnvironmentProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellEnvironmentProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellEnvironmentProcess
literal: 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.

AnnotationAssertion
IRI: .owl#CellEnvironmentProcess
literal: CellEnvironmentProcess

AnnotationAssertion
IRI: .owl#CellExport
literal: jps

AnnotationAssertion
IRI: .owl#CellExport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellExport
literal: 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.

AnnotationAssertion
IRI: .owl#CellExport
literal: CellExport

AnnotationAssertion
IRI: .owl#CellFusion
literal: jps

AnnotationAssertion
IRI: .owl#CellFusion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellFusion
literal: 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.

AnnotationAssertion
IRI: .owl#CellFusion
literal: urn:miriam:obo.go:0000768

AnnotationAssertion
IRI: .owl#CellFusion
literal: CellFusion

AnnotationAssertion
IRI: .owl#CellGrowth
literal: jps

AnnotationAssertion
IRI: .owl#CellGrowth
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellGrowth
literal: 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.

AnnotationAssertion
IRI: .owl#CellGrowth
literal: PATO:0001489

AnnotationAssertion
IRI: .owl#CellGrowth
literal: urn:miriam:obo.go:0016049

AnnotationAssertion
IRI: .owl#CellGrowth
literal: CellGrowth

AnnotationAssertion
IRI: .owl#CellGrowth
literal: subclass of: BFO:span:fiat_process_part

AnnotationAssertion
IRI: .owl#CellImport
literal: jps

AnnotationAssertion
IRI: .owl#CellImport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellImport
literal: 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.

AnnotationAssertion
IRI: .owl#CellImport
literal: CellImport

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixAdhesion
literal: jps

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixAdhesion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixAdhesion
literal: 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.

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixAdhesion
literal: CellInterstitialMatrixAdhesion

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixContact
literal: jps

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixContact
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixContact
literal: 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).

AnnotationAssertion
IRI: .owl#CellInterstitialMatrixContact
literal: CellInterstitialMatrixContact

AnnotationAssertion
IRI: .owl#CellMembrane
literal: jps

AnnotationAssertion
IRI: .owl#CellMembrane
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellMembrane
literal: 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.

AnnotationAssertion
IRI: .owl#CellMembrane
literal: urn:miriam:obo.fma:63841

AnnotationAssertion
IRI: .owl#CellMembrane
literal: urn:miriam:obo.go:0005886

AnnotationAssertion
IRI: .owl#CellMembrane
literal: CellMembrane

AnnotationAssertion
IRI: .owl#CellMembraneLocalStructure
literal: jps

AnnotationAssertion
IRI: .owl#CellMembraneLocalStructure
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellMembraneLocalStructure
literal: A CellMembraneLocalStructure is a CBO_Object 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.

AnnotationAssertion
IRI: .owl#CellMembraneLocalStructure
literal: urn:miriam:obo.go:0042995

AnnotationAssertion
IRI: .owl#CellMembraneLocalStructure
literal: CellMembraneLocalStructure

AnnotationAssertion
IRI: .owl#CellMembraneLocalStructure
literal: subclass of: BFO:snap:specifically_dependent_continuant

AnnotationAssertion
IRI: .owl#CellMembranePart
literal: jps

AnnotationAssertion
IRI: .owl#CellMembranePart
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellMembranePart
literal: 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.

AnnotationAssertion
IRI: .owl#CellMembranePart
literal: urn:miriam:obo.go:0044459

AnnotationAssertion
IRI: .owl#CellMembranePart
literal: CellMembranePart

AnnotationAssertion
IRI: .owl#CellMembranePart
literal: subclass of: BFO:snap:specifically_dependent_continuant

AnnotationAssertion
IRI: .owl#CellMotility
literal: jps

AnnotationAssertion
IRI: .owl#CellMotility
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellMotility
literal: 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.

AnnotationAssertion
IRI: .owl#CellMotility
literal: urn:miriam:obo.go:0048870

AnnotationAssertion
IRI: .owl#CellMotility
literal: CellMotility

AnnotationAssertion
IRI: .owl#CellMovement
literal: jps

AnnotationAssertion
IRI: .owl#CellMovement
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellMovement
literal: 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.

AnnotationAssertion
IRI: .owl#CellMovement
literal: CellMovement

AnnotationAssertion
IRI: .owl#CellNonCellAdhesion
literal: jps

AnnotationAssertion
IRI: .owl#CellNonCellAdhesion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellNonCellAdhesion
literal: 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.

AnnotationAssertion
IRI: .owl#CellNonCellAdhesion
literal: urn:miriam:obo.go:0031589

AnnotationAssertion
IRI: .owl#CellNonCellAdhesion
literal: CellNonCellAdhesion

AnnotationAssertion
IRI: .owl#CellNonCellContact
literal: jps

AnnotationAssertion
IRI: .owl#CellNonCellContact
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellNonCellContact
literal: 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).

AnnotationAssertion
IRI: .owl#CellNonCellContact
literal: CellNonCellContact

AnnotationAssertion
IRI: .owl#CellOrientationChange
literal: jps

AnnotationAssertion
IRI: .owl#CellOrientationChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellOrientationChange
literal: 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.

AnnotationAssertion
IRI: .owl#CellOrientationChange
literal: CellOrientationChange

AnnotationAssertion
IRI: .owl#CellPart
literal: jps

AnnotationAssertion
IRI: .owl#CellPart
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellPart
literal: CellPart is a CBO_Object including any constituent part of a Cell.

AnnotationAssertion
IRI: .owl#CellPart
literal: urn:miriam:obo.fma:61764

AnnotationAssertion
IRI: .owl#CellPart
literal: CellPart

AnnotationAssertion
IRI: .owl#CellPart
literal: subclass of: BFO:snap:specifically_dependent_continuant

AnnotationAssertion
IRI: .owl#CellProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellProcess
literal: CellProcess is a CBO_Process (span:process) describing a process characteristic of a CBO:Cell.

AnnotationAssertion
IRI: .owl#CellProcess
literal: CellProcess

AnnotationAssertion
IRI: .owl#CellProcess
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#CellRegion
literal: jps

AnnotationAssertion
IRI: .owl#CellRegion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellRegion
literal: CellRegion is a CBL:GeometricalEntity class that includes descriptors for various fiat regions. (A fiat region generally does not have clear boundaries.)

AnnotationAssertion
IRI: .owl#CellRegion
literal: CellRegion

AnnotationAssertion
IRI: .owl#CellRegion
literal: subclass of: BFO:snap:fiat_object_part

AnnotationAssertion
IRI: .owl#CellRelatedTransport
literal: jps

AnnotationAssertion
IRI: .owl#CellRelatedTransport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellRelatedTransport
literal: 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.

AnnotationAssertion
IRI: .owl#CellRelatedTransport
literal: urn:miriam:obo.go:0006810

AnnotationAssertion
IRI: .owl#CellRelatedTransport
literal: CellRelatedTransport

AnnotationAssertion
IRI: .owl#CellRotation
literal: jps

AnnotationAssertion
IRI: .owl#CellRotation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellRotation
literal: CellRotation is a CellMovement resulting in a Rotation of a cell about it center (center of mass or center of Volume).

AnnotationAssertion
IRI: .owl#CellRotation
literal: urn:miriam:obo.pato:0001599

AnnotationAssertion
IRI: .owl#CellRotation
literal: CellRotation

AnnotationAssertion
IRI: .owl#CellShapeChange
literal: jps

AnnotationAssertion
IRI: .owl#CellShapeChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellShapeChange
literal: 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.

AnnotationAssertion
IRI: .owl#CellShapeChange
literal: CellShapeChange

AnnotationAssertion
IRI: .owl#CellState
literal: jps

AnnotationAssertion
IRI: .owl#CellState
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellState
literal: A CellState is aCBO_Object (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.

AnnotationAssertion
IRI: .owl#CellState
literal: CellState

AnnotationAssertion
IRI: .owl#CellState
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#CellVolumeChange
literal: jps

AnnotationAssertion
IRI: .owl#CellVolumeChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellVolumeChange
literal: deprecated

AnnotationAssertion
IRI: .owl#CellVolumeChange
literal: CellVolumeChange

AnnotationAssertion
IRI: .owl#CellWall
literal: jps

AnnotationAssertion
IRI: .owl#CellWall
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellWall
literal: 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?

AnnotationAssertion
IRI: .owl#CellWall
literal: urn:miriam:obo.go:0005618

AnnotationAssertion
IRI: .owl#CellWall
literal: CellWall

AnnotationAssertion
IRI: .owl#CellularChemicalProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellularChemicalProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellularChemicalProcess
literal: CellularChemicalProcess is a CellEnvironmentProcess in which an environmental (local) chemical (or chemical gradient) changes a process or quality of a cell.

AnnotationAssertion
IRI: .owl#CellularChemicalProcess
literal: CellularChemicalProcess

AnnotationAssertion
IRI: .owl#CellularElectricalProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellularElectricalProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellularElectricalProcess
literal: CellularElectricalProcess is a CellEnvironmentProcess that results in a change in an electrical quality of the cell.

AnnotationAssertion
IRI: .owl#CellularElectricalProcess
literal: CellularElectricalProcess

AnnotationAssertion
IRI: .owl#CellularKineticProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellularKineticProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellularKineticProcess
literal: CellularKineticProcess is a CellularPropertyProcess that changes a kinetic dependence.

AnnotationAssertion
IRI: .owl#CellularKineticProcess
literal: CellularKineticProcess

AnnotationAssertion
IRI: .owl#CellularMechanicalProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellularMechanicalProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellularMechanicalProcess
literal: CellularMechanicalProcess is a CellularPropertyProcess that results in a change in a mechanical property of a cell.

AnnotationAssertion
IRI: .owl#CellularMechanicalProcess
literal: CellularMechanicalProcess

AnnotationAssertion
IRI: .owl#CellularPropertyProcess
literal: jps

AnnotationAssertion
IRI: .owl#CellularPropertyProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CellularPropertyProcess
literal: CellularPropertyProcess is a CellProcess that results in a change in a property of a cell. For example, CellMovement changes the property of location.

AnnotationAssertion
IRI: .owl#CellularPropertyProcess
literal: CellularPropertyProcess

AnnotationAssertion
IRI: .owl#CenterModelPlatform
literal: jps

AnnotationAssertion
IRI: .owl#CenterModelPlatform
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#CenterModelPlatform
literal: 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.

AnnotationAssertion
IRI: .owl#CenterModelPlatform
literal: CenterModelPlatform

AnnotationAssertion
IRI: .owl#CenterOfMass
literal: jps

AnnotationAssertion
IRI: .owl#CenterOfMass
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CenterOfMass
literal: 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.

AnnotationAssertion
IRI: .owl#CenterOfMass
literal: CenterOfMass

AnnotationAssertion
IRI: .owl#CenterOfVolume
literal: jps

AnnotationAssertion
IRI: .owl#CenterOfVolume
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CenterOfVolume
literal: 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.

AnnotationAssertion
IRI: .owl#CenterOfVolume
literal: CenterOfVolume

AnnotationAssertion
IRI: .owl#Charge
literal: jps

AnnotationAssertion
IRI: .owl#Charge
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Charge
literal: 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.

AnnotationAssertion
IRI: .owl#Charge
literal: urn:miriam:obo:pato:0002193

AnnotationAssertion
IRI: .owl#Charge
literal: urn:miriam:opb:'Charge amount'

AnnotationAssertion
IRI: .owl#Charge
literal: Charge

AnnotationAssertion
IRI: .owl#ChemicalAffinity
literal: jps

AnnotationAssertion
IRI: .owl#ChemicalAffinity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ChemicalAffinity
literal: ChemicalAffinity is a ChemicalProperty that describes an affinity (atraction, repulsion) between a molecule and another object.

AnnotationAssertion
IRI: .owl#ChemicalAffinity
literal: ChemicalAffinity

AnnotationAssertion
IRI: .owl#ChemicalDensity
literal: jps

AnnotationAssertion
IRI: .owl#ChemicalDensity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ChemicalDensity
literal: ChemicalDensity is a ChemicalProperty that describes the concentration (mass or number of molecules) per unit volume.

AnnotationAssertion
IRI: .owl#ChemicalDensity
literal: ChemicalDensity

AnnotationAssertion
IRI: .owl#ChemicalLocalization
literal: jps

AnnotationAssertion
IRI: .owl#ChemicalLocalization
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ChemicalLocalization
literal: ChemicalLocalization is a ChemicalProperty that describes a tendency for the chemical species to localize in a particular region (e.g., cell membrane).

AnnotationAssertion
IRI: .owl#ChemicalLocalization
literal: ChemicalLocalization

AnnotationAssertion
IRI: .owl#ChemicalPattern
literal: jps

AnnotationAssertion
IRI: .owl#ChemicalPattern
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ChemicalPattern
literal: ChemicalPattern is a ChemicalProperty that describes a tendency for the chemical species to organize or partition in a particular pattern.

AnnotationAssertion
IRI: .owl#ChemicalPattern
literal: ChemicalPattern

AnnotationAssertion
IRI: .owl#ChemicalPatternGradient
literal: jps

AnnotationAssertion
IRI: .owl#ChemicalPatternGradient
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ChemicalPatternGradient
literal: ChemicalPatternGradient is a ChemicalPattern that describes a tendency for the chemical species to organize or partition in a particular pattern that includes a gradient in concentration.

AnnotationAssertion
IRI: .owl#ChemicalPatternGradient
literal: ChemicalPatternGradient

AnnotationAssertion
IRI: .owl#ChemicalProperty
literal: jps

AnnotationAssertion
IRI: .owl#ChemicalProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ChemicalProperty
literal: 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.

AnnotationAssertion
IRI: .owl#ChemicalProperty
literal: ChemicalProperty

AnnotationAssertion
IRI: .owl#Chemotaxis
literal: jps

AnnotationAssertion
IRI: .owl#Chemotaxis
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Chemotaxis
literal: 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).

AnnotationAssertion
IRI: .owl#Chemotaxis

AnnotationAssertion
IRI: .owl#Chemotaxis
literal: urn:miriam:obo.go:0006935

AnnotationAssertion
IRI: .owl#Chemotaxis
literal: urn:miriam:obo.go:0060326

AnnotationAssertion
IRI: .owl#Chemotaxis
literal: Chemotaxis

AnnotationAssertion
IRI: .owl#Compucell3D
literal: jps

AnnotationAssertion
IRI: .owl#Compucell3D
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#Compucell3D
literal: Compucell3D is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.Compucell3D.org

AnnotationAssertion
IRI: .owl#Compucell3D
literal: Compucell3D

AnnotationAssertion
IRI: .owl#ComputationalPlatform
literal: jps

AnnotationAssertion
IRI: .owl#ComputationalPlatform
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#ComputationalPlatform
literal: ComputationalPlatform is a SystemQuality class describing a particular computational platform.

AnnotationAssertion
IRI: .owl#ComputationalPlatform
literal: ComputationalPlatform

AnnotationAssertion
IRI: .owl#ComputationalPlatformQualities
literal: jps

AnnotationAssertion
IRI: .owl#ComputationalPlatformQualities
literal: 27 Jul. 2012

AnnotationAssertion
IRI: .owl#ComputationalPlatformQualities
literal: ComputationalPlatformQuality is a CBO class describing qualities of computational platforms for preforming multicell modeling.

AnnotationAssertion
IRI: .owl#ComputationalPlatformQualities
literal: ComputationalPlatformQuality

AnnotationAssertion
IRI: .owl#ContactSurfaceArea
literal: jps

AnnotationAssertion
IRI: .owl#ContactSurfaceArea
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ContactSurfaceArea
literal: ContactSurfaceArea is a CBO:GeometricalProperty describing the scalar value of two objects contact surface area at a particular instant in time.

AnnotationAssertion
IRI: .owl#ContactSurfaceArea
literal: ContactSurfaceArea

AnnotationAssertion
IRI: .owl#ContinousPlatform
literal: jps

AnnotationAssertion
IRI: .owl#ContinousPlatform
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#ContinousPlatform
literal: 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

AnnotationAssertion
IRI: .owl#ContinousPlatform
literal: DiscreteModelPlatform

AnnotationAssertion
IRI: .owl#ContinuousEntity
literal: jps

AnnotationAssertion
IRI: .owl#ContinuousEntity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ContinuousEntity
literal: 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).

AnnotationAssertion
IRI: .owl#ContinuousEntity
literal: ContinuousEntity

AnnotationAssertion
IRI: .owl#ContinuousExtent
literal: jps

AnnotationAssertion
IRI: .owl#ContinuousExtent
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ContinuousExtent
literal: ContinousExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionaly sensitive quantity in an infinitely finely grained coordinate System. Compare with DiscreteExtent.

AnnotationAssertion
IRI: .owl#ContinuousExtent
literal: ContinuousExtent

AnnotationAssertion
IRI: .owl#Contraction
literal: jps

AnnotationAssertion
IRI: .owl#Contraction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Contraction
literal: Contraction is a VolumeChange resulting in a decrease in Volume occupied by an object.

AnnotationAssertion
IRI: .owl#Contraction
literal: Contraction

AnnotationAssertion
IRI: .owl#CorpuscularEntity
literal: jps

AnnotationAssertion
IRI: .owl#CorpuscularEntity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#CorpuscularEntity
literal: A CorpuscularEntity is a PhysicalEntityType (BFO:snap:object) that has a particular Location and Volume at a particular time. CorpuscularEntities 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.

AnnotationAssertion
IRI: .owl#CorpuscularEntity
literal: CorpuscularEntity

AnnotationAssertion
IRI: .owl#Creation
literal: jps

AnnotationAssertion
IRI: .owl#Creation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Creation
literal: Creation is a FundamentalPhysicalProcess resulting in the Creation of a new object. Often this will involve an increase in count of an object.

AnnotationAssertion
IRI: .owl#Creation
literal: Creation

AnnotationAssertion
IRI: .owl#Cytoplasm
literal: jps

AnnotationAssertion
IRI: .owl#Cytoplasm
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Cytoplasm
literal: FMA: Cell component which consists of cytosol and Cytoplasmic organelles.

AnnotationAssertion
IRI: .owl#Cytoplasm
literal: Cytoplasm

AnnotationAssertion
IRI: .owl#Deletion
literal: jps

AnnotationAssertion
IRI: .owl#Deletion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Deletion
literal: Deletion is a FundamentalPhysicalProcess resulting in the Deletion of an object. Often this will involve a decrease in count of an object.

AnnotationAssertion
IRI: .owl#Deletion
literal: Deletion

AnnotationAssertion
IRI: .owl#DiffuseEntity
literal: jps

AnnotationAssertion
IRI: .owl#DiffuseEntity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#DiffuseEntity
literal: 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.

AnnotationAssertion
IRI: .owl#DiffuseEntity
literal: DiffuseEntity

AnnotationAssertion
IRI: .owl#Diffusion
literal: jps

AnnotationAssertion
IRI: .owl#Diffusion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Diffusion
literal: Diffusion is a Movement arising from random motion, either thermal or motive (cf. motility), of an object.

AnnotationAssertion
IRI: .owl#Diffusion
literal: Diffusion

AnnotationAssertion
IRI: .owl#Dimension1d
literal: jps

AnnotationAssertion
IRI: .owl#Dimension1d
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Dimension1d
literal: Dimension1d is a CBO:Dimensionality quality for a System with one spatial dimension.

AnnotationAssertion
IRI: .owl#Dimension1d
literal: urn:miriam:opb:'One dimensional spatial coordinate System'

AnnotationAssertion
IRI: .owl#Dimension1d
literal: Dimension1d

AnnotationAssertion
IRI: .owl#Dimension2d
literal: jps

AnnotationAssertion
IRI: .owl#Dimension2d
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Dimension2d
literal: Dimension2d is a CBO:Dimensionality quality for a System with two spatial dimensions.

AnnotationAssertion
IRI: .owl#Dimension2d
literal: urn:miriam:opb:'Two dimensional spatial coordinate System'

AnnotationAssertion
IRI: .owl#Dimension2d
literal: Dimension2d

AnnotationAssertion
IRI: .owl#Dimension3d
literal: jps

AnnotationAssertion
IRI: .owl#Dimension3d
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Dimension3d
literal: Dimension3d is a CBO:Dimensionality quality for a System with three spatial dimensions.

AnnotationAssertion
IRI: .owl#Dimension3d
literal: urn:miriam:opb:'Three dimensional spatial coordinate System'

AnnotationAssertion
IRI: .owl#Dimension3d
literal: Dimension3d

AnnotationAssertion
IRI: .owl#Dimensionality
literal: jps

AnnotationAssertion
IRI: .owl#Dimensionality
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Dimensionality
literal: Dimensionality is a CBO:GeometricalProperty that describes the number of independent spatial axis in a model or System.

AnnotationAssertion
IRI: .owl#Dimensionality
literal: urn:miriam:opb:'Spatial coordinate System'

AnnotationAssertion
IRI: .owl#Dimensionality
literal: Dimensionality

AnnotationAssertion
IRI: .owl#DiscreteExtent
literal: jps

AnnotationAssertion
IRI: .owl#DiscreteExtent
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#DiscreteExtent
literal: DiscreteExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionally sensitive quantity in a finitely grained coordinate System. Compare with ContinuousExtent.

AnnotationAssertion
IRI: .owl#DiscreteExtent
literal: DiscreteExtent

AnnotationAssertion
IRI: .owl#Divisible
literal: jps

AnnotationAssertion
IRI: .owl#Divisible
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Divisible
literal: 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.

AnnotationAssertion
IRI: .owl#Divisible
literal: Divisible

AnnotationAssertion
IRI: .owl#Dorsal
literal: jps

AnnotationAssertion
IRI: .owl#Dorsal
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Dorsal
literal: Dorsal is a CBO:OrganismalRegion characteristic of the back of an object relative to the body it is contained in. For example Dorsal fin.

AnnotationAssertion
IRI: .owl#Dorsal
literal: urn:miriam:obo.fma:74535

AnnotationAssertion
IRI: .owl#Dorsal
literal: Dorsal

AnnotationAssertion
IRI: .owl#ElectricalProperty
literal: jps

AnnotationAssertion
IRI: .owl#ElectricalProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ElectricalProperty
literal: ElectricalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the electrical qualities of objects. ElectricalProperty are intrinsic to the object.

AnnotationAssertion
IRI: .owl#ElectricalProperty
literal: urn:miriam:opb:'Electrical entity'

AnnotationAssertion
IRI: .owl#ElectricalProperty
literal: ElectricalProperty

AnnotationAssertion
IRI: .owl#ElectromechanicalField
literal: jps

AnnotationAssertion
IRI: .owl#ElectromechanicalField
literal: 8/1/2012

AnnotationAssertion
IRI: .owl#ElectromechanicalField
literal: A ElectromechanicalField is a CBO:Field class for the description of electric and mechanical fields that span 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 ElectromechanicalField may be described as having a position dependent concentration or density function. Unlike a CBO:Cell, a ElectromechanicalField 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 ElectromechanicalField 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 transmembrane electrical field.

AnnotationAssertion
IRI: .owl#ElectromechanicalField
literal: ElectromechanicalField

AnnotationAssertion
IRI: .owl#Energy
literal: jps

AnnotationAssertion
IRI: .owl#Energy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Energy
literal: An Energy is a CBO:PhysicalObjectQuality is the Energy of the object for which it is a quality.

AnnotationAssertion
IRI: .owl#Energy
literal: urn:miriam:opb:'Energy amount'

AnnotationAssertion
IRI: .owl#Energy
literal: Energy

AnnotationAssertion
IRI: .owl#EnergyFunction
literal: jps

AnnotationAssertion
IRI: .owl#EnergyFunction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#EnergyFunction
literal: An EnergyFunction is a CBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the mathematical form used to define a particular EnergyQuality.

AnnotationAssertion
IRI: .owl#EnergyFunction
literal: Energy

AnnotationAssertion
IRI: .owl#EnergyFunction
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#EnergyQuality
literal: jps

AnnotationAssertion
IRI: .owl#EnergyQuality
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#EnergyQuality
literal: A EnergyQuality is a CBO_Object (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.

AnnotationAssertion
IRI: .owl#EnergyQuality
literal: EnergyQuality

AnnotationAssertion
IRI: .owl#EnergyQuality
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#ExistentialCellProcesses
literal: jps

AnnotationAssertion
IRI: .owl#ExistentialCellProcesses
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ExistentialCellProcesses
literal: ExistentialCellProcesses is a CellProcess that is assumed, without formal proof, to be a process of a cell.

AnnotationAssertion
IRI: .owl#ExistentialCellProcesses
literal: ExistentialCellProcesses

AnnotationAssertion
IRI: .owl#Expansion
literal: jps

AnnotationAssertion
IRI: .owl#Expansion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Expansion
literal: Expansion is a VolumeChange resulting in an increase in Volume occupied by an object.

AnnotationAssertion
IRI: .owl#Expansion
literal: Expansion

AnnotationAssertion
IRI: .owl#ExtentGeometrical
literal: jps

AnnotationAssertion
IRI: .owl#ExtentGeometrical
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ExtentGeometrical
literal: ExtentGeometrical is a CBO:GeometricalProperty that describes the basic granularity of the coordinate System.

AnnotationAssertion
IRI: .owl#ExtentGeometrical
literal: ExtentGeometrical

AnnotationAssertion
IRI: .owl#ExtraCellularFluid
literal: jps

AnnotationAssertion
IRI: .owl#ExtraCellularFluid
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ExtraCellularFluid
literal: 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.

AnnotationAssertion
IRI: .owl#ExtraCellularFluid
literal: ExtraCellularFluid

AnnotationAssertion
IRI: .owl#ExtraCellularMatrix
literal: jps

AnnotationAssertion
IRI: .owl#ExtraCellularMatrix
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ExtraCellularMatrix
literal: 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.

AnnotationAssertion
IRI: .owl#ExtraCellularMatrix
literal: urn:miriam:obo.fma:9672

AnnotationAssertion
IRI: .owl#ExtraCellularMatrix
literal: urn:miriam:obo.go:0031012

AnnotationAssertion
IRI: .owl#ExtraCellularMatrix
literal: ExtraCellularMatrix

AnnotationAssertion
IRI: .owl#ExtracellularMatrixProcess
literal: jps

AnnotationAssertion
IRI: .owl#ExtracellularMatrixProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ExtracellularMatrixProcess
literal: ExtracellularMatrixProcess is a CBO_Process involving a change in the qualities, or quantity of extracellular matrix and its components.

AnnotationAssertion
IRI: .owl#ExtracellularMatrixProcess
literal: ExtracellularMatrixProcess

AnnotationAssertion
IRI: .owl#ExtracellularMatrixProcess
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#Field
literal: jps

AnnotationAssertion
IRI: .owl#Field
literal: 19 Jul. 2012

AnnotationAssertion
IRI: .owl#Field
literal: A Field is a CBO_Object 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.

AnnotationAssertion
IRI: .owl#Field
literal: subclass of: BFO:snap:object

AnnotationAssertion
IRI: .owl#FieldProcess
literal: jps

AnnotationAssertion
IRI: .owl#FieldProcess
literal: 11/8/2012

AnnotationAssertion
IRI: .owl#FieldProcess
literal: FieldProcess is a CBO_Process (span:process) describing a process characteristic of a CBO:Field.

AnnotationAssertion
IRI: .owl#FieldProcess
literal: FieldProcess

AnnotationAssertion
IRI: .owl#FieldProcess
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#FieldQuality
literal: jps

AnnotationAssertion
IRI: .owl#FieldQuality
literal: 11/8/2012

AnnotationAssertion
IRI: .owl#FieldQuality
literal: A FieldQuality is a CBO_Object (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.

AnnotationAssertion
IRI: .owl#FieldQuality
literal: FieldQuality

AnnotationAssertion
IRI: .owl#FieldQuality
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#Fill
literal: jps

AnnotationAssertion
IRI: .owl#Fill
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Fill
literal: 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.

AnnotationAssertion
IRI: .owl#Fill
literal: Fill

AnnotationAssertion
IRI: .owl#Filopodium
literal: jps

AnnotationAssertion
IRI: .owl#Filopodium
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Filopodium
literal: 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

AnnotationAssertion
IRI: .owl#Filopodium
literal: urn:miriam:obo.go:0030175

AnnotationAssertion
IRI: .owl#Filopodium
literal: Filopodium

AnnotationAssertion
IRI: .owl#FirstOrderRate
literal: jps

AnnotationAssertion
IRI: .owl#FirstOrderRate
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#FirstOrderRate
literal: 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.

AnnotationAssertion
IRI: .owl#FirstOrderRate
literal: FirstOrderRate

AnnotationAssertion
IRI: .owl#Fission
literal: jps

AnnotationAssertion
IRI: .owl#Fission
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Fission
literal: 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.

AnnotationAssertion
IRI: .owl#Fission
literal: Fission

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: jps

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: A FundamentalPhysicalProcess is a CBO_Process (span:Process) that changes a quality or characteristic of an object.

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: urn:miriam:dummy:1

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: urn:miriam:dummy:2

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: urn:miriam:dummy:3

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: FundamentalPhysicalProcess

AnnotationAssertion
IRI: .owl#FundamentalPhysicalProcess
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#GapJunction
literal: jps

AnnotationAssertion
IRI: .owl#GapJunction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#GapJunction
literal: 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.

AnnotationAssertion
IRI: .owl#GapJunction
literal: urn:miriam:obo.fma:67423

AnnotationAssertion
IRI: .owl#GapJunction
literal: urn:miriam:obo.go:0005921

AnnotationAssertion
IRI: .owl#GapJunction
literal: GapJunction

AnnotationAssertion
IRI: .owl#GenerationalAge
literal: jps

AnnotationAssertion
IRI: .owl#GenerationalAge
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#GenerationalAge
literal: 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.

AnnotationAssertion
IRI: .owl#GenerationalAge
literal: urn:miriam:obo.go:0001302

AnnotationAssertion
IRI: .owl#GenerationalAge
literal: GenerationalAge

AnnotationAssertion
IRI: .owl#GeometricalCellProcess
literal: jps

AnnotationAssertion
IRI: .owl#GeometricalCellProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#GeometricalCellProcess
literal: GeometricalCellProcess is a CellularPropertyProcess that results in a change in the geometry of a cell.

AnnotationAssertion
IRI: .owl#GeometricalCellProcess
literal: GeometricalCellProcess

AnnotationAssertion
IRI: .owl#GeometricalEntity
literal: jps

AnnotationAssertion
IRI: .owl#GeometricalEntity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#GeometricalEntity
literal: GeometricalEntity is a CBO_Object for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions.

AnnotationAssertion
IRI: .owl#GeometricalEntity
literal: GeometricalEntity

AnnotationAssertion
IRI: .owl#GeometricalEntity
literal: subclass of: BFO:snap:independent_continuant

AnnotationAssertion
IRI: .owl#GeometricalProperty
literal: jps

AnnotationAssertion
IRI: .owl#GeometricalProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#GeometricalProperty
literal: 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.

AnnotationAssertion
IRI: .owl#GeometricalProperty
literal: GeometricalProperty

AnnotationAssertion
IRI: .owl#GradientTexture
literal: jps

AnnotationAssertion
IRI: .owl#GradientTexture
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#GradientTexture
literal: GradientTexture is a CBO:Texture consisting of a Texture description that varies smoothly across one or more dimensions.

AnnotationAssertion
IRI: .owl#GradientTexture
literal: GradientTexture

AnnotationAssertion
IRI: .owl#Hamlitonian
literal: jps

AnnotationAssertion
IRI: .owl#Hamlitonian
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Hamlitonian
literal: 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.

AnnotationAssertion
IRI: .owl#Hamlitonian
literal: Hamiltonian

AnnotationAssertion
IRI: .owl#Haptotaxis
literal: jps

AnnotationAssertion
IRI: .owl#Haptotaxis
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Haptotaxis
literal: 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.

AnnotationAssertion
IRI: .owl#Haptotaxis
literal: Haptotaxis

AnnotationAssertion
IRI: .owl#HarmonicEnergy
literal: jps

AnnotationAssertion
IRI: .owl#HarmonicEnergy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#HarmonicEnergy
literal: 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.

AnnotationAssertion
IRI: .owl#HarmonicEnergy
literal: HarmonicEnergy

AnnotationAssertion
IRI: .owl#InterentityExport
literal: jps

AnnotationAssertion
IRI: .owl#InterentityExport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterentityExport
literal: 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.

AnnotationAssertion
IRI: .owl#InterentityExport
literal: InterentityExport

AnnotationAssertion
IRI: .owl#InterentityImport
literal: jps

AnnotationAssertion
IRI: .owl#InterentityImport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterentityImport
literal: 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.

AnnotationAssertion
IRI: .owl#InterentityImport
literal: InterentityImport

AnnotationAssertion
IRI: .owl#InterentityTransport
literal: jps

AnnotationAssertion
IRI: .owl#InterentityTransport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterentityTransport
literal: InterentityTransport is a Transport of an object across a bona fide boundary. For example, from within a bone to the space outside the bone.

AnnotationAssertion
IRI: .owl#InterentityTransport
literal: InterentityTransport

AnnotationAssertion
IRI: .owl#InterentityTransport
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#InterstitialMatrix
literal: jps

AnnotationAssertion
IRI: .owl#InterstitialMatrix
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterstitialMatrix
literal: 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.

AnnotationAssertion
IRI: .owl#InterstitialMatrix
literal: urn:miriam:obo.go:0005614

AnnotationAssertion
IRI: .owl#InterstitialMatrix
literal: InterstitialMatrix

AnnotationAssertion
IRI: .owl#InterstitialMatrixChange
literal: jps

AnnotationAssertion
IRI: .owl#InterstitialMatrixChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterstitialMatrixChange
literal: InterstitialMatrixChange is an InterstitialMatrixProcess involving a change in the components or characteristics of the interstitial matrix components.

AnnotationAssertion
IRI: .owl#InterstitialMatrixChange
literal: InterstitialMatrixChange

AnnotationAssertion
IRI: .owl#InterstitialMatrixCreation
literal: jps

AnnotationAssertion
IRI: .owl#InterstitialMatrixCreation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterstitialMatrixCreation
literal: InterstitialMatrixCreation is an InterstitialMatrixProcess involving an increase in the quantity of the interstitial matrix and its components.

AnnotationAssertion
IRI: .owl#InterstitialMatrixCreation
literal: InterstitialMatrixCreation

AnnotationAssertion
IRI: .owl#InterstitialMatrixDeletion
literal: jps

AnnotationAssertion
IRI: .owl#InterstitialMatrixDeletion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterstitialMatrixDeletion
literal: InterstitialMatrixDeletion is an InterstitialMatrixProcess involving a decrease in the quantity of the interstitial matrix and its components.

AnnotationAssertion
IRI: .owl#InterstitialMatrixDeletion
literal: InterstitialMatrixDeletion

AnnotationAssertion
IRI: .owl#InterstitialMatrixProcess
literal: jps

AnnotationAssertion
IRI: .owl#InterstitialMatrixProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#InterstitialMatrixProcess
literal: InterstitialMatrixProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of interstitial matrix and its components.

AnnotationAssertion
IRI: .owl#InterstitialMatrixProcess
literal: InterstitialMatrixProcess

AnnotationAssertion
IRI: .owl#IntraentityTransport
literal: jps

AnnotationAssertion
IRI: .owl#IntraentityTransport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IntraentityTransport
literal: 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.

AnnotationAssertion
IRI: .owl#IntraentityTransport
literal: IntraentityTransport

AnnotationAssertion
IRI: .owl#IonChannel
literal: jps

AnnotationAssertion
IRI: .owl#IonChannel
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IonChannel
literal: 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.

AnnotationAssertion
IRI: .owl#IonChannel
literal: urn:miriam:obo.go:0022831

AnnotationAssertion
IRI: .owl#IonChannel
literal: IonChannel

AnnotationAssertion
IRI: .owl#IsApoptotic
literal: jps

AnnotationAssertion
IRI: .owl#IsApoptotic
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IsApoptotic
literal: 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.

AnnotationAssertion
IRI: .owl#IsApoptotic
literal: IsApoptotic

AnnotationAssertion
IRI: .owl#IsDebris
literal: jps

AnnotationAssertion
IRI: .owl#IsDebris
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IsDebris
literal: 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.

AnnotationAssertion
IRI: .owl#IsDebris
literal: IsDebris

AnnotationAssertion
IRI: .owl#IsGrowing
literal: jps

AnnotationAssertion
IRI: .owl#IsGrowing
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IsGrowing
literal: 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.

AnnotationAssertion
IRI: .owl#IsGrowing
literal: IsGrowing

AnnotationAssertion
IRI: .owl#IsHypoxic
literal: jps

AnnotationAssertion
IRI: .owl#IsHypoxic
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IsHypoxic
literal: 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.

AnnotationAssertion
IRI: .owl#IsHypoxic
literal: IsHypoxic

AnnotationAssertion
IRI: .owl#IsNecrotic
literal: jps

AnnotationAssertion
IRI: .owl#IsNecrotic
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IsNecrotic
literal: 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.

AnnotationAssertion
IRI: .owl#IsNecrotic
literal: IsNecrotic

AnnotationAssertion
IRI: .owl#IsQuiescent
literal: jps

AnnotationAssertion
IRI: .owl#IsQuiescent
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#IsQuiescent
literal: 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.

AnnotationAssertion
IRI: .owl#IsQuiescent
literal: IsQuiescent

AnnotationAssertion
IRI: .owl#Isotropy
literal: jps

AnnotationAssertion
IRI: .owl#Isotropy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Isotropy
literal: 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.

AnnotationAssertion
IRI: .owl#Isotropy
literal: Isotropy

AnnotationAssertion
IRI: .owl#KineticProperty
literal: jps

AnnotationAssertion
IRI: .owl#KineticProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#KineticProperty
literal: KineticProperty is a CBO:PhysicalObjectQuality describing a kinetic characteristic of an object.

AnnotationAssertion
IRI: .owl#KineticProperty
literal: urn:miriam:opb:'Kinetic manifestation'

AnnotationAssertion
IRI: .owl#KineticProperty
literal: KineticProperty

AnnotationAssertion
IRI: .owl#LJ_6_12Energy
literal: jps

AnnotationAssertion
IRI: .owl#LJ_6_12Energy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#LJ_6_12Energy
literal: 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.

AnnotationAssertion
IRI: .owl#LJ_6_12Energy
literal: LJ_6_12Energy

AnnotationAssertion
IRI: .owl#LateralPart
literal: jps

AnnotationAssertion
IRI: .owl#LateralPart
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#LateralPart
literal: LateralPart is a CBO:CellRegion that is between the CBO:BasalPart and CBO:LateralPart.

AnnotationAssertion
IRI: .owl#LateralPart
literal: LateralPart

AnnotationAssertion
IRI: .owl#LinearEnergy
literal: jps

AnnotationAssertion
IRI: .owl#LinearEnergy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#LinearEnergy
literal: 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.

AnnotationAssertion
IRI: .owl#LinearEnergy
literal: LinearEnergy

AnnotationAssertion
IRI: .owl#Location
literal: jps

AnnotationAssertion
IRI: .owl#Location
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Location
literal: 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

AnnotationAssertion
IRI: .owl#Location
literal: Location

AnnotationAssertion
IRI: .owl#Mass
literal: jps

AnnotationAssertion
IRI: .owl#Mass
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Mass
literal: Mass is a CBO:PhysicalObjectQuality describing the Mass of the object.

AnnotationAssertion
IRI: .owl#Mass
literal: PATO:0000125

AnnotationAssertion
IRI: .owl#Mass
literal: urn:miriam:opb:'Discrete solid Mass'

AnnotationAssertion
IRI: .owl#Mass
literal: Mass

AnnotationAssertion
IRI: .owl#MechanicalProperty
literal: jps

AnnotationAssertion
IRI: .owl#MechanicalProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MechanicalProperty
literal: 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.

AnnotationAssertion
IRI: .owl#MechanicalProperty
literal: MechanicalProperty

AnnotationAssertion
IRI: .owl#MedialPart
literal: jps

AnnotationAssertion
IRI: .owl#MedialPart
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MedialPart
literal: MedialPart is a CBO:CellRegion located near the center of the Cell.

AnnotationAssertion
IRI: .owl#MedialPart
literal: MedialPart

AnnotationAssertion
IRI: .owl#Meiosis
literal: jps

AnnotationAssertion
IRI: .owl#Meiosis
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Meiosis
literal: 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.

AnnotationAssertion
IRI: .owl#Meiosis
literal: urn:miriam:obo.go:0007126

AnnotationAssertion
IRI: .owl#Meiosis
literal: Meiosis

AnnotationAssertion
IRI: .owl#MembraneReceptor
literal: jps

AnnotationAssertion
IRI: .owl#MembraneReceptor
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MembraneReceptor
literal: 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.

AnnotationAssertion
IRI: .owl#MembraneReceptor
literal: MembraneReceptor

AnnotationAssertion
IRI: .owl#MinimizationAcceptanceFunction
literal: jps

AnnotationAssertion
IRI: .owl#MinimizationAcceptanceFunction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MinimizationAcceptanceFunction
literal: 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.

AnnotationAssertion
IRI: .owl#MinimizationAcceptanceFunction
literal: MinimizationAcceptanceFunction

AnnotationAssertion
IRI: .owl#Mitosis
literal: jps

AnnotationAssertion
IRI: .owl#Mitosis
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Mitosis
literal: 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.

AnnotationAssertion
IRI: .owl#Mitosis
literal: urn:miriam:obo.go:0007067

AnnotationAssertion
IRI: .owl#Mitosis
literal: Mitosis

AnnotationAssertion
IRI: .owl#MolecularField
literal: jps

AnnotationAssertion
IRI: .owl#MolecularField
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MolecularField
literal: 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.

AnnotationAssertion
IRI: .owl#MolecularField
literal: MolecularField

AnnotationAssertion
IRI: .owl#MolecularField
literal: subclass of: BFO:snap:object

AnnotationAssertion
IRI: .owl#MolecularTargeting
literal: jps

AnnotationAssertion
IRI: .owl#MolecularTargeting
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MolecularTargeting
literal: MolecularTargeting is an IntraentityTransport in which a molecule is actively directed from one place in a cell to another.

AnnotationAssertion
IRI: .owl#MolecularTargeting
literal: urn:miriam:obo.go:0006605

AnnotationAssertion
IRI: .owl#MolecularTargeting
literal: MolecularTargeting

AnnotationAssertion
IRI: .owl#Molecule
literal: jps

AnnotationAssertion
IRI: .owl#Molecule
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Molecule
literal: Molecule is a CBO:BioEntityType class OPB: ...that is a polyatomic entity.

AnnotationAssertion
IRI: .owl#Molecule
literal: urn:miriam:opb:'Molecule'

AnnotationAssertion
IRI: .owl#Molecule
literal: Molecule

AnnotationAssertion
IRI: .owl#MoleculeBarrierCrossing
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeBarrierCrossing
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeBarrierCrossing
literal: MoleculeBarrierCrossing is a MoleculeProcess describing the transfer of a molecule across a bona fide boundary such as a basement membrane or a cell wall.

AnnotationAssertion
IRI: .owl#MoleculeBarrierCrossing
literal: MoleculeBarrierCrossing

AnnotationAssertion
IRI: .owl#MoleculeChange
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeChange
literal: MoleculeChange is a MoleculeProcess that results in a phenotypic change in the molecule. For example, changes in the ionization state of an acid.

AnnotationAssertion
IRI: .owl#MoleculeChange
literal: MoleculeChange

AnnotationAssertion
IRI: .owl#MoleculeCreation
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeCreation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeCreation
literal: MoleculeCreation is a MoleculeProcess that results in the Creation of a new molecule or an increase in a molecule's concentration.

AnnotationAssertion
IRI: .owl#MoleculeCreation
literal: MoleculeCreation

AnnotationAssertion
IRI: .owl#MoleculeDeletion
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeDeletion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeDeletion
literal: MoleculeDeletion is a MoleculeProcess that results in the Deletion of a molecule, or a decrease in a molecule's concentration.

AnnotationAssertion
IRI: .owl#MoleculeDeletion
literal: MoleculeDeletion

AnnotationAssertion
IRI: .owl#MoleculeDiffusion
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeDiffusion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeDiffusion
literal: 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.

AnnotationAssertion
IRI: .owl#MoleculeDiffusion
literal: MoleculeDiffusion

AnnotationAssertion
IRI: .owl#MoleculeDiffusion
literal: subclass of: BFO:span:fiat_process_part

AnnotationAssertion
IRI: .owl#MoleculeMoleculeAdhesion
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeMoleculeAdhesion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeMoleculeAdhesion
literal: 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.

AnnotationAssertion
IRI: .owl#MoleculeMoleculeAdhesion
literal: MoleculeMoleculeAdhesion

AnnotationAssertion
IRI: .owl#MoleculeProcess
literal: jps

AnnotationAssertion
IRI: .owl#MoleculeProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MoleculeProcess
literal: MoleculeProcess is a CBO_Process that involves a molecule.

AnnotationAssertion
IRI: .owl#MoleculeProcess
literal: MoleculeProcess

AnnotationAssertion
IRI: .owl#MoleculeProcess
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#Movement
literal: jps

AnnotationAssertion
IRI: .owl#Movement
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Movement
literal: Movement is a FundamentalPhysicalProcess resulting in the change in location or Shape of a physical object.

AnnotationAssertion
IRI: .owl#Movement
literal: Movement

AnnotationAssertion
IRI: .owl#Movement
literal: subclass of: BFO:span:fiat_process_part

AnnotationAssertion
IRI: .owl#MovementField
literal: jps

AnnotationAssertion
IRI: .owl#MovementField
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#MovementField
literal: 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.

AnnotationAssertion
IRI: .owl#MovementField
literal: MovementField

AnnotationAssertion
IRI: .owl#Necrosis
literal: jps

AnnotationAssertion
IRI: .owl#Necrosis
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Necrosis
literal: Necrosis is a CellDeath caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin.

AnnotationAssertion
IRI: .owl#Necrosis
literal: PATO:0000647

AnnotationAssertion
IRI: .owl#Necrosis
literal: Necrosis

AnnotationAssertion
IRI: .owl#Nucleus
literal: jps

AnnotationAssertion
IRI: .owl#Nucleus
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Nucleus
literal: 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.

AnnotationAssertion
IRI: .owl#Nucleus
literal: urn:miriam:obo.fma:63840

AnnotationAssertion
IRI: .owl#Nucleus
literal: urn:miriam:obo.go:0005634

AnnotationAssertion
IRI: .owl#Nucleus
literal: Nucleus

AnnotationAssertion
IRI: .owl#OpenAlea
literal: jps

AnnotationAssertion
IRI: .owl#OpenAlea
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#OpenAlea
literal: 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

AnnotationAssertion
IRI: .owl#OpenAlea
literal: OpenAlea

AnnotationAssertion
IRI: .owl#OpenSourcePlatform
literal: jps

AnnotationAssertion
IRI: .owl#OpenSourcePlatform
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#OpenSourcePlatform
literal: OpenSourceModelPlatform is a CBO:ComputationalPlatformQuality class for compuational platforms which are open source.

AnnotationAssertion
IRI: .owl#OpenSourcePlatform
literal: OpenSourceModelPlatform

AnnotationAssertion
IRI: .owl#OrganismalRegion
literal: jps

AnnotationAssertion
IRI: .owl#OrganismalRegion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#OrganismalRegion
literal: OrganismalRegion is a CBO:GeometricalEntity class for regions of an animal.

AnnotationAssertion
IRI: .owl#OrganismalRegion
literal: OrganismalRegion

AnnotationAssertion
IRI: .owl#OrganismalRegion
literal: subclass of: BFO:snap:fiat_object_part

AnnotationAssertion
IRI: .owl#Orientation
literal: jps

AnnotationAssertion
IRI: .owl#Orientation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Orientation
literal: 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.

AnnotationAssertion
IRI: .owl#Orientation
literal: Orientation

AnnotationAssertion
IRI: .owl#Other
literal: jps

AnnotationAssertion
IRI: .owl#Other
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#Other
literal: 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.

AnnotationAssertion
IRI: .owl#Other
literal: OtherComputationalPlatform

AnnotationAssertion
IRI: .owl#OtherPublicationReference
literal: jps

AnnotationAssertion
IRI: .owl#OtherPublicationReference
literal: 23 Jul. 2012

AnnotationAssertion
IRI: .owl#OtherPublicationReference
literal: OtherPublicationReference is a CBO:ComputationalPlatformQuality class for computational platforms referenced only by a literature citation.

AnnotationAssertion
IRI: .owl#OtherPublicationReference
literal: OtherPublicationReference

AnnotationAssertion
IRI: .owl#PatternTexture
literal: jps

AnnotationAssertion
IRI: .owl#PatternTexture
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#PatternTexture
literal: PatternTexture is a CBO:Texture consisting of a positionally repetitive Texture description.

AnnotationAssertion
IRI: .owl#PatternTexture
literal: PatternTexture

AnnotationAssertion
IRI: .owl#PhenotypicChange
literal: jps

AnnotationAssertion
IRI: .owl#PhenotypicChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#PhenotypicChange
literal: 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.

AnnotationAssertion
IRI: .owl#PhenotypicChange
literal: PhenotypicChange

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: jps

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: A PhysicalEntityType is a CBO_Object class of physical objects. For example, a Cell, a basement membrane of a diffusible Molecule.

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: urn:miriam:dummy:1

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: urn:miriam:dummy:2

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: urn:miriam:dummy:3

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: PhysicalEntityType

AnnotationAssertion
IRI: .owl#PhysicalEntityType
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#PhysicalObjectQuality
literal: jps

AnnotationAssertion
IRI: .owl#PhysicalObjectQuality
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#PhysicalObjectQuality
literal: A PhysicalObjectQuality is a CBO_Object (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.

AnnotationAssertion
IRI: .owl#PhysicalObjectQuality
literal: PhysicalObjectQuality

AnnotationAssertion
IRI: .owl#PhysicalObjectQuality
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#PoissonRatio
literal: jps

AnnotationAssertion
IRI: .owl#PoissonRatio
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#PoissonRatio
literal: 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).

AnnotationAssertion
IRI: .owl#PoissonRatio
literal: PoissonRatio

AnnotationAssertion
IRI: .owl#PressureMechanical
literal: jps

AnnotationAssertion
IRI: .owl#PressureMechanical
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#PressureMechanical
literal: PressureMechanical is a CBO:MechanicalProperty describing the barometric pressure of an object or Location in space.

AnnotationAssertion
IRI: .owl#PressureMechanical
literal: PressureMechanical

AnnotationAssertion
IRI: .owl#Protrusion
literal: jps

AnnotationAssertion
IRI: .owl#Protrusion
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Protrusion
literal: Protrusion is a GeometricalProperty describing an extension from an otherwise simpler CBO:BodyShape description. For example, a transient pseudopodia or a persistent neuronal axon.

AnnotationAssertion
IRI: .owl#Protrusion
literal: Protrusion

AnnotationAssertion
IRI: .owl#Pseudopodium
literal: jps

AnnotationAssertion
IRI: .owl#Pseudopodium
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Pseudopodium
literal: 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

AnnotationAssertion
IRI: .owl#Pseudopodium
literal: urn:miriam:obo.go:0031143

AnnotationAssertion
IRI: .owl#Pseudopodium
literal: Pseudopodium

AnnotationAssertion
IRI: .owl#Pump
literal: jps

AnnotationAssertion
IRI: .owl#Pump
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Pump
literal: 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.

AnnotationAssertion
IRI: .owl#Pump
literal: MeSH: D12.776.157.530

AnnotationAssertion
IRI: .owl#Pump
literal: MeSH:'Membrane Transport Proteins'

AnnotationAssertion
IRI: .owl#Pump
literal: Pump

AnnotationAssertion
IRI: .owl#Random
literal: jps

AnnotationAssertion
IRI: .owl#Random
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Random
literal: Random is a CBO:StatisticalProperty class that describes a quality of randomness to an object or process.

AnnotationAssertion
IRI: .owl#Random
literal: Random

AnnotationAssertion
IRI: .owl#RateFunction
literal: jps

AnnotationAssertion
IRI: .owl#RateFunction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#RateFunction
literal: An RateFunction is a CBO_Object (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.

AnnotationAssertion
IRI: .owl#RateFunction
literal: RateFunction

AnnotationAssertion
IRI: .owl#RateFunction
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#Rotation
literal: jps

AnnotationAssertion
IRI: .owl#Rotation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Rotation
literal: Rotation is a Movement resulting in a change in orientation of an object.

AnnotationAssertion
IRI: .owl#Rotation
literal: Rotation

AnnotationAssertion
IRI: .owl#SecondOrderRate
literal: jps

AnnotationAssertion
IRI: .owl#SecondOrderRate
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#SecondOrderRate
literal: 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.

AnnotationAssertion
IRI: .owl#SecondOrderRate
literal: SecondOrderRate

AnnotationAssertion
IRI: .owl#Shape
literal: jps

AnnotationAssertion
IRI: .owl#Shape
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Shape
literal: 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.

AnnotationAssertion
IRI: .owl#Shape
literal: PATO:0000052

AnnotationAssertion
IRI: .owl#Shape
literal: urn:miriam:opb:'bounded Volume Shape'

AnnotationAssertion
IRI: .owl#Shape
literal: Shape

AnnotationAssertion
IRI: .owl#ShapeChange
literal: jps

AnnotationAssertion
IRI: .owl#ShapeChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ShapeChange
literal: ShapeChange is a FundamentalPhysicalProcess resulting in the change in the Shape, including extents, of an object.

AnnotationAssertion
IRI: .owl#ShapeChange
literal: ShapeChange

AnnotationAssertion
IRI: .owl#ShapeChange
literal: subclass of: BFO:span:fiat_process_part

AnnotationAssertion
IRI: .owl#SpacialExclusive
literal: jps

AnnotationAssertion
IRI: .owl#SpacialExclusive
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#SpacialExclusive
literal: 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.

AnnotationAssertion
IRI: .owl#SpacialExclusive
literal: SpacialExclusive

AnnotationAssertion
IRI: .owl#StatisticalProperty
literal: jps

AnnotationAssertion
IRI: .owl#StatisticalProperty
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#StatisticalProperty
literal: StatisticalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the statistical qualities of objects. StatisticalProperty are intrinsic to the object.

AnnotationAssertion
IRI: .owl#StatisticalProperty
literal: StatisticalProperty

AnnotationAssertion
IRI: .owl#StiffnessMechanical
literal: jps

AnnotationAssertion
IRI: .owl#StiffnessMechanical
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#StiffnessMechanical
literal: StiffnessMechanical is a CBO:MechanicalProperty that describes an elastic object's resistance to deformation by an applied force along a given direction.

AnnotationAssertion
IRI: .owl#StiffnessMechanical
literal: StiffnessMechanical

AnnotationAssertion
IRI: .owl#StructuralProcess
literal: jps

AnnotationAssertion
IRI: .owl#StructuralProcess
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#StructuralProcess
literal: StructuralProcess is a CBO_Process (span:process) that results does not result in a change in the identity of the Object, but the Object does change in its DATA structure.

AnnotationAssertion
IRI: .owl#StructuralProcess
literal: StructuralProcess

AnnotationAssertion
IRI: .owl#StructuralProcess
literal: subclass of: BFO:span:process

AnnotationAssertion
IRI: .owl#SurfaceArea
literal: jps

AnnotationAssertion
IRI: .owl#SurfaceArea
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#SurfaceArea
literal: SurfaceArea is a CBO:GeometricalProperty describing the scalar value of the object's surface area at a particular instant in time.

AnnotationAssertion
IRI: .owl#SurfaceArea
literal: urn:miriam:opb:'Area of surface region'

AnnotationAssertion
IRI: .owl#SurfaceArea
literal: SurfaceArea

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionOrientedCleavagePlane
literal: jps

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionOrientedCleavagePlane
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionOrientedCleavagePlane
literal: 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.

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionOrientedCleavagePlane
literal: SymmetricCellDivisionOrientedCleavagePlane

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionRandomCleavagePlane
literal: jps

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionRandomCleavagePlane
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionRandomCleavagePlane
literal: 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.

AnnotationAssertion
IRI: .owl#SymmetricCellDivisionRandomCleavagePlane
literal: SymmetricCellDivisionRandomCleavagePlane

AnnotationAssertion
IRI: .owl#System
literal: jps

AnnotationAssertion
IRI: .owl#System
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#System
literal: System is a CBO_Object 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.

AnnotationAssertion
IRI: .owl#System
literal: System

AnnotationAssertion
IRI: .owl#System
literal: subclass of: BFO:snap:object

AnnotationAssertion
IRI: .owl#SystemBoundary
literal: jps

AnnotationAssertion
IRI: .owl#SystemBoundary
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemBoundary
literal: SystemBoundary is a SystemQuality that describes the edges (boundary) of a computational model.

AnnotationAssertion
IRI: .owl#SystemBoundary
literal: SystemBoundary

AnnotationAssertion
IRI: .owl#SystemExtent
literal: jps

AnnotationAssertion
IRI: .owl#SystemExtent
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemExtent
literal: 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.

AnnotationAssertion
IRI: .owl#SystemExtent
literal: SystemExtent

AnnotationAssertion
IRI: .owl#SystemExtentX
literal: jps

AnnotationAssertion
IRI: .owl#SystemExtentX
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemExtentX
literal: 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.

AnnotationAssertion
IRI: .owl#SystemExtentX
literal: SystemExtentX

AnnotationAssertion
IRI: .owl#SystemExtentY
literal: jps

AnnotationAssertion
IRI: .owl#SystemExtentY
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemExtentY
literal: 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.

AnnotationAssertion
IRI: .owl#SystemExtentY
literal: SystemExtentY

AnnotationAssertion
IRI: .owl#SystemExtentZ
literal: jps

AnnotationAssertion
IRI: .owl#SystemExtentZ
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemExtentZ
literal: 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.

AnnotationAssertion
IRI: .owl#SystemExtentZ
literal: SystemExtentZ

AnnotationAssertion
IRI: .owl#SystemPeriodic
literal: jps

AnnotationAssertion
IRI: .owl#SystemPeriodic
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemPeriodic
literal: 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.

AnnotationAssertion
IRI: .owl#SystemPeriodic
literal: SystemPeriodic

AnnotationAssertion
IRI: .owl#SystemPeriodicX
literal: jpos

AnnotationAssertion
IRI: .owl#SystemPeriodicX
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemPeriodicX
literal: 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.

AnnotationAssertion
IRI: .owl#SystemPeriodicX
literal: SystemPeriodicX

AnnotationAssertion
IRI: .owl#SystemPeriodicY
literal: jps

AnnotationAssertion
IRI: .owl#SystemPeriodicY
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemPeriodicY
literal: 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.

AnnotationAssertion
IRI: .owl#SystemPeriodicY
literal: SystemPeriodicY

AnnotationAssertion
IRI: .owl#SystemPeriodicZ
literal: jps

AnnotationAssertion
IRI: .owl#SystemPeriodicZ
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemPeriodicZ
literal: 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.

AnnotationAssertion
IRI: .owl#SystemPeriodicZ
literal: SystemPeriodicZ

AnnotationAssertion
IRI: .owl#SystemPixelDistanceScale
literal: jps

AnnotationAssertion
IRI: .owl#SystemPixelDistanceScale
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemPixelDistanceScale
literal: 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.

AnnotationAssertion
IRI: .owl#SystemPixelDistanceScale
literal: SystemPixel2DistanceScale

AnnotationAssertion
IRI: .owl#SystemQualities
literal: jps

AnnotationAssertion
IRI: .owl#SystemQualities
literal: 24 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemQualities
literal: SystemQualities is CBO_Object class that describes the computational platform (suite of code or a standalone computational tool) and instantiation of a particular model.

AnnotationAssertion
IRI: .owl#SystemQualities
literal: SystemQuality

AnnotationAssertion
IRI: .owl#SystemQualities
literal: subclass of: BFO:snap:quality

AnnotationAssertion
IRI: .owl#SystemWall
literal: jps

AnnotationAssertion
IRI: .owl#SystemWall
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemWall
literal: 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.

AnnotationAssertion
IRI: .owl#SystemWall
literal: SystemWall

AnnotationAssertion
IRI: .owl#SystemWallX
literal: jps

AnnotationAssertion
IRI: .owl#SystemWallX
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemWallX
literal: 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.

AnnotationAssertion
IRI: .owl#SystemWallX
literal: SystemWallX

AnnotationAssertion
IRI: .owl#SystemWallY
literal: jps

AnnotationAssertion
IRI: .owl#SystemWallY
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemWallY
literal: 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.

AnnotationAssertion
IRI: .owl#SystemWallY
literal: SystemWallY

AnnotationAssertion
IRI: .owl#SystemWallZ
literal: jps

AnnotationAssertion
IRI: .owl#SystemWallZ
literal: 25 Jul. 2012

AnnotationAssertion
IRI: .owl#SystemWallZ
literal: 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.

AnnotationAssertion
IRI: .owl#SystemWallZ
literal: SystemWallZ

AnnotationAssertion
IRI: .owl#TemperatureField
literal: jps

AnnotationAssertion
IRI: .owl#TemperatureField
literal: 19 Jul. 2012

AnnotationAssertion
IRI: .owl#TemperatureField
literal: 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.)

AnnotationAssertion
IRI: .owl#TemperatureField
literal: 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.)

AnnotationAssertion
IRI: .owl#TemperatureField
literal: TemperatureField

AnnotationAssertion
IRI: .owl#TemporalAge
literal: jps

AnnotationAssertion
IRI: .owl#TemporalAge
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#TemporalAge
literal: 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.

AnnotationAssertion
IRI: .owl#TemporalAge
literal: urn:miriam:obo.pato:0000011

AnnotationAssertion
IRI: .owl#TemporalAge
literal: TemporalAge

AnnotationAssertion
IRI: .owl#TemporalEntity
literal: jps

AnnotationAssertion
IRI: .owl#TemporalEntity
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#TemporalEntity
literal: TemporalEntity is a CBO_Processt that OPB: ...is a moment or span of time.

AnnotationAssertion
IRI: .owl#TemporalEntity
literal: urn:miriam:opb:'temporal entity'

AnnotationAssertion
IRI: .owl#TemporalEntity
literal: TemporalEntity

AnnotationAssertion
IRI: .owl#TemporalEntity
literal: subclass of: BFO:span:connected_temporal_region

AnnotationAssertion
IRI: .owl#TemporalInstant
literal: jps

AnnotationAssertion
IRI: .owl#TemporalInstant
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#TemporalInstant
literal: OPB: ...is a point in time.

AnnotationAssertion
IRI: .owl#TemporalInstant
literal: urn:miriam:opb:'temporal instant'

AnnotationAssertion
IRI: .owl#TemporalInstant
literal: TemporalInstant

AnnotationAssertion
IRI: .owl#TemporalInstant
literal: subclass of: BFO:snap:TemporalInstant

AnnotationAssertion
IRI: .owl#TemporalInterval
literal: jps

AnnotationAssertion
IRI: .owl#TemporalInterval
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#TemporalInterval
literal: OPB: ...is a period of time bounded by two temporal moments (that may be the same moment).

AnnotationAssertion
IRI: .owl#TemporalInterval
literal: urn:miriam:opb:'temporal interval'

AnnotationAssertion
IRI: .owl#TemporalInterval
literal: TemporalInterval

AnnotationAssertion
IRI: .owl#TemporalInterval
literal: subclass of: BFO:snap:TemporalInterval

AnnotationAssertion
IRI: .owl#TensionMechanical
literal: jps

AnnotationAssertion
IRI: .owl#TensionMechanical
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#TensionMechanical
literal: TensionMechanical is a CBO:MechanicalProperty that describes the pulling force exerted on an entity (a stretching or distorting force).

AnnotationAssertion
IRI: .owl#TensionMechanical
literal: TensionMechanical

AnnotationAssertion
IRI: .owl#Texture
literal: jps

AnnotationAssertion
IRI: .owl#Texture
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Texture
literal: Texture is a CBO:GeometricalProperty describing the characteristics of a surface Texture.

AnnotationAssertion
IRI: .owl#Texture
literal: Texture

AnnotationAssertion
IRI: .owl#TightJunction
literal: jps

AnnotationAssertion
IRI: .owl#TightJunction
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#TightJunction
literal: 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)

AnnotationAssertion
IRI: .owl#TightJunction
literal: urn:miriam:obo.go:0005923

AnnotationAssertion
IRI: .owl#TightJunction
literal: TightJunction

AnnotationAssertion
IRI: .owl#Translation
literal: jps

AnnotationAssertion
IRI: .owl#Translation
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Translation
literal: Translation is a Movement resulting in a change in the spatial location of an object.

AnnotationAssertion
IRI: .owl#Translation
literal: Translation

AnnotationAssertion
IRI: .owl#Transport
literal: jps

AnnotationAssertion
IRI: .owl#Transport
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Transport
literal: 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).

AnnotationAssertion
IRI: .owl#Transport
literal: TransportProcess

AnnotationAssertion
IRI: .owl#UniformTexture
literal: jps

AnnotationAssertion
IRI: .owl#UniformTexture
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#UniformTexture
literal: UniformTexture is a CBO:Texture consisting of a positionally independent Texture description.

AnnotationAssertion
IRI: .owl#UniformTexture
literal: UniformTexture

AnnotationAssertion
IRI: .owl#VTK_FileName
literal: JPS

AnnotationAssertion
IRI: .owl#VTK_FileName
literal: 10/25/2012

AnnotationAssertion
IRI: .owl#VTK_FileName
literal: 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.

AnnotationAssertion
IRI: .owl#VTK_FileName
literal: VTK_FileName

AnnotationAssertion
IRI: .owl#VTK_FileRoot
literal: JPS

AnnotationAssertion
IRI: .owl#VTK_FileRoot
literal: 10/25/2012

AnnotationAssertion
IRI: .owl#VTK_FileRoot
literal: VTK_FileRoot is a CBO:SystemQuality:VTK_Quality giving the root name for the VTK files associated with the particular model.

AnnotationAssertion
IRI: .owl#VTK_FileRoot
literal: VTK_FileRoot

AnnotationAssertion
IRI: .owl#VTK_FileTimeStep
literal: JPS

AnnotationAssertion
IRI: .owl#VTK_FileTimeStep
literal: 10/25/2012

AnnotationAssertion
IRI: .owl#VTK_FileTimeStep
literal: 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).

AnnotationAssertion
IRI: .owl#VTK_FileTimeStep
literal: VTK_FileTimeStep

AnnotationAssertion
IRI: .owl#VTK_InitialCondition
literal: jps

AnnotationAssertion
IRI: .owl#VTK_InitialCondition
literal: 10/25/2012

AnnotationAssertion
IRI: .owl#VTK_InitialCondition
literal: 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.

AnnotationAssertion
IRI: .owl#VTK_InitialCondition
literal: VTK_InitialCondition

AnnotationAssertion
IRI: .owl#VTK_Quality
literal: JPS

AnnotationAssertion
IRI: .owl#VTK_Quality
literal: 10/29/2012

AnnotationAssertion
IRI: .owl#VTK_Quality
literal: VTK_Quality is a CBO:SystemQuality that includes classes for specificying the name, ilneage and time of a VTK snap(shot) of the simulation.

AnnotationAssertion
IRI: .owl#VTK_Quality
literal: VTK_Quality

AnnotationAssertion
IRI: .owl#Ventral
literal: jps

AnnotationAssertion
IRI: .owl#Ventral
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Ventral
literal: 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.

AnnotationAssertion
IRI: .owl#Ventral
literal: Ventral

AnnotationAssertion
IRI: .owl#Volume
literal: jps

AnnotationAssertion
IRI: .owl#Volume
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#Volume
literal: Volume is a GeometricalProperty describing the total Volume of spaced occupied by the object at a particular instant in time.

AnnotationAssertion
IRI: .owl#Volume
literal: PATO:0000918

AnnotationAssertion
IRI: .owl#Volume
literal: urn:miriam:opb:'Volume of Volume region'

AnnotationAssertion
IRI: .owl#Volume
literal: Volume

AnnotationAssertion
IRI: .owl#VolumeChange
literal: jps

AnnotationAssertion
IRI: .owl#VolumeChange
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#VolumeChange
literal: VolumeChange is a FundamentalPhysicalProcess resulting in a change, an increase or decrease, in the Volume occupied by an object.

AnnotationAssertion
IRI: .owl#VolumeChange
literal: VolumeChange

AnnotationAssertion
IRI: .owl#VolumeChange
literal: subclass of: BFO:span:fiat_process_part

AnnotationAssertion
IRI: .owl#VolumeEnergy
literal: jps

AnnotationAssertion
IRI: .owl#VolumeEnergy
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#VolumeEnergy
literal: A VolumeEnergy is a CBO:EnergyQuality representing the energy associated with a given volume entity.

AnnotationAssertion
IRI: .owl#VolumeEnergy
literal: VolumeEnergy

AnnotationAssertion
IRI: .owl#YieldingThreshold
literal: jps

AnnotationAssertion
IRI: .owl#YieldingThreshold
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#YieldingThreshold
literal: YieldingThreshold (Yield stress threshold, Y) is a CBO:MechanicalProperty describing the rheological yield stress of an object.

AnnotationAssertion
IRI: .owl#YieldingThreshold
literal: YieldingThreshold

AnnotationAssertion
IRI: .owl#YoungsModulus
literal: jps

AnnotationAssertion
IRI: .owl#YoungsModulus
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#YoungsModulus
literal: 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)

AnnotationAssertion
IRI: .owl#YoungsModulus
literal: YoungsModulus

AnnotationAssertion
IRI: .owl#ZerothOrderRate
literal: jps

AnnotationAssertion
IRI: .owl#ZerothOrderRate
literal: 24 Aug. 2011

AnnotationAssertion
IRI: .owl#ZerothOrderRate
literal: 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.

AnnotationAssertion
IRI: .owl#ZerothOrderRate
literal: ZerothOrderRate

AnnotationAssertion
IRI: .owl#hasExtentValueSet1D
literal: 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.

AnnotationAssertion
IRI: .owl#hasExtentValueSet1D
literal: hasExtentValueSet1D

AnnotationAssertion
IRI: .owl#hasExtentValueSet2D
literal: 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.

AnnotationAssertion
IRI: .owl#hasExtentValueSet2D
literal: hasExtentValueSet2D

AnnotationAssertion
IRI: .owl#hasExtentValueSet3D
literal: 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.

AnnotationAssertion
IRI: .owl#hasExtentValueSet3D
literal: hasExtentValueSet3D

AnnotationAssertion
IRI: .owl#hasFloatValue
literal: A single floating point number.

AnnotationAssertion
IRI: .owl#hasFloatValue
literal: hasFloatValue

AnnotationAssertion
IRI: .owl#hasFloatValueTarget
literal: A single floating point number representing the target value of a quality or function.

AnnotationAssertion
IRI: .owl#hasFloatValueTarget
literal: hasFloatValueTarget

AnnotationAssertion
IRI: .owl#hasIntValue
literal: A single integer number.

AnnotationAssertion
IRI: .owl#hasIntValue
literal: hasIntValue

AnnotationAssertion
IRI: .owl#hasIntValueTarget
literal: A single integer number representing the target value of a quality or function.

AnnotationAssertion
IRI: .owl#hasIntValueTarget
literal: hasIntValueTarget

AnnotationAssertion
IRI: .owl#hasLocationValueSet1D
literal: 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.

AnnotationAssertion
IRI: .owl#hasLocationValueSet1D
literal: hasLocationValueSet1D

AnnotationAssertion
IRI: .owl#hasLocationValueSet2D
literal: 2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string.

AnnotationAssertion
IRI: .owl#hasLocationValueSet2D
literal: hasLocationValueSet2D

AnnotationAssertion
IRI: .owl#hasLocationValueSet3D
literal: 3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string.

AnnotationAssertion
IRI: .owl#hasLocationValueSet3D
literal: hasLocationValueSet3D

AnnotationAssertion
IRI: .owl#hasLocationValueSetND
literal: 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.

AnnotationAssertion
IRI: .owl#hasLocationValueSetND
literal: hasLocationValueSetND

AnnotationAssertion
IRI: .owl#hasParameterValueSetND
literal: 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.

AnnotationAssertion
IRI: .owl#hasParameterValueSetND
literal: hasParameterValueSetND

AnnotationAssertion
IRI: .owl#hasPointsValueSetND
literal: 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.

AnnotationAssertion
IRI: .owl#hasPointsValueSetND
literal: hasPointsValueSetND

AnnotationAssertion
IRI: .owl#hasUnit
literal: A unit name, for example, "meter", "micrometer*micrometer", "hour". Stored as a text string.

AnnotationAssertion
IRI: .owl#hasUnit
literal: hasUnit

AnnotationAssertion
IRI: .owl#hasVTKfieldID
literal: jps

AnnotationAssertion
IRI: .owl#hasVTKfieldID
literal: 11/9/2012

AnnotationAssertion
IRI: .owl#hasVTKfieldID
literal: 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".

AnnotationAssertion
IRI: .owl#hasVTKfieldID
literal: hasVTKfieldID

AnnotationAssertion
IRI: .owl#hasVTKtypeID
literal: JPS

AnnotationAssertion
IRI: .owl#hasVTKtypeID
literal: 10/25/2012

AnnotationAssertion
IRI: .owl#hasVTKtypeID
literal: 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.

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: OBO_REL_adjacent_to

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: OBO_REL_adjacents_to

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: OBO_REL_adjacented_to

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: OBO_REL:0000012

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_adjacent_to
literal: adjacent_to

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_agent_in
literal: OBO_REL_agent_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_agent_in
literal: OBO_REL_agents_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_agent_in
literal: OBO_REL_agented_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_agent_in
literal: OBO_REL:has_agent

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_agent_in
literal: OBO_REL:0000022

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_agent_in
literal: agent_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: OBO_REL_contained_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: OBO_REL_containeds_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: OBO_REL_containeded_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: OBO_REL:contains

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: OBO_REL:0000010

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: "C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contained_in
literal: contained_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contains
literal: OBO_REL_contains

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contains
literal: OBO_REL_containses

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contains
literal: OBO_REL_containsed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contains
literal: OBO_REL:contained_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contains
literal: OBO_REL:0000011

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_contains
literal: contains

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derived_into
literal: OBO_REL_derived_into

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derived_into
literal: OBO_REL_deriveds_into

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derived_into
literal: OBO_REL_deriveded_into

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derived_into
literal: OBO_REL:derives_from

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derived_into
literal: OBO_REL:0000016

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derived_into
literal: derived_into

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: OBO_REL_derives_from

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: OBO_REL_deriveses_from

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: OBO_REL_derivesed_from

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: OBO_REL:derived_into

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: OBO_REL:0000015

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'." [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: "derived_from" []

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_derives_from
literal: derives_from

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: OBO_REL_has_agent

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: OBO_REL_has_agents

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: OBO_REL_has_agented

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: OBO_REL:agent_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: OBO_REL:0000021

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_agent
literal: has_agent

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: OBO_REL_has_improper_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: OBO_REL_has_improper_parts

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: OBO_REL_has_improper_parted

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: OBO_REL:improper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: OBO_REL:0000024

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: See reasons for obsoletion of improper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_improper_part
literal: has_improper_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: OBO_REL_has_integral_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: OBO_REL_has_integral_parts

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: OBO_REL_has_integral_parted

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: OBO_REL:integral_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: OBO_REL:0000005

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_integral_part
literal: has_integral_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: OBO_REL_has_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: OBO_REL_has_parts

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: OBO_REL_has_parted

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: OBO_REL:part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: OBO_REL:0000003

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_part
literal: has_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: OBO_REL_has_participant

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: OBO_REL_has_participants

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: OBO_REL_has_participanted

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: OBO_REL:participates_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: OBO_REL:0000019

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_participant
literal: has_participant

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_proper_part
literal: OBO_REL_has_proper_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_proper_part
literal: OBO_REL_has_proper_parts

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_proper_part
literal: OBO_REL_has_proper_parted

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_proper_part
literal: OBO_REL:proper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_proper_part
literal: OBO_REL:0000007

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_has_proper_part
literal: has_proper_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: OBO_REL_improper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: OBO_REL_improper_part_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: OBO_REL_improper_part_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: OBO_REL:has_improper_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: OBO_REL:0000025

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: "As for part_of, with the additional constraint that subject and object may be identical" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_improper_part_of
literal: improper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: OBO_REL_instance_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: OBO_REL_instance_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: OBO_REL_instance_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: OBO_REL:0000023

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: The instance_of relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for completeness

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: "A relation between an instance and a class. For components: a primitive relation between a component instance and a class which it instantiates at a specific time. For processes: a primitive relation, between a process instance and a class which it instantiates, holding independently of time" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_instance_of
literal: instance_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: OBO_REL_integral_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: OBO_REL_integral_part_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: OBO_REL_integral_part_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: OBO_REL:has_integral_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: OBO_REL:0000004

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_integral_part_of
literal: integral_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: OBO_REL_is_a

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: OBO_REL_is_as

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: OBO_REL_is_aed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: OBO_REL:0000001

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: The is_a relationship is considered axiomatic by the obo file format specification. In the representation of obo in OWL, where obo terms are represented as OWL classes, is_a is mapped on to the subClassOf axiom

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: "For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'." [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: "is_subtype_of" []

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: owl:subClassOf

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_is_a
literal: is_a

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: OBO_REL_located_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: OBO_REL_locateds_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: OBO_REL_locateded_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: OBO_REL:location_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: OBO_REL:0000008

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_located_in
literal: located_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_location_of
literal: OBO_REL_location_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_location_of
literal: OBO_REL_location_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_location_of
literal: OBO_REL_location_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_location_of
literal: OBO_REL:located_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_location_of
literal: OBO_REL:0000009

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_location_of
literal: location_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: OBO_REL_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: OBO_REL_part_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: OBO_REL_part_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: OBO_REL:has_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: true

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: OBO_REL:0000002

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_part_of
literal: part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_participates_in
literal: OBO_REL_participates_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_participates_in
literal: OBO_REL_participateses_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_participates_in
literal: OBO_REL_participatesed_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_participates_in
literal: OBO_REL:has_participant

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_participates_in
literal: OBO_REL:0000020

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_participates_in
literal: participates_in

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: OBO_REL_preceded_by

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: OBO_REL_preceded_bies

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: OBO_REL_preceded_bied

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: OBO_REL:precedes

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: OBO_REL:0000017

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_preceded_by
literal: preceded_by

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_precedes
literal: OBO_REL_precedes

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_precedes
literal: OBO_REL_precedeses

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_precedes
literal: OBO_REL_precedesed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_precedes
literal: OBO_REL:preceded_by

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_precedes
literal: OBO_REL:0000018

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_precedes
literal: precedes

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: OBO_REL_proper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: OBO_REL_proper_part_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: OBO_REL_proper_part_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: OBO_REL:has_proper_part

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: OBO_REL:0000006

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_proper_part_of
literal: proper_part_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: OBO_REL_transformation_of

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: OBO_REL_transformation_ofs

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: OBO_REL_transformation_ofed

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: OBO_REL:0000013

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874]

AnnotationAssertion
abbreviated IRI: relationship:OBO_REL_transformation_of
literal: transformation_of

AnnotationAssertion
abbreviated IRI: snap:IndependentContinuant
literal: CBO_Process is the top level CBO class for processes and process qualities. CBO_Object is BFO:continuant (endurant). CBO_Process is euivalent to BFO:occurrent.

AnnotationAssertion
abbreviated IRI: owl:topObjectProperty
literal: Note that OWL DL does not support antiymetric properties so those have been removed from the OBO Relation defintiions for the properties.