J Sluka, Biocomplexity Insitute, Indiana University
21 Sept 2021
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.
https://creativecommons.org/licenses/by/3.0/
OBO_REL http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry"
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
This work was supported by US National Institute of Health grant R01GM76692, US Environmental Protection Agency grant R835001,
Indiana University, Bloomington (IUB) and the Biocomplexity Institute
at IUB.
This work used the Protege resource, supported by grant LM007885 from
the US National Library of Medicine to Stanford University.
1.3
release version 1.1.2
jps
1.1.1
1.1.2
Version 1.1.2 added license info.
Version 1.1.1 added fuding sources.
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".
#OMEtiff_FileName
JPS
#OMEtiff_FileName
10/10/2017
#OMEtiff_FileName
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.
#OMEtiff_FileRoot
JPS
#OMEtiff_FileRoot
10/10/2017
#OMEtiff_FileRoot
OMEtiff_FileRoot is a CBO:SystemQuality:OMEtiff_Quality giving the root name for the OMERO-Tiff files associated with the particular model.
#OMEtiff_FileTimeStep
JPS
#OMEtiff_FileTimeStep
10/10/2017
#OMEtiff_FileTimeStep
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).
#OMEtiff_InitialCondition
jps
#OMEtiff_InitialCondition
10/10/2017
#OMEtiff_InitialCondition
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.
#OMEtiff_Quality
JPS
#OMEtiff_Quality
10/10/2017
#OMEtiff_Quality
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.
#has_Quality
jps
#has_Quality
1/24/2012
#has_Quality
has_Quality links an instance of a CBO quality to a class or individual.
#has_Quality
has_Quality links an instance of a CBO quality to a class or individual.
#has_Quality
has_Quality
.owl#AcceptanceFunction
jps
.owl#AcceptanceFunction
24 Aug. 2011
.owl#AcceptanceFunction
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.
.owl#AcceptanceFunction
AcceptanceFunction
.owl#AdhesionEnergy
jps
.owl#AdhesionEnergy
24 Aug. 2011
.owl#AdhesionEnergy
An AdhesionEnergy is a CBO:EnergyQuality representing the energy associated with the contact between two physical objects.
.owl#AdhesionEnergy
AdhesionEnergy
.owl#AdhesionMolecule
jps
.owl#AdhesionMolecule
24 Aug. 2011
.owl#AdhesionMolecule
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.
.owl#AdhesionMolecule
urn:miriam:obo.fma:67214
.owl#AdhesionMolecule
AdhesionMolecule
.owl#AdhesiveProperty
jps
.owl#AdhesiveProperty
24 Aug. 2011
.owl#AdhesiveProperty
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.
.owl#AdhesiveProperty
AdhesiveProperty
.owl#Advection
jps
.owl#Advection
29 Oct. 2012
.owl#Advection
Advection is a Movement that is caused by a carrying medium (such as blood) that results in a change in location.
.owl#Advection
Advection
.owl#Advection
CellAdvection
.owl#Age
jps
.owl#Age
24 Aug. 2011
.owl#Age
Age is a CBO:PhysicalObjectQuality class that describes the chronological or generational Age of a physical object.
.owl#Age
Age
.owl#Anisotropy
jps
.owl#Anisotropy
24 Aug. 2011
.owl#Anisotropy
Anisotropy is a GeometricalProperty describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:Isotropy.
.owl#Anisotropy
Anisotropy
.owl#ApicalPart
jps
.owl#ApicalPart
24 Aug. 2011
.owl#ApicalPart
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.
.owl#ApicalPart
ApicalPart
.owl#Apoptosis
jps
.owl#Apoptosis
24 Aug. 2011
.owl#Apoptosis
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.
.owl#Apoptosis
PATO:0000638
.owl#Apoptosis
urn:miriam:obo.go:0006915
.owl#Apoptosis
Apoptosis
.owl#AreaEnergy
jps
.owl#AreaEnergy
24 Aug. 2011
.owl#AreaEnergy
A AreaEnergy is a CBO:EnergyQuality representing the energy associated with a given area entity.
.owl#AreaEnergy
AreaEnergy
.owl#AsymmetricCellDivisionOrientedCleavagePlane
jps
.owl#AsymmetricCellDivisionOrientedCleavagePlane
24 Aug. 2011
.owl#AsymmetricCellDivisionOrientedCleavagePlane
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.
.owl#AsymmetricCellDivisionOrientedCleavagePlane
AsymmetricCellDivisionOrientedCleavagePlane
.owl#AsymmetricCellDivisionRandomCleavagePlane
jps
.owl#AsymmetricCellDivisionRandomCleavagePlane
24 Aug. 2011
.owl#AsymmetricCellDivisionRandomCleavagePlane
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.
.owl#AsymmetricCellDivisionRandomCleavagePlane
AsymmetricCellDivisionRandomCleavagePlane
.owl#AutophagicDeath
jps
.owl#AutophagicDeath
24 Aug. 2011
.owl#AutophagicDeath
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.
.owl#AutophagicDeath
urn:miriam:obo.go:0048102
.owl#AutophagicDeath
AutophagicDeath
.owl#BarrierCrossing
jps
.owl#BarrierCrossing
24 Aug. 2011
.owl#BarrierCrossing
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.
.owl#BarrierCrossing
BarrierCrossing
.owl#BasalPart
jps
.owl#BasalPart
24 Aug. 2011
.owl#BasalPart
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.
.owl#BasalPart
urn:miriam:obo.fma:72558
.owl#BasalPart
urn:miriam:obo.go:0045178
.owl#BasalPart
BasalPart
.owl#BasementLaminaChange
jps
.owl#BasementLaminaChange
24 Aug. 2011
.owl#BasementLaminaChange
BasementLaminaChange is an BasementLaminaProcess involving a change in the components or characteristics of the basement lamina components.
.owl#BasementLaminaChange
BasementLaminaChange
.owl#BasementLaminaCreation
jps
.owl#BasementLaminaCreation
24 Aug. 2011
.owl#BasementLaminaCreation
BasementLaminaCreation is a BasementLaminaProcess involving an increase in the quantity of the basement lamina and its components.
.owl#BasementLaminaCreation
BasementLaminaCreation
.owl#BasementLaminaDeletion
jps
.owl#BasementLaminaDeletion
24 Aug. 2011
.owl#BasementLaminaDeletion
BasementLaminaDeletion is a BasementLaminaProcess involving a decrease in the quantity of the basement lamina and its components.
.owl#BasementLaminaDeletion
BasementLaminaDeletion
.owl#BasementLaminaProcess
jps
.owl#BasementLaminaProcess
24 Aug. 2011
.owl#BasementLaminaProcess
BasementLaminaProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of a basement membrane or its components.
.owl#BasementLaminaProcess
BasementLaminaProcess
.owl#BasementMembrane
jps
.owl#BasementMembrane
24 Aug. 2011
.owl#BasementMembrane
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.
.owl#BasementMembrane
urn:miriam:obo.go:0005605
.owl#BasementMembrane
BasementMembrane
.owl#BioEntityType
jps
.owl#BioEntityType
11/8/2012
.owl#BioEntityType
BioEntityType is a CBO_Object for biological concepts such as Cell and ECM.
.owl#BioEntityType
BioEntityType
.owl#BioEntityType
subclass of: BFO:snap:object
.owl#BodyShape
jps
.owl#BodyShape
24 Aug. 2011
.owl#BodyShape
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.
.owl#BodyShape
urn:miriam:opb:'bounded Volume Shape'
.owl#BodyShape
BodyShape
.owl#BoltzmannFactor
jps
.owl#BoltzmannFactor
24 Aug. 2011
.owl#BoltzmannFactor
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).
.owl#BoltzmannFactor
BoltzmannFactor
.owl#Boundary
jps
.owl#Boundary
24 Aug. 2011
.owl#Boundary
Boundary is a CBO:GeometricalEntity that demarks the interface between two bona fide physical objects.
.owl#Boundary
Boundary
.owl#Boundary
subclass of: BFO:snap:object_Boundary
.owl#BrushBorder
jps
.owl#BrushBorder
24 Aug. 2011
.owl#BrushBorder
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
.owl#BrushBorder
urn:miriam:obo.fma:70977
.owl#BrushBorder
urn:miriam:obo.go:0005903
.owl#BrushBorder
BrushBorder
.owl#CBO_Object
jps
.owl#CBO_Object
24 Aug. 2011
.owl#CBO_Object
CBO_Object is the top level CBO class for physical objects and object qualities. CBO_Object is BFO:continuant (endurant).
.owl#CBO_Object
CBO_Object
.owl#CBO_Object
subclass of: BFO:continuant
.owl#CBO_Process
jps
.owl#CBO_Process
24 Aug. 2011
.owl#CBO_Process
CBO_Process is the top level CBO class for processes. CBO_Process is BFO:occurant (processual).
.owl#CBO_Process
CBO_Process
.owl#CBO_Process
subclass of: BFO:occurrent
.owl#CHASTEcenter
jps
.owl#CHASTEcenter
23 Jul. 2012
.owl#CHASTEcenter
CHASTERcenter is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.cs.ox.ac.uk/chaste/sysbio_index.html
.owl#CHASTEcenter
CHASTEcenter
.owl#Cell
jps
.owl#Cell
24 Aug. 2011
.owl#Cell
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.
.owl#Cell
urn:miriam:obo.clo:0000000
.owl#Cell
urn:miriam:obo.fma:68646
.owl#Cell
urn:miriam:obo.go:0005623
.owl#Cell
Cell
.owl#CellAdhesion
jps
.owl#CellAdhesion
24 Aug. 2011
.owl#CellAdhesion
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.
.owl#CellAdhesion
PATO:0001531
.owl#CellAdhesion
urn:miriam:obo.go:0007155
.owl#CellAdhesion
CellAdhesion
.owl#CellAdvection
jps
.owl#CellAdvection
24 Aug. 2011
.owl#CellAdvection
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.
.owl#CellAdvection
CellAdvection
.owl#CellBasementLaminaContact
jps
.owl#CellBasementLaminaContact
24 Aug. 2011
.owl#CellBasementLaminaContact
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).
.owl#CellBasementLaminaContact
CellBasementLaminaContact
.owl#CellBasementMembraneAdhesion
jps
.owl#CellBasementMembraneAdhesion
24 Aug. 2011
.owl#CellBasementMembraneAdhesion
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.
.owl#CellBasementMembraneAdhesion
CellBasementMembraneAdhesion
.owl#CellBorder
jps
.owl#CellBorder
24 Aug. 2011
.owl#CellBorder
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.
.owl#CellBorder
CellBorder
.owl#CellCellAdhesion
jps
.owl#CellCellAdhesion
24 Aug. 2011
.owl#CellCellAdhesion
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.
.owl#CellCellAdhesion
PATO:0001531
.owl#CellCellAdhesion
urn:miriam:obo.go:0016337
.owl#CellCellAdhesion
CellCellAdhesion
.owl#CellCellContact
jps
.owl#CellCellContact
24 Aug. 2011
.owl#CellCellContact
CellCellContact is a CellContact involving the direct physical contact between two cells. Note that contact is distinct from adhesion (see CBO:CellAdhesion).
.owl#CellCellContact
CellCellContact
.owl#CellCellProcess
jps
.owl#CellCellProcess
24 Aug. 2011
.owl#CellCellProcess
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.
.owl#CellCellProcess
CellCellProcess
.owl#CellContact
jps
.owl#CellContact
24 Aug. 2011
.owl#CellContact
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).
.owl#CellContact
CellContact
.owl#CellContact
subclass of: BFO:span:fiat_process_part
.owl#CellDeath
jps
.owl#CellDeath
24 Aug. 2011
.owl#CellDeath
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.
.owl#CellDeath
urn:miriam:obo.go:0008219
.owl#CellDeath
CellDeath
.owl#CellDifferentiation
jps
.owl#CellDifferentiation
24 Aug. 2011
.owl#CellDifferentiation
CellDifferentiation is an existential_CellProcess in which the type (CBO:Phenotype) of a cell is changed.
.owl#CellDifferentiation
CellDifferentiation
.owl#CellDisplacement
jps
.owl#CellDisplacement
24 Aug. 2011
.owl#CellDisplacement
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.
.owl#CellDisplacement
CellDisplacement
.owl#CellDivision
jps
.owl#CellDivision
24 Aug. 2011
.owl#CellDivision
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.
.owl#CellDivision
urn:miriam:obo.go:0051301
.owl#CellDivision
CellDivision
.owl#CellEnvironmentProcess
jps
.owl#CellEnvironmentProcess
24 Aug. 2011
.owl#CellEnvironmentProcess
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.
.owl#CellEnvironmentProcess
CellEnvironmentProcess
.owl#CellExport
jps
.owl#CellExport
24 Aug. 2011
.owl#CellExport
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.
.owl#CellExport
CellExport
.owl#CellFusion
jps
.owl#CellFusion
24 Aug. 2011
.owl#CellFusion
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.
.owl#CellFusion
urn:miriam:obo.go:0000768
.owl#CellFusion
CellFusion
.owl#CellGrowth
jps
.owl#CellGrowth
24 Aug. 2011
.owl#CellGrowth
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.
.owl#CellGrowth
PATO:0001489
.owl#CellGrowth
urn:miriam:obo.go:0016049
.owl#CellGrowth
CellGrowth
.owl#CellGrowth
subclass of: BFO:span:fiat_process_part
.owl#CellImport
jps
.owl#CellImport
24 Aug. 2011
.owl#CellImport
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.
.owl#CellImport
CellImport
.owl#CellInterstitialMatrixAdhesion
jps
.owl#CellInterstitialMatrixAdhesion
24 Aug. 2011
.owl#CellInterstitialMatrixAdhesion
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.
.owl#CellInterstitialMatrixAdhesion
CellInterstitialMatrixAdhesion
.owl#CellInterstitialMatrixContact
jps
.owl#CellInterstitialMatrixContact
24 Aug. 2011
.owl#CellInterstitialMatrixContact
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).
.owl#CellInterstitialMatrixContact
CellInterstitialMatrixContact
.owl#CellMembrane
jps
.owl#CellMembrane
24 Aug. 2011
.owl#CellMembrane
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.
.owl#CellMembrane
urn:miriam:obo.fma:63841
.owl#CellMembrane
urn:miriam:obo.go:0005886
.owl#CellMembrane
CellMembrane
.owl#CellMembraneLocalStructure
jps
.owl#CellMembraneLocalStructure
24 Aug. 2011
.owl#CellMembraneLocalStructure
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.
.owl#CellMembraneLocalStructure
urn:miriam:obo.go:0042995
.owl#CellMembraneLocalStructure
CellMembraneLocalStructure
.owl#CellMembraneLocalStructure
subclass of: BFO:snap:specifically_dependent_continuant
.owl#CellMembranePart
jps
.owl#CellMembranePart
24 Aug. 2011
.owl#CellMembranePart
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.
.owl#CellMembranePart
urn:miriam:obo.go:0044459
.owl#CellMembranePart
CellMembranePart
.owl#CellMembranePart
subclass of: BFO:snap:specifically_dependent_continuant
.owl#CellMotility
jps
.owl#CellMotility
24 Aug. 2011
.owl#CellMotility
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.
.owl#CellMotility
urn:miriam:obo.go:0048870
.owl#CellMotility
CellMotility
.owl#CellMovement
jps
.owl#CellMovement
24 Aug. 2011
.owl#CellMovement
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.
.owl#CellMovement
CellMovement
.owl#CellNonCellAdhesion
jps
.owl#CellNonCellAdhesion
24 Aug. 2011
.owl#CellNonCellAdhesion
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.
.owl#CellNonCellAdhesion
urn:miriam:obo.go:0031589
.owl#CellNonCellAdhesion
CellNonCellAdhesion
.owl#CellNonCellContact
jps
.owl#CellNonCellContact
24 Aug. 2011
.owl#CellNonCellContact
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).
.owl#CellNonCellContact
CellNonCellContact
.owl#CellOrientationChange
jps
.owl#CellOrientationChange
24 Aug. 2011
.owl#CellOrientationChange
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.
.owl#CellOrientationChange
CellOrientationChange
.owl#CellPart
jps
.owl#CellPart
24 Aug. 2011
.owl#CellPart
CellPart is a CBO_Object including any constituent part of a Cell.
.owl#CellPart
urn:miriam:obo.fma:61764
.owl#CellPart
CellPart
.owl#CellPart
subclass of: BFO:snap:specifically_dependent_continuant
.owl#CellProcess
jps
.owl#CellProcess
24 Aug. 2011
.owl#CellProcess
CellProcess is a CBO_Process (span:process) describing a process characteristic of a CBO:Cell.
.owl#CellProcess
CellProcess
.owl#CellProcess
subclass of: BFO:span:process
.owl#CellRegion
jps
.owl#CellRegion
24 Aug. 2011
.owl#CellRegion
CellRegion is a CBL:GeometricalEntity class that includes descriptors for various fiat regions. (A fiat region generally does not have clear boundaries.)
.owl#CellRegion
CellRegion
.owl#CellRegion
subclass of: BFO:snap:fiat_object_part
.owl#CellRelatedTransport
jps
.owl#CellRelatedTransport
24 Aug. 2011
.owl#CellRelatedTransport
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.
.owl#CellRelatedTransport
urn:miriam:obo.go:0006810
.owl#CellRelatedTransport
CellRelatedTransport
.owl#CellRotation
jps
.owl#CellRotation
24 Aug. 2011
.owl#CellRotation
CellRotation is a CellMovement resulting in a Rotation of a cell about it center (center of mass or center of Volume).
.owl#CellRotation
urn:miriam:obo.pato:0001599
.owl#CellRotation
CellRotation
.owl#CellShapeChange
jps
.owl#CellShapeChange
24 Aug. 2011
.owl#CellShapeChange
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.
.owl#CellShapeChange
CellShapeChange
.owl#CellState
jps
.owl#CellState
24 Aug. 2011
.owl#CellState
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.
.owl#CellState
CellState
.owl#CellState
subclass of: BFO:snap:quality
.owl#CellVolumeChange
jps
.owl#CellVolumeChange
24 Aug. 2011
.owl#CellVolumeChange
deprecated
.owl#CellVolumeChange
CellVolumeChange
.owl#CellWall
jps
.owl#CellWall
24 Aug. 2011
.owl#CellWall
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?
.owl#CellWall
urn:miriam:obo.go:0005618
.owl#CellWall
CellWall
.owl#CellularChemicalProcess
jps
.owl#CellularChemicalProcess
24 Aug. 2011
.owl#CellularChemicalProcess
CellularChemicalProcess is a CellEnvironmentProcess in which an environmental (local) chemical (or chemical gradient) changes a process or quality of a cell.
.owl#CellularChemicalProcess
CellularChemicalProcess
.owl#CellularElectricalProcess
jps
.owl#CellularElectricalProcess
24 Aug. 2011
.owl#CellularElectricalProcess
CellularElectricalProcess is a CellEnvironmentProcess that results in a change in an electrical quality of the cell.
.owl#CellularElectricalProcess
CellularElectricalProcess
.owl#CellularKineticProcess
jps
.owl#CellularKineticProcess
24 Aug. 2011
.owl#CellularKineticProcess
CellularKineticProcess is a CellularPropertyProcess that changes a kinetic dependence.
.owl#CellularKineticProcess
CellularKineticProcess
.owl#CellularMechanicalProcess
jps
.owl#CellularMechanicalProcess
24 Aug. 2011
.owl#CellularMechanicalProcess
CellularMechanicalProcess is a CellularPropertyProcess that results in a change in a mechanical property of a cell.
.owl#CellularMechanicalProcess
CellularMechanicalProcess
.owl#CellularPropertyProcess
jps
.owl#CellularPropertyProcess
24 Aug. 2011
.owl#CellularPropertyProcess
CellularPropertyProcess is a CellProcess that results in a change in a property of a cell. For example, CellMovement changes the property of location.
.owl#CellularPropertyProcess
CellularPropertyProcess
.owl#CenterModelPlatform
jps
.owl#CenterModelPlatform
23 Jul. 2012
.owl#CenterModelPlatform
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.
.owl#CenterModelPlatform
CenterModelPlatform
.owl#CenterOfMass
jps
.owl#CenterOfMass
24 Aug. 2011
.owl#CenterOfMass
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.
.owl#CenterOfMass
CenterOfMass
.owl#CenterOfVolume
jps
.owl#CenterOfVolume
24 Aug. 2011
.owl#CenterOfVolume
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.
.owl#CenterOfVolume
CenterOfVolume
.owl#Charge
jps
.owl#Charge
24 Aug. 2011
.owl#Charge
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.
.owl#Charge
urn:miriam:obo:pato:0002193
.owl#Charge
urn:miriam:opb:'Charge amount'
.owl#Charge
Charge
.owl#ChemicalAffinity
jps
.owl#ChemicalAffinity
24 Aug. 2011
.owl#ChemicalAffinity
ChemicalAffinity is a ChemicalProperty that describes an affinity (atraction, repulsion) between a molecule and another object.
.owl#ChemicalAffinity
ChemicalAffinity
.owl#ChemicalDensity
jps
.owl#ChemicalDensity
24 Aug. 2011
.owl#ChemicalDensity
ChemicalDensity is a ChemicalProperty that describes the concentration (mass or number of molecules) per unit volume.
.owl#ChemicalDensity
ChemicalDensity
.owl#ChemicalLocalization
jps
.owl#ChemicalLocalization
24 Aug. 2011
.owl#ChemicalLocalization
ChemicalLocalization is a ChemicalProperty that describes a tendency for the chemical species to localize in a particular region (e.g., cell membrane).
.owl#ChemicalLocalization
ChemicalLocalization
.owl#ChemicalPattern
jps
.owl#ChemicalPattern
24 Aug. 2011
.owl#ChemicalPattern
ChemicalPattern is a ChemicalProperty that describes a tendency for the chemical species to organize or partition in a particular pattern.
.owl#ChemicalPattern
ChemicalPattern
.owl#ChemicalPatternGradient
jps
.owl#ChemicalPatternGradient
24 Aug. 2011
.owl#ChemicalPatternGradient
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.
.owl#ChemicalPatternGradient
ChemicalPatternGradient
.owl#ChemicalProperty
jps
.owl#ChemicalProperty
24 Aug. 2011
.owl#ChemicalProperty
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.
.owl#ChemicalProperty
ChemicalProperty
.owl#Chemotaxis
jps
.owl#Chemotaxis
24 Aug. 2011
.owl#Chemotaxis
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).
.owl#Chemotaxis
.owl#Chemotaxis
urn:miriam:obo.go:0006935
.owl#Chemotaxis
urn:miriam:obo.go:0060326
.owl#Chemotaxis
Chemotaxis
.owl#Compucell3D
jps
.owl#Compucell3D
23 Jul. 2012
.owl#Compucell3D
Compucell3D is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.Compucell3D.org
.owl#Compucell3D
Compucell3D
.owl#ComputationalPlatform
jps
.owl#ComputationalPlatform
23 Jul. 2012
.owl#ComputationalPlatform
ComputationalPlatform is a SystemQuality class describing a particular computational platform.
.owl#ComputationalPlatform
ComputationalPlatform
.owl#ComputationalPlatformQualities
jps
.owl#ComputationalPlatformQualities
27 Jul. 2012
.owl#ComputationalPlatformQualities
ComputationalPlatformQuality is a CBO class describing qualities of computational platforms for preforming multicell modeling.
.owl#ComputationalPlatformQualities
ComputationalPlatformQuality
.owl#ContactSurfaceArea
jps
.owl#ContactSurfaceArea
24 Aug. 2011
.owl#ContactSurfaceArea
ContactSurfaceArea is a CBO:GeometricalProperty describing the scalar value of two objects contact surface area at a particular instant in time.
.owl#ContactSurfaceArea
ContactSurfaceArea
.owl#ContinousPlatform
jps
.owl#ContinousPlatform
23 Jul. 2012
.owl#ContinousPlatform
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
.owl#ContinousPlatform
DiscreteModelPlatform
.owl#ContinuousEntity
jps
.owl#ContinuousEntity
24 Aug. 2011
.owl#ContinuousEntity
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).
.owl#ContinuousEntity
ContinuousEntity
.owl#ContinuousExtent
jps
.owl#ContinuousExtent
24 Aug. 2011
.owl#ContinuousExtent
ContinousExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionaly sensitive quantity in an infinitely finely grained coordinate System. Compare with DiscreteExtent.
.owl#ContinuousExtent
ContinuousExtent
.owl#Contraction
jps
.owl#Contraction
24 Aug. 2011
.owl#Contraction
Contraction is a VolumeChange resulting in a decrease in Volume occupied by an object.
.owl#Contraction
Contraction
.owl#CorpuscularEntity
jps
.owl#CorpuscularEntity
24 Aug. 2011
.owl#CorpuscularEntity
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.
.owl#CorpuscularEntity
CorpuscularEntity
.owl#Creation
jps
.owl#Creation
24 Aug. 2011
.owl#Creation
Creation is a FundamentalPhysicalProcess resulting in the Creation of a new object. Often this will involve an increase in count of an object.
.owl#Creation
Creation
.owl#Cytoplasm
jps
.owl#Cytoplasm
24 Aug. 2011
.owl#Cytoplasm
FMA: Cell component which consists of cytosol and Cytoplasmic organelles.
.owl#Cytoplasm
Cytoplasm
.owl#Deletion
jps
.owl#Deletion
24 Aug. 2011
.owl#Deletion
Deletion is a FundamentalPhysicalProcess resulting in the Deletion of an object. Often this will involve a decrease in count of an object.
.owl#Deletion
Deletion
.owl#DiffuseEntity
jps
.owl#DiffuseEntity
24 Aug. 2011
.owl#DiffuseEntity
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.
.owl#DiffuseEntity
DiffuseEntity
.owl#Diffusion
jps
.owl#Diffusion
24 Aug. 2011
.owl#Diffusion
Diffusion is a Movement arising from random motion, either thermal or motive (cf. motility), of an object.
.owl#Diffusion
Diffusion
.owl#Dimension1d
jps
.owl#Dimension1d
24 Aug. 2011
.owl#Dimension1d
Dimension1d is a CBO:Dimensionality quality for a System with one spatial dimension.
.owl#Dimension1d
urn:miriam:opb:'One dimensional spatial coordinate System'
.owl#Dimension1d
Dimension1d
.owl#Dimension2d
jps
.owl#Dimension2d
24 Aug. 2011
.owl#Dimension2d
Dimension2d is a CBO:Dimensionality quality for a System with two spatial dimensions.
.owl#Dimension2d
urn:miriam:opb:'Two dimensional spatial coordinate System'
.owl#Dimension2d
Dimension2d
.owl#Dimension3d
jps
.owl#Dimension3d
24 Aug. 2011
.owl#Dimension3d
Dimension3d is a CBO:Dimensionality quality for a System with three spatial dimensions.
.owl#Dimension3d
urn:miriam:opb:'Three dimensional spatial coordinate System'
.owl#Dimension3d
Dimension3d
.owl#Dimensionality
jps
.owl#Dimensionality
24 Aug. 2011
.owl#Dimensionality
Dimensionality is a CBO:GeometricalProperty that describes the number of independent spatial axis in a model or System.
.owl#Dimensionality
urn:miriam:opb:'Spatial coordinate System'
.owl#Dimensionality
Dimensionality
.owl#DiscreteExtent
jps
.owl#DiscreteExtent
24 Aug. 2011
.owl#DiscreteExtent
DiscreteExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionally sensitive quantity in a finitely grained coordinate System. Compare with ContinuousExtent.
.owl#DiscreteExtent
DiscreteExtent
.owl#Divisible
jps
.owl#Divisible
24 Aug. 2011
.owl#Divisible
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.
.owl#Divisible
Divisible
.owl#Dorsal
jps
.owl#Dorsal
24 Aug. 2011
.owl#Dorsal
Dorsal is a CBO:OrganismalRegion characteristic of the back of an object relative to the body it is contained in. For example Dorsal fin.
.owl#Dorsal
urn:miriam:obo.fma:74535
.owl#Dorsal
Dorsal
.owl#ElectricalProperty
jps
.owl#ElectricalProperty
24 Aug. 2011
.owl#ElectricalProperty
ElectricalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the electrical qualities of objects. ElectricalProperty are intrinsic to the object.
.owl#ElectricalProperty
urn:miriam:opb:'Electrical entity'
.owl#ElectricalProperty
ElectricalProperty
.owl#ElectromechanicalField
jps
.owl#ElectromechanicalField
8/1/2012
.owl#ElectromechanicalField
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.
.owl#ElectromechanicalField
ElectromechanicalField
.owl#Energy
jps
.owl#Energy
24 Aug. 2011
.owl#Energy
An Energy is a CBO:PhysicalObjectQuality is the Energy of the object for which it is a quality.
.owl#Energy
urn:miriam:opb:'Energy amount'
.owl#Energy
Energy
.owl#EnergyFunction
jps
.owl#EnergyFunction
24 Aug. 2011
.owl#EnergyFunction
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.
.owl#EnergyFunction
Energy
.owl#EnergyFunction
subclass of: BFO:snap:quality
.owl#EnergyQuality
jps
.owl#EnergyQuality
24 Aug. 2011
.owl#EnergyQuality
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.
.owl#EnergyQuality
EnergyQuality
.owl#EnergyQuality
subclass of: BFO:snap:quality
.owl#ExistentialCellProcesses
jps
.owl#ExistentialCellProcesses
24 Aug. 2011
.owl#ExistentialCellProcesses
ExistentialCellProcesses is a CellProcess that is assumed, without formal proof, to be a process of a cell.
.owl#ExistentialCellProcesses
ExistentialCellProcesses
.owl#Expansion
jps
.owl#Expansion
24 Aug. 2011
.owl#Expansion
Expansion is a VolumeChange resulting in an increase in Volume occupied by an object.
.owl#Expansion
Expansion
.owl#ExtentGeometrical
jps
.owl#ExtentGeometrical
24 Aug. 2011
.owl#ExtentGeometrical
ExtentGeometrical is a CBO:GeometricalProperty that describes the basic granularity of the coordinate System.
.owl#ExtentGeometrical
ExtentGeometrical
.owl#ExtraCellularFluid
jps
.owl#ExtraCellularFluid
24 Aug. 2011
.owl#ExtraCellularFluid
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.
.owl#ExtraCellularFluid
ExtraCellularFluid
.owl#ExtraCellularMatrix
jps
.owl#ExtraCellularMatrix
24 Aug. 2011
.owl#ExtraCellularMatrix
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.
.owl#ExtraCellularMatrix
urn:miriam:obo.fma:9672
.owl#ExtraCellularMatrix
urn:miriam:obo.go:0031012
.owl#ExtraCellularMatrix
ExtraCellularMatrix
.owl#ExtracellularMatrixProcess
jps
.owl#ExtracellularMatrixProcess
24 Aug. 2011
.owl#ExtracellularMatrixProcess
ExtracellularMatrixProcess is a CBO_Process involving a change in the qualities, or quantity of extracellular matrix and its components.
.owl#ExtracellularMatrixProcess
ExtracellularMatrixProcess
.owl#ExtracellularMatrixProcess
subclass of: BFO:span:process
.owl#Field
jps
.owl#Field
19 Jul. 2012
.owl#Field
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.
.owl#Field
subclass of: BFO:snap:object
.owl#FieldProcess
jps
.owl#FieldProcess
11/8/2012
.owl#FieldProcess
FieldProcess is a CBO_Process (span:process) describing a process characteristic of a CBO:Field.
.owl#FieldProcess
FieldProcess
.owl#FieldProcess
subclass of: BFO:span:process
.owl#FieldQuality
jps
.owl#FieldQuality
11/8/2012
.owl#FieldQuality
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.
.owl#FieldQuality
FieldQuality
.owl#FieldQuality
subclass of: BFO:snap:quality
.owl#Fill
jps
.owl#Fill
24 Aug. 2011
.owl#Fill
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.
.owl#Fill
Fill
.owl#Filopodium
jps
.owl#Filopodium
24 Aug. 2011
.owl#Filopodium
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
.owl#Filopodium
urn:miriam:obo.go:0030175
.owl#Filopodium
Filopodium
.owl#FirstOrderRate
jps
.owl#FirstOrderRate
24 Aug. 2011
.owl#FirstOrderRate
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.
.owl#FirstOrderRate
FirstOrderRate
.owl#Fission
jps
.owl#Fission
24 Aug. 2011
.owl#Fission
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.
.owl#Fission
Fission
.owl#FundamentalPhysicalProcess
jps
.owl#FundamentalPhysicalProcess
24 Aug. 2011
.owl#FundamentalPhysicalProcess
A FundamentalPhysicalProcess is a CBO_Process (span:Process) that changes a quality or characteristic of an object.
.owl#FundamentalPhysicalProcess
urn:miriam:dummy:1
.owl#FundamentalPhysicalProcess
urn:miriam:dummy:2
.owl#FundamentalPhysicalProcess
urn:miriam:dummy:3
.owl#FundamentalPhysicalProcess
FundamentalPhysicalProcess
.owl#FundamentalPhysicalProcess
subclass of: BFO:span:process
.owl#GapJunction
jps
.owl#GapJunction
24 Aug. 2011
.owl#GapJunction
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.
.owl#GapJunction
urn:miriam:obo.fma:67423
.owl#GapJunction
urn:miriam:obo.go:0005921
.owl#GapJunction
GapJunction
.owl#GenerationalAge
jps
.owl#GenerationalAge
24 Aug. 2011
.owl#GenerationalAge
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.
.owl#GenerationalAge
urn:miriam:obo.go:0001302
.owl#GenerationalAge
GenerationalAge
.owl#GeometricalCellProcess
jps
.owl#GeometricalCellProcess
24 Aug. 2011
.owl#GeometricalCellProcess
GeometricalCellProcess is a CellularPropertyProcess that results in a change in the geometry of a cell.
.owl#GeometricalCellProcess
GeometricalCellProcess
.owl#GeometricalEntity
jps
.owl#GeometricalEntity
24 Aug. 2011
.owl#GeometricalEntity
GeometricalEntity is a CBO_Object for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions.
.owl#GeometricalEntity
GeometricalEntity
.owl#GeometricalEntity
subclass of: BFO:snap:independent_continuant
.owl#GeometricalProperty
jps
.owl#GeometricalProperty
24 Aug. 2011
.owl#GeometricalProperty
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.
.owl#GeometricalProperty
GeometricalProperty
.owl#GradientTexture
jps
.owl#GradientTexture
24 Aug. 2011
.owl#GradientTexture
GradientTexture is a CBO:Texture consisting of a Texture description that varies smoothly across one or more dimensions.
.owl#GradientTexture
GradientTexture
.owl#Hamlitonian
jps
.owl#Hamlitonian
24 Aug. 2011
.owl#Hamlitonian
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.
.owl#Hamlitonian
Hamiltonian
.owl#Haptotaxis
jps
.owl#Haptotaxis
24 Aug. 2011
.owl#Haptotaxis
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.
.owl#Haptotaxis
Haptotaxis
.owl#HarmonicEnergy
jps
.owl#HarmonicEnergy
24 Aug. 2011
.owl#HarmonicEnergy
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.
.owl#HarmonicEnergy
HarmonicEnergy
.owl#InterentityExport
jps
.owl#InterentityExport
24 Aug. 2011
.owl#InterentityExport
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.
.owl#InterentityExport
InterentityExport
.owl#InterentityImport
jps
.owl#InterentityImport
24 Aug. 2011
.owl#InterentityImport
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.
.owl#InterentityImport
InterentityImport
.owl#InterentityTransport
jps
.owl#InterentityTransport
24 Aug. 2011
.owl#InterentityTransport
InterentityTransport is a Transport of an object across a bona fide boundary. For example, from within a bone to the space outside the bone.
.owl#InterentityTransport
InterentityTransport
.owl#InterentityTransport
subclass of: BFO:span:process
.owl#InterstitialMatrix
jps
.owl#InterstitialMatrix
24 Aug. 2011
.owl#InterstitialMatrix
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.
.owl#InterstitialMatrix
urn:miriam:obo.go:0005614
.owl#InterstitialMatrix
InterstitialMatrix
.owl#InterstitialMatrixChange
jps
.owl#InterstitialMatrixChange
24 Aug. 2011
.owl#InterstitialMatrixChange
InterstitialMatrixChange is an InterstitialMatrixProcess involving a change in the components or characteristics of the interstitial matrix components.
.owl#InterstitialMatrixChange
InterstitialMatrixChange
.owl#InterstitialMatrixCreation
jps
.owl#InterstitialMatrixCreation
24 Aug. 2011
.owl#InterstitialMatrixCreation
InterstitialMatrixCreation is an InterstitialMatrixProcess involving an increase in the quantity of the interstitial matrix and its components.
.owl#InterstitialMatrixCreation
InterstitialMatrixCreation
.owl#InterstitialMatrixDeletion
jps
.owl#InterstitialMatrixDeletion
24 Aug. 2011
.owl#InterstitialMatrixDeletion
InterstitialMatrixDeletion is an InterstitialMatrixProcess involving a decrease in the quantity of the interstitial matrix and its components.
.owl#InterstitialMatrixDeletion
InterstitialMatrixDeletion
.owl#InterstitialMatrixProcess
jps
.owl#InterstitialMatrixProcess
24 Aug. 2011
.owl#InterstitialMatrixProcess
InterstitialMatrixProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of interstitial matrix and its components.
.owl#InterstitialMatrixProcess
InterstitialMatrixProcess
.owl#IntraentityTransport
jps
.owl#IntraentityTransport
24 Aug. 2011
.owl#IntraentityTransport
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.
.owl#IntraentityTransport
IntraentityTransport
.owl#IonChannel
jps
.owl#IonChannel
24 Aug. 2011
.owl#IonChannel
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.
.owl#IonChannel
urn:miriam:obo.go:0022831
.owl#IonChannel
IonChannel
.owl#IsApoptotic
jps
.owl#IsApoptotic
24 Aug. 2011
.owl#IsApoptotic
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.
.owl#IsApoptotic
IsApoptotic
.owl#IsDebris
jps
.owl#IsDebris
24 Aug. 2011
.owl#IsDebris
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.
.owl#IsDebris
IsDebris
.owl#IsGrowing
jps
.owl#IsGrowing
24 Aug. 2011
.owl#IsGrowing
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.
.owl#IsGrowing
IsGrowing
.owl#IsHypoxic
jps
.owl#IsHypoxic
24 Aug. 2011
.owl#IsHypoxic
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.
.owl#IsHypoxic
IsHypoxic
.owl#IsNecrotic
jps
.owl#IsNecrotic
24 Aug. 2011
.owl#IsNecrotic
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.
.owl#IsNecrotic
IsNecrotic
.owl#IsQuiescent
jps
.owl#IsQuiescent
24 Aug. 2011
.owl#IsQuiescent
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.
.owl#IsQuiescent
IsQuiescent
.owl#Isotropy
jps
.owl#Isotropy
24 Aug. 2011
.owl#Isotropy
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.
.owl#Isotropy
Isotropy
.owl#KineticProperty
jps
.owl#KineticProperty
24 Aug. 2011
.owl#KineticProperty
KineticProperty is a CBO:PhysicalObjectQuality describing a kinetic characteristic of an object.
.owl#KineticProperty
urn:miriam:opb:'Kinetic manifestation'
.owl#KineticProperty
KineticProperty
.owl#LJ_6_12Energy
jps
.owl#LJ_6_12Energy
24 Aug. 2011
.owl#LJ_6_12Energy
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.
.owl#LJ_6_12Energy
LJ_6_12Energy
.owl#LateralPart
jps
.owl#LateralPart
24 Aug. 2011
.owl#LateralPart
LateralPart is a CBO:CellRegion that is between the CBO:BasalPart and CBO:LateralPart.
.owl#LateralPart
LateralPart
.owl#LinearEnergy
jps
.owl#LinearEnergy
24 Aug. 2011
.owl#LinearEnergy
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.
.owl#LinearEnergy
LinearEnergy
.owl#Location
jps
.owl#Location
24 Aug. 2011
.owl#Location
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
.owl#Location
Location
.owl#Mass
jps
.owl#Mass
24 Aug. 2011
.owl#Mass
Mass is a CBO:PhysicalObjectQuality describing the Mass of the object.
.owl#Mass
PATO:0000125
.owl#Mass
urn:miriam:opb:'Discrete solid Mass'
.owl#Mass
Mass
.owl#MechanicalProperty
jps
.owl#MechanicalProperty
24 Aug. 2011
.owl#MechanicalProperty
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.
.owl#MechanicalProperty
MechanicalProperty
.owl#MedialPart
jps
.owl#MedialPart
24 Aug. 2011
.owl#MedialPart
MedialPart is a CBO:CellRegion located near the center of the Cell.
.owl#MedialPart
MedialPart
.owl#Meiosis
jps
.owl#Meiosis
24 Aug. 2011
.owl#Meiosis
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.
.owl#Meiosis
urn:miriam:obo.go:0007126
.owl#Meiosis
Meiosis
.owl#MembraneReceptor
jps
.owl#MembraneReceptor
24 Aug. 2011
.owl#MembraneReceptor
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.
.owl#MembraneReceptor
MembraneReceptor
.owl#MinimizationAcceptanceFunction
jps
.owl#MinimizationAcceptanceFunction
24 Aug. 2011
.owl#MinimizationAcceptanceFunction
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.
.owl#MinimizationAcceptanceFunction
MinimizationAcceptanceFunction
.owl#Mitosis
jps
.owl#Mitosis
24 Aug. 2011
.owl#Mitosis
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.
.owl#Mitosis
urn:miriam:obo.go:0007067
.owl#Mitosis
Mitosis
.owl#MolecularField
jps
.owl#MolecularField
24 Aug. 2011
.owl#MolecularField
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.
.owl#MolecularField
MolecularField
.owl#MolecularField
subclass of: BFO:snap:object
.owl#MolecularTargeting
jps
.owl#MolecularTargeting
24 Aug. 2011
.owl#MolecularTargeting
MolecularTargeting is an IntraentityTransport in which a molecule is actively directed from one place in a cell to another.
.owl#MolecularTargeting
urn:miriam:obo.go:0006605
.owl#MolecularTargeting
MolecularTargeting
.owl#Molecule
jps
.owl#Molecule
24 Aug. 2011
.owl#Molecule
Molecule is a CBO:BioEntityType class OPB: ...that is a polyatomic entity.
.owl#Molecule
urn:miriam:opb:'Molecule'
.owl#Molecule
Molecule
.owl#MoleculeBarrierCrossing
jps
.owl#MoleculeBarrierCrossing
24 Aug. 2011
.owl#MoleculeBarrierCrossing
MoleculeBarrierCrossing is a MoleculeProcess describing the transfer of a molecule across a bona fide boundary such as a basement membrane or a cell wall.
.owl#MoleculeBarrierCrossing
MoleculeBarrierCrossing
.owl#MoleculeChange
jps
.owl#MoleculeChange
24 Aug. 2011
.owl#MoleculeChange
MoleculeChange is a MoleculeProcess that results in a phenotypic change in the molecule. For example, changes in the ionization state of an acid.
.owl#MoleculeChange
MoleculeChange
.owl#MoleculeCreation
jps
.owl#MoleculeCreation
24 Aug. 2011
.owl#MoleculeCreation
MoleculeCreation is a MoleculeProcess that results in the Creation of a new molecule or an increase in a molecule's concentration.
.owl#MoleculeCreation
MoleculeCreation
.owl#MoleculeDeletion
jps
.owl#MoleculeDeletion
24 Aug. 2011
.owl#MoleculeDeletion
MoleculeDeletion is a MoleculeProcess that results in the Deletion of a molecule, or a decrease in a molecule's concentration.
.owl#MoleculeDeletion
MoleculeDeletion
.owl#MoleculeDiffusion
jps
.owl#MoleculeDiffusion
24 Aug. 2011
.owl#MoleculeDiffusion
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.
.owl#MoleculeDiffusion
MoleculeDiffusion
.owl#MoleculeDiffusion
subclass of: BFO:span:fiat_process_part
.owl#MoleculeMoleculeAdhesion
jps
.owl#MoleculeMoleculeAdhesion
24 Aug. 2011
.owl#MoleculeMoleculeAdhesion
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.
.owl#MoleculeMoleculeAdhesion
MoleculeMoleculeAdhesion
.owl#MoleculeProcess
jps
.owl#MoleculeProcess
24 Aug. 2011
.owl#MoleculeProcess
MoleculeProcess is a CBO_Process that involves a molecule.
.owl#MoleculeProcess
MoleculeProcess
.owl#MoleculeProcess
subclass of: BFO:span:process
.owl#Movement
jps
.owl#Movement
24 Aug. 2011
.owl#Movement
Movement is a FundamentalPhysicalProcess resulting in the change in location or Shape of a physical object.
.owl#Movement
Movement
.owl#Movement
subclass of: BFO:span:fiat_process_part
.owl#MovementField
jps
.owl#MovementField
24 Aug. 2011
.owl#MovementField
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.
.owl#MovementField
MovementField
.owl#Necrosis
jps
.owl#Necrosis
24 Aug. 2011
.owl#Necrosis
Necrosis is a CellDeath caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin.
.owl#Necrosis
PATO:0000647
.owl#Necrosis
Necrosis
.owl#Nucleus
jps
.owl#Nucleus
24 Aug. 2011
.owl#Nucleus
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.
.owl#Nucleus
urn:miriam:obo.fma:63840
.owl#Nucleus
urn:miriam:obo.go:0005634
.owl#Nucleus
Nucleus
.owl#OpenAlea
jps
.owl#OpenAlea
23 Jul. 2012
.owl#OpenAlea
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
.owl#OpenAlea
OpenAlea
.owl#OpenSourcePlatform
jps
.owl#OpenSourcePlatform
23 Jul. 2012
.owl#OpenSourcePlatform
OpenSourceModelPlatform is a CBO:ComputationalPlatformQuality class for compuational platforms which are open source.
.owl#OpenSourcePlatform
OpenSourceModelPlatform
.owl#OrganismalRegion
jps
.owl#OrganismalRegion
24 Aug. 2011
.owl#OrganismalRegion
OrganismalRegion is a CBO:GeometricalEntity class for regions of an animal.
.owl#OrganismalRegion
OrganismalRegion
.owl#OrganismalRegion
subclass of: BFO:snap:fiat_object_part
.owl#Orientation
jps
.owl#Orientation
24 Aug. 2011
.owl#Orientation
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.
.owl#Orientation
Orientation
.owl#Other
jps
.owl#Other
23 Jul. 2012
.owl#Other
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.
.owl#Other
OtherComputationalPlatform
.owl#OtherPublicationReference
jps
.owl#OtherPublicationReference
23 Jul. 2012
.owl#OtherPublicationReference
OtherPublicationReference is a CBO:ComputationalPlatformQuality class for computational platforms referenced only by a literature citation.
.owl#OtherPublicationReference
OtherPublicationReference
.owl#PatternTexture
jps
.owl#PatternTexture
24 Aug. 2011
.owl#PatternTexture
PatternTexture is a CBO:Texture consisting of a positionally repetitive Texture description.
.owl#PatternTexture
PatternTexture
.owl#PhenotypicChange
jps
.owl#PhenotypicChange
24 Aug. 2011
.owl#PhenotypicChange
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.
.owl#PhenotypicChange
PhenotypicChange
.owl#PhysicalEntityType
jps
.owl#PhysicalEntityType
24 Aug. 2011
.owl#PhysicalEntityType
A PhysicalEntityType is a CBO_Object class of physical objects. For example, a Cell, a basement membrane of a diffusible Molecule.
.owl#PhysicalEntityType
urn:miriam:dummy:1
.owl#PhysicalEntityType
urn:miriam:dummy:2
.owl#PhysicalEntityType
urn:miriam:dummy:3
.owl#PhysicalEntityType
PhysicalEntityType
.owl#PhysicalEntityType
subclass of: BFO:snap:quality
.owl#PhysicalObjectQuality
jps
.owl#PhysicalObjectQuality
24 Aug. 2011
.owl#PhysicalObjectQuality
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.
.owl#PhysicalObjectQuality
PhysicalObjectQuality
.owl#PhysicalObjectQuality
subclass of: BFO:snap:quality
.owl#PoissonRatio
jps
.owl#PoissonRatio
24 Aug. 2011
.owl#PoissonRatio
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).
.owl#PoissonRatio
PoissonRatio
.owl#PressureMechanical
jps
.owl#PressureMechanical
24 Aug. 2011
.owl#PressureMechanical
PressureMechanical is a CBO:MechanicalProperty describing the barometric pressure of an object or Location in space.
.owl#PressureMechanical
PressureMechanical
.owl#Protrusion
jps
.owl#Protrusion
24 Aug. 2011
.owl#Protrusion
Protrusion is a GeometricalProperty describing an extension from an otherwise simpler CBO:BodyShape description. For example, a transient pseudopodia or a persistent neuronal axon.
.owl#Protrusion
Protrusion
.owl#Pseudopodium
jps
.owl#Pseudopodium
24 Aug. 2011
.owl#Pseudopodium
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
.owl#Pseudopodium
urn:miriam:obo.go:0031143
.owl#Pseudopodium
Pseudopodium
.owl#Pump
jps
.owl#Pump
24 Aug. 2011
.owl#Pump
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.
.owl#Pump
MeSH: D12.776.157.530
.owl#Pump
MeSH:'Membrane Transport Proteins'
.owl#Pump
Pump
.owl#Random
jps
.owl#Random
24 Aug. 2011
.owl#Random
Random is a CBO:StatisticalProperty class that describes a quality of randomness to an object or process.
.owl#Random
Random
.owl#RateFunction
jps
.owl#RateFunction
24 Aug. 2011
.owl#RateFunction
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.
.owl#RateFunction
RateFunction
.owl#RateFunction
subclass of: BFO:snap:quality
.owl#Rotation
jps
.owl#Rotation
24 Aug. 2011
.owl#Rotation
Rotation is a Movement resulting in a change in orientation of an object.
.owl#Rotation
Rotation
.owl#SecondOrderRate
jps
.owl#SecondOrderRate
24 Aug. 2011
.owl#SecondOrderRate
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.
.owl#SecondOrderRate
SecondOrderRate
.owl#Shape
jps
.owl#Shape
24 Aug. 2011
.owl#Shape
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.
.owl#Shape
PATO:0000052
.owl#Shape
urn:miriam:opb:'bounded Volume Shape'
.owl#Shape
Shape
.owl#ShapeChange
jps
.owl#ShapeChange
24 Aug. 2011
.owl#ShapeChange
ShapeChange is a FundamentalPhysicalProcess resulting in the change in the Shape, including extents, of an object.
.owl#ShapeChange
ShapeChange
.owl#ShapeChange
subclass of: BFO:span:fiat_process_part
.owl#SpacialExclusive
jps
.owl#SpacialExclusive
24 Aug. 2011
.owl#SpacialExclusive
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.
.owl#SpacialExclusive
SpacialExclusive
.owl#StatisticalProperty
jps
.owl#StatisticalProperty
24 Aug. 2011
.owl#StatisticalProperty
StatisticalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the statistical qualities of objects. StatisticalProperty are intrinsic to the object.
.owl#StatisticalProperty
StatisticalProperty
.owl#StiffnessMechanical
jps
.owl#StiffnessMechanical
24 Aug. 2011
.owl#StiffnessMechanical
StiffnessMechanical is a CBO:MechanicalProperty that describes an elastic object's resistance to deformation by an applied force along a given direction.
.owl#StiffnessMechanical
StiffnessMechanical
.owl#StructuralProcess
jps
.owl#StructuralProcess
24 Aug. 2011
.owl#StructuralProcess
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.
.owl#StructuralProcess
StructuralProcess
.owl#StructuralProcess
subclass of: BFO:span:process
.owl#SurfaceArea
jps
.owl#SurfaceArea
24 Aug. 2011
.owl#SurfaceArea
SurfaceArea is a CBO:GeometricalProperty describing the scalar value of the object's surface area at a particular instant in time.
.owl#SurfaceArea
urn:miriam:opb:'Area of surface region'
.owl#SurfaceArea
SurfaceArea
.owl#SymmetricCellDivisionOrientedCleavagePlane
jps
.owl#SymmetricCellDivisionOrientedCleavagePlane
24 Aug. 2011
.owl#SymmetricCellDivisionOrientedCleavagePlane
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.
.owl#SymmetricCellDivisionOrientedCleavagePlane
SymmetricCellDivisionOrientedCleavagePlane
.owl#SymmetricCellDivisionRandomCleavagePlane
jps
.owl#SymmetricCellDivisionRandomCleavagePlane
24 Aug. 2011
.owl#SymmetricCellDivisionRandomCleavagePlane
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.
.owl#SymmetricCellDivisionRandomCleavagePlane
SymmetricCellDivisionRandomCleavagePlane
.owl#System
jps
.owl#System
24 Aug. 2011
.owl#System
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.
.owl#System
System
.owl#System
subclass of: BFO:snap:object
.owl#SystemBoundary
jps
.owl#SystemBoundary
25 Jul. 2012
.owl#SystemBoundary
SystemBoundary is a SystemQuality that describes the edges (boundary) of a computational model.
.owl#SystemBoundary
SystemBoundary
.owl#SystemExtent
jps
.owl#SystemExtent
25 Jul. 2012
.owl#SystemExtent
SystemExtent classes are SystemQualties the describe the extent of the model in two or three dimensions. SystemExtent can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
.owl#SystemExtent
SystemExtent
.owl#SystemExtentX
jps
.owl#SystemExtentX
25 Jul. 2012
.owl#SystemExtentX
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.
.owl#SystemExtentX
SystemExtentX
.owl#SystemExtentY
jps
.owl#SystemExtentY
25 Jul. 2012
.owl#SystemExtentY
SystemExtentY is a are SystemExtent the describe the extent of the model in the Y dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
.owl#SystemExtentY
SystemExtentY
.owl#SystemExtentZ
jps
.owl#SystemExtentZ
25 Jul. 2012
.owl#SystemExtentZ
SystemExtentZ is a are SystemExtent the describe the extent of the model in the Y dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents.
.owl#SystemExtentZ
SystemExtentZ
.owl#SystemPeriodic
jps
.owl#SystemPeriodic
25 Jul. 2012
.owl#SystemPeriodic
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.
.owl#SystemPeriodic
SystemPeriodic
.owl#SystemPeriodicX
jpos
.owl#SystemPeriodicX
25 Jul. 2012
.owl#SystemPeriodicX
SystemPeriodicX is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the X-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side.
.owl#SystemPeriodicX
SystemPeriodicX
.owl#SystemPeriodicY
jps
.owl#SystemPeriodicY
25 Jul. 2012
.owl#SystemPeriodicY
SystemPeriodicY is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the Y-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side.
.owl#SystemPeriodicY
SystemPeriodicY
.owl#SystemPeriodicZ
jps
.owl#SystemPeriodicZ
25 Jul. 2012
.owl#SystemPeriodicZ
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.
.owl#SystemPeriodicZ
SystemPeriodicZ
.owl#SystemPixelDistanceScale
jps
.owl#SystemPixelDistanceScale
25 Jul. 2012
.owl#SystemPixelDistanceScale
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.
.owl#SystemPixelDistanceScale
SystemPixel2DistanceScale
.owl#SystemQualities
jps
.owl#SystemQualities
24 Jul. 2012
.owl#SystemQualities
SystemQualities is CBO_Object class that describes the computational platform (suite of code or a standalone computational tool) and instantiation of a particular model.
.owl#SystemQualities
SystemQuality
.owl#SystemQualities
subclass of: BFO:snap:quality
.owl#SystemWall
jps
.owl#SystemWall
25 Jul. 2012
.owl#SystemWall
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.
.owl#SystemWall
SystemWall
.owl#SystemWallX
jps
.owl#SystemWallX
25 Jul. 2012
.owl#SystemWallX
SystemWallX is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the X-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall.
.owl#SystemWallX
SystemWallX
.owl#SystemWallY
jps
.owl#SystemWallY
25 Jul. 2012
.owl#SystemWallY
SystemWallY is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the Y-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall.
.owl#SystemWallY
SystemWallY
.owl#SystemWallZ
jps
.owl#SystemWallZ
25 Jul. 2012
.owl#SystemWallZ
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.
.owl#SystemWallZ
SystemWallZ
.owl#TemperatureField
jps
.owl#TemperatureField
19 Jul. 2012
.owl#TemperatureField
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.)
.owl#TemperatureField
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.)
.owl#TemperatureField
TemperatureField
.owl#TemporalAge
jps
.owl#TemporalAge
24 Aug. 2011
.owl#TemporalAge
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.
.owl#TemporalAge
urn:miriam:obo.pato:0000011
.owl#TemporalAge
TemporalAge
.owl#TemporalEntity
jps
.owl#TemporalEntity
24 Aug. 2011
.owl#TemporalEntity
TemporalEntity is a CBO_Processt that OPB: ...is a moment or span of time.
.owl#TemporalEntity
urn:miriam:opb:'temporal entity'
.owl#TemporalEntity
TemporalEntity
.owl#TemporalEntity
subclass of: BFO:span:connected_temporal_region
.owl#TemporalInstant
jps
.owl#TemporalInstant
24 Aug. 2011
.owl#TemporalInstant
OPB: ...is a point in time.
.owl#TemporalInstant
urn:miriam:opb:'temporal instant'
.owl#TemporalInstant
TemporalInstant
.owl#TemporalInstant
subclass of: BFO:snap:TemporalInstant
.owl#TemporalInterval
jps
.owl#TemporalInterval
24 Aug. 2011
.owl#TemporalInterval
OPB: ...is a period of time bounded by two temporal moments (that may be the same moment).
.owl#TemporalInterval
urn:miriam:opb:'temporal interval'
.owl#TemporalInterval
TemporalInterval
.owl#TemporalInterval
subclass of: BFO:snap:TemporalInterval
.owl#TensionMechanical
jps
.owl#TensionMechanical
24 Aug. 2011
.owl#TensionMechanical
TensionMechanical is a CBO:MechanicalProperty that describes the pulling force exerted on an entity (a stretching or distorting force).
.owl#TensionMechanical
TensionMechanical
.owl#Texture
jps
.owl#Texture
24 Aug. 2011
.owl#Texture
Texture is a CBO:GeometricalProperty describing the characteristics of a surface Texture.
.owl#Texture
Texture
.owl#TightJunction
jps
.owl#TightJunction
24 Aug. 2011
.owl#TightJunction
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)
.owl#TightJunction
urn:miriam:obo.go:0005923
.owl#TightJunction
TightJunction
.owl#Translation
jps
.owl#Translation
24 Aug. 2011
.owl#Translation
Translation is a Movement resulting in a change in the spatial location of an object.
.owl#Translation
Translation
.owl#Transport
jps
.owl#Transport
24 Aug. 2011
.owl#Transport
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).
.owl#Transport
TransportProcess
.owl#UniformTexture
jps
.owl#UniformTexture
24 Aug. 2011
.owl#UniformTexture
UniformTexture is a CBO:Texture consisting of a positionally independent Texture description.
.owl#UniformTexture
UniformTexture
.owl#VTK_FileName
JPS
.owl#VTK_FileName
10/25/2012
.owl#VTK_FileName
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.
.owl#VTK_FileName
VTK_FileName
.owl#VTK_FileRoot
JPS
.owl#VTK_FileRoot
10/25/2012
.owl#VTK_FileRoot
VTK_FileRoot is a CBO:SystemQuality:VTK_Quality giving the root name for the VTK files associated with the particular model.
.owl#VTK_FileRoot
VTK_FileRoot
.owl#VTK_FileTimeStep
JPS
.owl#VTK_FileTimeStep
10/25/2012
.owl#VTK_FileTimeStep
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).
.owl#VTK_FileTimeStep
VTK_FileTimeStep
.owl#VTK_InitialCondition
jps
.owl#VTK_InitialCondition
10/25/2012
.owl#VTK_InitialCondition
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.
.owl#VTK_InitialCondition
VTK_InitialCondition
.owl#VTK_Quality
JPS
.owl#VTK_Quality
10/29/2012
.owl#VTK_Quality
VTK_Quality is a CBO:SystemQuality that includes classes for specificying the name, ilneage and time of a VTK snap(shot) of the simulation.
.owl#VTK_Quality
VTK_Quality
.owl#Ventral
jps
.owl#Ventral
24 Aug. 2011
.owl#Ventral
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.
.owl#Ventral
Ventral
.owl#Volume
jps
.owl#Volume
24 Aug. 2011
.owl#Volume
Volume is a GeometricalProperty describing the total Volume of spaced occupied by the object at a particular instant in time.
.owl#Volume
PATO:0000918
.owl#Volume
urn:miriam:opb:'Volume of Volume region'
.owl#Volume
Volume
.owl#VolumeChange
jps
.owl#VolumeChange
24 Aug. 2011
.owl#VolumeChange
VolumeChange is a FundamentalPhysicalProcess resulting in a change, an increase or decrease, in the Volume occupied by an object.
.owl#VolumeChange
VolumeChange
.owl#VolumeChange
subclass of: BFO:span:fiat_process_part
.owl#VolumeEnergy
jps
.owl#VolumeEnergy
24 Aug. 2011
.owl#VolumeEnergy
A VolumeEnergy is a CBO:EnergyQuality representing the energy associated with a given volume entity.
.owl#VolumeEnergy
VolumeEnergy
.owl#YieldingThreshold
jps
.owl#YieldingThreshold
24 Aug. 2011
.owl#YieldingThreshold
YieldingThreshold (Yield stress threshold, Y) is a CBO:MechanicalProperty describing the rheological yield stress of an object.
.owl#YieldingThreshold
YieldingThreshold
.owl#YoungsModulus
jps
.owl#YoungsModulus
24 Aug. 2011
.owl#YoungsModulus
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)
.owl#YoungsModulus
YoungsModulus
.owl#ZerothOrderRate
jps
.owl#ZerothOrderRate
24 Aug. 2011
.owl#ZerothOrderRate
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.
.owl#ZerothOrderRate
ZerothOrderRate
.owl#hasExtentValueSet1D
1 value (included for completeness, probably best to just use hasFloatValue or hasIntValue). For example, the 1D length of an object of "3.2". Stored as a text string. Value is assumed to be X in a square coordinate system.
.owl#hasExtentValueSet1D
hasExtentValueSet1D
.owl#hasExtentValueSet2D
2 Comma separated values (CSV). For example, the extent of a 2D region (area) "5,10". Stored as a text string. Values are assumed to be X,Y in a square coordinate system.
.owl#hasExtentValueSet2D
hasExtentValueSet2D
.owl#hasExtentValueSet3D
3 Comma separated values (CSV). For example, the extent of a 3D region (volume) "5,5,10". Stored as a text string. Values are assumed to be X,Y,Z in a square coordinate system.
.owl#hasExtentValueSet3D
hasExtentValueSet3D
.owl#hasFloatValue
A single floating point number.
.owl#hasFloatValue
hasFloatValue
.owl#hasFloatValueTarget
A single floating point number representing the target value of a quality or function.
.owl#hasFloatValueTarget
hasFloatValueTarget
.owl#hasIntValue
A single integer number.
.owl#hasIntValue
hasIntValue
.owl#hasIntValueTarget
A single integer number representing the target value of a quality or function.
.owl#hasIntValueTarget
hasIntValueTarget
.owl#hasLocationValueSet1D
1 value (included for completeness, probably best to just use hasFloatValue or hasIntValue). For example, the location of a point "3.2". Stored as a text string.
.owl#hasLocationValueSet1D
hasLocationValueSet1D
.owl#hasLocationValueSet2D
2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string.
.owl#hasLocationValueSet2D
hasLocationValueSet2D
.owl#hasLocationValueSet3D
3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string.
.owl#hasLocationValueSet3D
hasLocationValueSet3D
.owl#hasLocationValueSetND
Comma separated values (CSV) with [CR] end of row markers. Dimension (rows and column counts) not explicitly stated. Assumed that all units are the same. Stored as a text string.
.owl#hasLocationValueSetND
hasLocationValueSetND
.owl#hasParameterValueSetND
Data is a list of n-tupes (one n-tuple/line) listing values of various kinds. For example, the list of interaction energies between a set of cell types. Comma separated values (CSV) with [CR] end of row markers. The dimensions (number of rows and columns) is not explicitly stated. Stored as a text string.
.owl#hasParameterValueSetND
hasParameterValueSetND
.owl#hasPointsValueSetND
Data is a list of n-tupes (one n-tuple/line) listing the coordinates of the elements within a set. For example, the list of x,y,z coordinates of a cell in a grid-based coordinate system. Comma separated values (CSV) with [CR] end of row markers. The dimensions (number of rows and columns) is not explicitly stated. Stored as a text string.
.owl#hasPointsValueSetND
hasPointsValueSetND
.owl#hasUnit
A unit name, for example, "meter", "micrometer*micrometer", "hour". Stored as a text string.
.owl#hasUnit
hasUnit
.owl#hasVTKfieldID
jps
.owl#hasVTKfieldID
11/9/2012
.owl#hasVTKfieldID
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".
.owl#hasVTKfieldID
hasVTKfieldID
.owl#hasVTKtypeID
JPS
.owl#hasVTKtypeID
10/25/2012
.owl#hasVTKtypeID
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.
relationship:OBO_REL_adjacent_to
OBO_REL_adjacent_to
relationship:OBO_REL_adjacent_to
OBO_REL_adjacents_to
relationship:OBO_REL_adjacent_to
OBO_REL_adjacented_to
relationship:OBO_REL_adjacent_to
true
relationship:OBO_REL_adjacent_to
OBO_REL:0000012
relationship:OBO_REL_adjacent_to
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
relationship:OBO_REL_adjacent_to
"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]
relationship:OBO_REL_adjacent_to
adjacent_to
relationship:OBO_REL_agent_in
OBO_REL_agent_in
relationship:OBO_REL_agent_in
OBO_REL_agents_in
relationship:OBO_REL_agent_in
OBO_REL_agented_in
relationship:OBO_REL_agent_in
OBO_REL:has_agent
relationship:OBO_REL_agent_in
OBO_REL:0000022
relationship:OBO_REL_agent_in
agent_in
relationship:OBO_REL_contained_in
OBO_REL_contained_in
relationship:OBO_REL_contained_in
OBO_REL_containeds_in
relationship:OBO_REL_contained_in
OBO_REL_containeded_in
relationship:OBO_REL_contained_in
OBO_REL:contains
relationship:OBO_REL_contained_in
OBO_REL:0000010
relationship:OBO_REL_contained_in
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):
relationship:OBO_REL_contained_in
"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]
relationship:OBO_REL_contained_in
contained_in
relationship:OBO_REL_contains
OBO_REL_contains
relationship:OBO_REL_contains
OBO_REL_containses
relationship:OBO_REL_contains
OBO_REL_containsed
relationship:OBO_REL_contains
OBO_REL:contained_in
relationship:OBO_REL_contains
OBO_REL:0000011
relationship:OBO_REL_contains
contains
relationship:OBO_REL_derived_into
OBO_REL_derived_into
relationship:OBO_REL_derived_into
OBO_REL_deriveds_into
relationship:OBO_REL_derived_into
OBO_REL_deriveded_into
relationship:OBO_REL_derived_into
OBO_REL:derives_from
relationship:OBO_REL_derived_into
OBO_REL:0000016
relationship:OBO_REL_derived_into
derived_into
relationship:OBO_REL_derives_from
OBO_REL_derives_from
relationship:OBO_REL_derives_from
OBO_REL_deriveses_from
relationship:OBO_REL_derives_from
OBO_REL_derivesed_from
relationship:OBO_REL_derives_from
OBO_REL:derived_into
relationship:OBO_REL_derives_from
OBO_REL:0000015
relationship:OBO_REL_derives_from
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.
relationship:OBO_REL_derives_from
"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]
relationship:OBO_REL_derives_from
"derived_from" []
relationship:OBO_REL_derives_from
derives_from
relationship:OBO_REL_has_agent
OBO_REL_has_agent
relationship:OBO_REL_has_agent
OBO_REL_has_agents
relationship:OBO_REL_has_agent
OBO_REL_has_agented
relationship:OBO_REL_has_agent
OBO_REL:agent_in
relationship:OBO_REL_has_agent
OBO_REL:0000021
relationship:OBO_REL_has_agent
"As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874]
relationship:OBO_REL_has_agent
has_agent
relationship:OBO_REL_has_improper_part
OBO_REL_has_improper_part
relationship:OBO_REL_has_improper_part
OBO_REL_has_improper_parts
relationship:OBO_REL_has_improper_part
OBO_REL_has_improper_parted
relationship:OBO_REL_has_improper_part
OBO_REL:improper_part_of
relationship:OBO_REL_has_improper_part
OBO_REL:0000024
relationship:OBO_REL_has_improper_part
See reasons for obsoletion of improper_part_of
relationship:OBO_REL_has_improper_part
true
relationship:OBO_REL_has_improper_part
has_improper_part
relationship:OBO_REL_has_integral_part
OBO_REL_has_integral_part
relationship:OBO_REL_has_integral_part
OBO_REL_has_integral_parts
relationship:OBO_REL_has_integral_part
OBO_REL_has_integral_parted
relationship:OBO_REL_has_integral_part
OBO_REL:integral_part_of
relationship:OBO_REL_has_integral_part
true
relationship:OBO_REL_has_integral_part
OBO_REL:0000005
relationship:OBO_REL_has_integral_part
has_integral_part
relationship:OBO_REL_has_part
OBO_REL_has_part
relationship:OBO_REL_has_part
OBO_REL_has_parts
relationship:OBO_REL_has_part
OBO_REL_has_parted
relationship:OBO_REL_has_part
OBO_REL:part_of
relationship:OBO_REL_has_part
true
relationship:OBO_REL_has_part
OBO_REL:0000003
relationship:OBO_REL_has_part
has_part
relationship:OBO_REL_has_participant
OBO_REL_has_participant
relationship:OBO_REL_has_participant
OBO_REL_has_participants
relationship:OBO_REL_has_participant
OBO_REL_has_participanted
relationship:OBO_REL_has_participant
OBO_REL:participates_in
relationship:OBO_REL_has_participant
OBO_REL:0000019
relationship:OBO_REL_has_participant
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.
relationship:OBO_REL_has_participant
"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]
relationship:OBO_REL_has_participant
has_participant
relationship:OBO_REL_has_proper_part
OBO_REL_has_proper_part
relationship:OBO_REL_has_proper_part
OBO_REL_has_proper_parts
relationship:OBO_REL_has_proper_part
OBO_REL_has_proper_parted
relationship:OBO_REL_has_proper_part
OBO_REL:proper_part_of
relationship:OBO_REL_has_proper_part
OBO_REL:0000007
relationship:OBO_REL_has_proper_part
has_proper_part
relationship:OBO_REL_improper_part_of
OBO_REL_improper_part_of
relationship:OBO_REL_improper_part_of
OBO_REL_improper_part_ofs
relationship:OBO_REL_improper_part_of
OBO_REL_improper_part_ofed
relationship:OBO_REL_improper_part_of
OBO_REL:has_improper_part
relationship:OBO_REL_improper_part_of
OBO_REL:0000025
relationship:OBO_REL_improper_part_of
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]
relationship:OBO_REL_improper_part_of
"As for part_of, with the additional constraint that subject and object may be identical" [PMID:15892874]
relationship:OBO_REL_improper_part_of
true
relationship:OBO_REL_improper_part_of
improper_part_of
relationship:OBO_REL_instance_of
OBO_REL_instance_of
relationship:OBO_REL_instance_of
OBO_REL_instance_ofs
relationship:OBO_REL_instance_of
OBO_REL_instance_ofed
relationship:OBO_REL_instance_of
OBO_REL:0000023
relationship:OBO_REL_instance_of
true
relationship:OBO_REL_instance_of
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
relationship:OBO_REL_instance_of
"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]
relationship:OBO_REL_instance_of
instance_of
relationship:OBO_REL_integral_part_of
OBO_REL_integral_part_of
relationship:OBO_REL_integral_part_of
OBO_REL_integral_part_ofs
relationship:OBO_REL_integral_part_of
OBO_REL_integral_part_ofed
relationship:OBO_REL_integral_part_of
OBO_REL:has_integral_part
relationship:OBO_REL_integral_part_of
true
relationship:OBO_REL_integral_part_of
OBO_REL:0000004
relationship:OBO_REL_integral_part_of
"C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874]
relationship:OBO_REL_integral_part_of
integral_part_of
relationship:OBO_REL_is_a
OBO_REL_is_a
relationship:OBO_REL_is_a
OBO_REL_is_as
relationship:OBO_REL_is_a
OBO_REL_is_aed
relationship:OBO_REL_is_a
true
relationship:OBO_REL_is_a
OBO_REL:0000001
relationship:OBO_REL_is_a
true
relationship:OBO_REL_is_a
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
relationship:OBO_REL_is_a
"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]
relationship:OBO_REL_is_a
"is_subtype_of" []
relationship:OBO_REL_is_a
owl:subClassOf
relationship:OBO_REL_is_a
is_a
relationship:OBO_REL_located_in
OBO_REL_located_in
relationship:OBO_REL_located_in
OBO_REL_locateds_in
relationship:OBO_REL_located_in
OBO_REL_locateded_in
relationship:OBO_REL_located_in
OBO_REL:location_of
relationship:OBO_REL_located_in
OBO_REL:0000008
relationship:OBO_REL_located_in
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
relationship:OBO_REL_located_in
"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]
relationship:OBO_REL_located_in
located_in
relationship:OBO_REL_location_of
OBO_REL_location_of
relationship:OBO_REL_location_of
OBO_REL_location_ofs
relationship:OBO_REL_location_of
OBO_REL_location_ofed
relationship:OBO_REL_location_of
OBO_REL:located_in
relationship:OBO_REL_location_of
OBO_REL:0000009
relationship:OBO_REL_location_of
location_of
relationship:OBO_REL_part_of
OBO_REL_part_of
relationship:OBO_REL_part_of
OBO_REL_part_ofs
relationship:OBO_REL_part_of
OBO_REL_part_ofed
relationship:OBO_REL_part_of
OBO_REL:has_part
relationship:OBO_REL_part_of
true
relationship:OBO_REL_part_of
OBO_REL:0000002
relationship:OBO_REL_part_of
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.
relationship:OBO_REL_part_of
"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]
relationship:OBO_REL_part_of
part_of
relationship:OBO_REL_participates_in
OBO_REL_participates_in
relationship:OBO_REL_participates_in
OBO_REL_participateses_in
relationship:OBO_REL_participates_in
OBO_REL_participatesed_in
relationship:OBO_REL_participates_in
OBO_REL:has_participant
relationship:OBO_REL_participates_in
OBO_REL:0000020
relationship:OBO_REL_participates_in
participates_in
relationship:OBO_REL_preceded_by
OBO_REL_preceded_by
relationship:OBO_REL_preceded_by
OBO_REL_preceded_bies
relationship:OBO_REL_preceded_by
OBO_REL_preceded_bied
relationship:OBO_REL_preceded_by
OBO_REL:precedes
relationship:OBO_REL_preceded_by
OBO_REL:0000017
relationship:OBO_REL_preceded_by
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.
relationship:OBO_REL_preceded_by
"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]
relationship:OBO_REL_preceded_by
preceded_by
relationship:OBO_REL_precedes
OBO_REL_precedes
relationship:OBO_REL_precedes
OBO_REL_precedeses
relationship:OBO_REL_precedes
OBO_REL_precedesed
relationship:OBO_REL_precedes
OBO_REL:preceded_by
relationship:OBO_REL_precedes
OBO_REL:0000018
relationship:OBO_REL_precedes
precedes
relationship:OBO_REL_proper_part_of
OBO_REL_proper_part_of
relationship:OBO_REL_proper_part_of
OBO_REL_proper_part_ofs
relationship:OBO_REL_proper_part_of
OBO_REL_proper_part_ofed
relationship:OBO_REL_proper_part_of
OBO_REL:has_proper_part
relationship:OBO_REL_proper_part_of
OBO_REL:0000006
relationship:OBO_REL_proper_part_of
"As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]
relationship:OBO_REL_proper_part_of
proper_part_of
relationship:OBO_REL_transformation_of
OBO_REL_transformation_of
relationship:OBO_REL_transformation_of
OBO_REL_transformation_ofs
relationship:OBO_REL_transformation_of
OBO_REL_transformation_ofed
relationship:OBO_REL_transformation_of
OBO_REL:0000013
relationship:OBO_REL_transformation_of
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.
relationship:OBO_REL_transformation_of
"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]
relationship:OBO_REL_transformation_of
transformation_of
snap:IndependentContinuant
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.
owl:topObjectProperty
Note that OWL DL does not support antiymetric properties so those have been removed from the OBO Relation defintiions for the properties.