CBO 1 0
type: Ontology
version info: 1.0.0
format-version: 1.2
date: 7 Feb. 2013
creator: J Sluka, Biocomplexity Insitute, Indiana University
idspace: OBO_REL http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry"
comment: The cell Behavior Ontology (CBO) is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.
description: The cell Behavior Ontology (CBO) is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.
version info: Version 1.0.0 is the initial release of the Cell Behavior Ontology (CBO).
saved-by: jps
remark: release version 1.0.0

has_Quality
type: ObjectProperty
date: 1/24/2012
def: has_Quality links an instance of a CBO quality to a class or individual.
creator: jps
description: has_Quality links an instance of a CBO quality to a class or individual.

adjacent_to
type: ObjectProperty
TV pl: OBO_REL_adjacent_to
def: "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]
TV vbg: OBO_REL_adjacented_to
instance level is transitive: true
alt id: OBO_REL:0000012
TV sg: OBO_REL_adjacents_to
comment: 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

agent_in
type: ObjectProperty
TV pl: OBO_REL_agent_in
TV sg: OBO_REL_agents_in
inverse of on instance level: OBO_REL:has_agent
alt id: OBO_REL:0000022
TV vbg: OBO_REL_agented_in
sub property of: participates_in

contained_in
type: ObjectProperty
TV sg: OBO_REL_containeds_in
comment: 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):
inverse of on instance level: OBO_REL:contains
TV vbg: OBO_REL_containeded_in
TV pl: OBO_REL_contained_in
def: "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]
alt id: OBO_REL:0000010

contains
type: ObjectProperty
alt id: OBO_REL:0000011
inverse of on instance level: OBO_REL:contained_in
TV pl: OBO_REL_contains
TV vbg: OBO_REL_containsed
TV sg: OBO_REL_containses

derived_into
type: ObjectProperty
type: TransitiveProperty
TV pl: OBO_REL_derived_into
inverse of on instance level: OBO_REL:derives_from
TV vbg: OBO_REL_deriveded_into
TV sg: OBO_REL_deriveds_into
alt id: OBO_REL:0000016

derives_from
type: ObjectProperty
type: TransitiveProperty
TV pl: OBO_REL_derives_from
inverse of on instance level: OBO_REL:derived_into
comment: 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.
exact synonym: "derived_from" []
def: "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]
TV vbg: OBO_REL_derivesed_from
TV sg: OBO_REL_deriveses_from
alt id: OBO_REL:0000015

has_agent
type: ObjectProperty
TV pl: OBO_REL_has_agent
alt id: OBO_REL:0000021
def: "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874]
inverse of on instance level: OBO_REL:agent_in
TV sg: OBO_REL_has_agents
TV vbg: OBO_REL_has_agented
sub property of: has_participant

has_improper_part
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
TV pl: OBO_REL_has_improper_part
TV sg: OBO_REL_has_improper_parts
alt id: OBO_REL:0000024
TV vbg: OBO_REL_has_improper_parted
inverse of on instance level: OBO_REL:improper_part_of
comment: See reasons for obsoletion of improper_part_of
is obsolete: true
sub property of: has_part

has_integral_part
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
TV vbg: OBO_REL_has_integral_parted
is anti symmetric: true
TV sg: OBO_REL_has_integral_parts
TV pl: OBO_REL_has_integral_part
alt id: OBO_REL:0000005
inverse of: OBO_REL:integral_part_of
sub property of: has_part

has_part
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
alt id: OBO_REL:0000003
TV vbg: OBO_REL_has_parted
TV sg: OBO_REL_has_parts
is anti symmetric: true
TV pl: OBO_REL_has_part
inverse of on instance level: OBO_REL:part_of

has_participant
type: ObjectProperty
TV pl: OBO_REL_has_participant
TV sg: OBO_REL_has_participants
alt id: OBO_REL:0000019
comment: 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.
inverse of on instance level: OBO_REL:participates_in
TV vbg: OBO_REL_has_participanted
def: "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]

has_proper_part
type: ObjectProperty
type: TransitiveProperty
TV sg: OBO_REL_has_proper_parts
TV pl: OBO_REL_has_proper_part
inverse of on instance level: OBO_REL:proper_part_of
TV vbg: OBO_REL_has_proper_parted
alt id: OBO_REL:0000007
sub property of: has_part

improper_part_of
type: ObjectProperty
type: ReflexiveProperty
is obsolete: true
TV sg: OBO_REL_improper_part_ofs
TV vbg: OBO_REL_improper_part_ofed
def: "As for part_of, with the additional constraint that subject and object may be identical" [PMID:15892874]
inverse of on instance level: OBO_REL:has_improper_part
alt id: OBO_REL:0000025
TV pl: OBO_REL_improper_part_of
comment: 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]
sub property of: part_of

instance_of
type: ObjectProperty
alt id: OBO_REL:0000023
TV pl: OBO_REL_instance_of
def: "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]
builtin: true
comment: 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
TV sg: OBO_REL_instance_ofs
TV vbg: OBO_REL_instance_ofed

integral_part_of
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
TV vbg: OBO_REL_integral_part_ofed
TV sg: OBO_REL_integral_part_ofs
TV pl: OBO_REL_integral_part_of
inverse of: OBO_REL:has_integral_part
alt id: OBO_REL:0000004
def: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874]
is anti symmetric: true
sub property of: part_of

is_a
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
xref: owl:subClassOf
builtin: true
alt id: OBO_REL:0000001
TV vbg: OBO_REL_is_aed
comment: 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
def: "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]
TV pl: OBO_REL_is_a
is anti symmetric: true
TV sg: OBO_REL_is_as
exact synonym: "is_subtype_of" []

located_in
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
def: "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]
TV sg: OBO_REL_locateds_in
inverse of on instance level: OBO_REL:location_of
comment: 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
TV pl: OBO_REL_located_in
alt id: OBO_REL:0000008
TV vbg: OBO_REL_locateded_in

location_of
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
TV sg: OBO_REL_location_ofs
TV pl: OBO_REL_location_of
inverse of on instance level: OBO_REL:located_in
alt id: OBO_REL:0000009
TV vbg: OBO_REL_location_ofed

part_of
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
comment: 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.
def: "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]
inverse of on instance level: OBO_REL:has_part
is anti symmetric: true
TV sg: OBO_REL_part_ofs
alt id: OBO_REL:0000002
TV vbg: OBO_REL_part_ofed
TV pl: OBO_REL_part_of

participates_in
type: ObjectProperty
alt id: OBO_REL:0000020
TV pl: OBO_REL_participates_in
TV vbg: OBO_REL_participatesed_in
inverse of on instance level: OBO_REL:has_participant
TV sg: OBO_REL_participateses_in

preceded_by
type: ObjectProperty
type: TransitiveProperty
TV vbg: OBO_REL_preceded_bied
inverse of on instance level: OBO_REL:precedes
TV sg: OBO_REL_preceded_bies
def: "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]
alt id: OBO_REL:0000017
comment: 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.
TV pl: OBO_REL_preceded_by

precedes
type: ObjectProperty
type: TransitiveProperty
inverse of on instance level: OBO_REL:preceded_by
alt id: OBO_REL:0000018
TV sg: OBO_REL_precedeses
TV vbg: OBO_REL_precedesed
TV pl: OBO_REL_precedes

proper_part_of
type: ObjectProperty
type: TransitiveProperty
inverse of on instance level: OBO_REL:has_proper_part
def: "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874]
alt id: OBO_REL:0000006
TV vbg: OBO_REL_proper_part_ofed
TV pl: OBO_REL_proper_part_of
TV sg: OBO_REL_proper_part_ofs
sub property of: part_of

transformation_of
type: ObjectProperty
type: TransitiveProperty
alt id: OBO_REL:0000013
comment: 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.
TV vbg: OBO_REL_transformation_ofed
TV sg: OBO_REL_transformation_ofs
def: "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]
TV pl: OBO_REL_transformation_of

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

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

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

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

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

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

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

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

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

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

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

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

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

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

hasVTKfieldID
type: DatatypeProperty
date: 11/9/2012
description: 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".
creator: jps

hasVTKtypeID
type: DatatypeProperty
type: FunctionalProperty
creator: JPS
description: 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.
date: 10/25/2012
range: int

AcceptanceFunction
type: Class
subclass of: EnergyFunction
description: 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.
creator: jps
date: 24 Aug. 2011

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

AdhesionMolecule
type: Class
subclass of: CellMembranePart
creator: jps
description: 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.
date: 24 Aug. 2011

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

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

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

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

ApicalPart
type: Class
subclass of: CellRegion
description: 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.
date: 24 Aug. 2011
creator: jps

Apoptosis
type: Class
subclass of: CellDeath
creator: jps
description: 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.
date: 24 Aug. 2011

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

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

AsymmetricCellDivisionRandomCleavagePlane
type: Class
subclass of: Mitosis
description: 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.
date: 24 Aug. 2011
creator: jps

AutophagicDeath
type: Class
subclass of: CellDeath
creator: jps
description: 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.
date: 24 Aug. 2011

BarrierCrossing
type: Class
subclass of: FundamentalPhysicalProcess
creator: jps
description: 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.
date: 24 Aug. 2011

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

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

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

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

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

BasementMembrane
type: Class
subclass of: ExtraCellularMatrix
disjoint with: InterstitialMatrix
description: 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.
date: 24 Aug. 2011
creator: jps

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

BodyShape
type: Class
subclass of: Shape
creator: jps
description: 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.
date: 24 Aug. 2011
is defined by: urn:miriam:opb:'bounded Volume Shape'

BoltzmannFactor
type: Class
subclass of: AcceptanceFunction
disjoint with: MinimizationAcceptanceFunction
description: 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).
date: 24 Aug. 2011
creator: jps

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

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

CBO_Object
type: Class
disjoint with: CBO_Process
see also: subclass of: BFO:continuant
date: 24 Aug. 2011
creator: jps
description: CBO_Object is the top level CBO class for physical objects and object qualities. CBO_Object is BFO:continuant (endurant).

CBO_Process
type: Class
date: 24 Aug. 2011
see also: subclass of: BFO:occurrent
description: CBO_Process is the top level CBO class for processes. CBO_Process is BFO:occurant (processual).
creator: jps

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

Cell
type: Class
subclass of: BioEntityType
see also: subclass of: BFO:snap:object
date: 24 Aug. 2011
creator: jps
description: 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.

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

CellAdvection
type: Class
subclass of: CellMovement
creator: jps
description: 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.
date: 24 Aug. 2011

CellBasementLaminaContact
type: Class
subclass of: CellNonCellContact
disjoint with: CellInterstitialMatrixContact
creator: jps
description: 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).
date: 24 Aug. 2011

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

CellBorder
type: Class
subclass of: CellPart
creator: jps
description: 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.
date: 24 Aug. 2011

CellCellAdhesion
type: Class
subclass of: CellAdhesion
disjoint with: CellNonCellAdhesion
description: 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.
date: 24 Aug. 2011
creator: jps

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

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

CellContact
type: Class
subclass of: CellEnvironmentProcess
see also: subclass of: BFO:span:fiat_process_part
date: 24 Aug. 2011
creator: jps
description: 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).

CellDeath
type: Class
subclass of: ExistentialCellProcesses
creator: jps
description: 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.
date: 24 Aug. 2011

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

CellDisplacement
type: Class
subclass of: CellMovement
date: 24 Aug. 2011
description: 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.
creator: jps

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

CellEnvironmentProcess
type: Class
subclass of: CellProcess
date: 24 Aug. 2011
description: 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.
creator: jps

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

CellFusion
type: Class
subclass of: ExistentialCellProcesses
creator: jps
description: 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.
date: 24 Aug. 2011

CellGrowth
type: Class
subclass of: ExistentialCellProcesses
creator: jps
see also: subclass of: BFO:span:fiat_process_part
description: 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.
date: 24 Aug. 2011

CellImport
type: Class
subclass of: CellRelatedTransport
description: 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.
creator: jps
date: 24 Aug. 2011

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

CellInterstitialMatrixContact
type: Class
subclass of: CellNonCellContact
description: 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).
date: 24 Aug. 2011
creator: jps

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

CellMembraneLocalStructure
type: Class
subclass of: CBO_Object
creator: jps
date: 24 Aug. 2011
description: 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.
see also: subclass of: BFO:snap:specifically_dependent_continuant

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

CellMotility
type: Class
subclass of: CellMovement
creator: jps
description: 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.
date: 24 Aug. 2011

CellMovement
type: Class
subclass of: GeometricalCellProcess
creator: jps
description: 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.
date: 24 Aug. 2011

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

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

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

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

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

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

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

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

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

CellState
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
description: 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.
see also: subclass of: BFO:snap:quality
creator: jps

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

CellWall
type: Class
subclass of: CellBorder
date: 24 Aug. 2011
description: 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?
creator: jps

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

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

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

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

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

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

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

CenterOfVolume
type: Class
subclass of: Location
description: 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.
date: 24 Aug. 2011
creator: jps

Charge
type: Class
subclass of: ElectricalProperty
creator: jps
description: 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.
date: 24 Aug. 2011
is defined by: urn:miriam:opb:'Charge amount'

ChemicalAffinity
type: Class
subclass of: ChemicalProperty
description: ChemicalAffinity is a ChemicalProperty that describes an affinity (atraction, repulsion) between a molecule and another object.
creator: jps
date: 24 Aug. 2011

ChemicalDensity
type: Class
subclass of: ChemicalProperty
creator: jps
description: ChemicalDensity is a ChemicalProperty that describes the concentration (mass or number of molecules) per unit volume.
date: 24 Aug. 2011

ChemicalLocalization
type: Class
subclass of: ChemicalProperty
date: 24 Aug. 2011
description: ChemicalLocalization is a ChemicalProperty that describes a tendency for the chemical species to localize in a particular region (e.g., cell membrane).
creator: jps

ChemicalPattern
type: Class
subclass of: ChemicalProperty
date: 24 Aug. 2011
creator: jps
description: ChemicalPattern is a ChemicalProperty that describes a tendency for the chemical species to organize or partition in a particular pattern.

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

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

Chemotaxis
type: Class
subclass of: CellMovement
description: 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).
date: 24 Aug. 2011
creator: jps

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

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

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

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

DiscreteModelPlatform
type: Class
subclass of: ComputationalPlatformQuality
description: 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
creator: jps
date: 23 Jul. 2012

ContinuousEntity
type: Class
subclass of: PhysicalEntityType
description: 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).
creator: jps
date: 24 Aug. 2011

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

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

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

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

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

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

DiffuseEntity
type: Class
subclass of: PhysicalEntityType
description: 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.
date: 24 Aug. 2011
creator: jps

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

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

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

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

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

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

Divisible
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
creator: jps
description: 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.

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

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

ElectromechanicalField
type: Class
subclass of: Field
date: 8/1/2012
description: 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.
creator: jps

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

EnergyFunction
type: Class
subclass of: CBO_Object
creator: jps
see also: subclass of: BFO:snap:quality
date: 24 Aug. 2011
description: 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.

EnergyQuality
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
see also: subclass of: BFO:snap:quality
creator: jps
description: 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.

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

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

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

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

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

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

Field
type: Class
subclass of: CBO_Object
creator: jps
date: 19 Jul. 2012
description: 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.

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

FieldQuality
type: Class
subclass of: CBO_Object
description: 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.
date: 11/8/2012
creator: jps

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

Filopodium
type: Class
subclass of: CellMembraneLocalStructure
disjoint with: Pseudopodium
description: 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
creator: jps
date: 24 Aug. 2011

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

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

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

GapJunction
type: Class
subclass of: CellMembranePart
description: 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.
creator: jps
date: 24 Aug. 2011

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

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

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

GeometricalProperty
type: Class
subclass of: PhysicalObjectQuality
date: 24 Aug. 2011
description: 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.
creator: jps

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

Hamiltonian
type: Class
subclass of: EnergyQuality
description: 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.
creator: jps
date: 24 Aug. 2011

Haptotaxis
type: Class
subclass of: CellMovement
description: 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.
date: 24 Aug. 2011
creator: jps

HarmonicEnergy
type: Class
subclass of: EnergyFunction
creator: jps
description: 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.
date: 24 Aug. 2011

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

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

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

InterstitialMatrix
type: Class
subclass of: ExtraCellularMatrix
description: 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.
date: 24 Aug. 2011
creator: jps

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

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

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

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

IntraentityTransport
type: Class
subclass of: Transport
description: 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.
creator: jps
date: 24 Aug. 2011

IonChannel
type: Class
subclass of: CellMembranePart
description: 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.
date: 24 Aug. 2011
creator: jps

IsApoptotic
type: Class
subclass of: CellState
description: 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.
creator: jps
date: 24 Aug. 2011

IsDebris
type: Class
subclass of: CellState
description: 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.
creator: jps
date: 24 Aug. 2011

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

IsHypoxic
type: Class
subclass of: CellState
date: 24 Aug. 2011
creator: jps
description: 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.

IsNecrotic
type: Class
subclass of: CellState
date: 24 Aug. 2011
creator: jps
description: 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.

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

Isotropy
type: Class
subclass of: BodyShape
creator: jps
description: 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.
date: 24 Aug. 2011

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

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

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

LinearEnergy
type: Class
subclass of: EnergyFunction
date: 24 Aug. 2011
creator: jps
description: 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.

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

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

MechanicalProperty
type: Class
subclass of: PhysicalObjectQuality
creator: jps
description: 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.
date: 24 Aug. 2011

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

Meiosis
type: Class
subclass of: CellDivision
date: 24 Aug. 2011
creator: jps
description: 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.

MembraneReceptor
type: Class
subclass of: CellMembranePart
creator: jps
description: 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.
date: 24 Aug. 2011

MinimizationAcceptanceFunction
type: Class
subclass of: AcceptanceFunction
description: 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.
creator: jps
date: 24 Aug. 2011

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

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

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

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

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

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

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

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

MoleculeDiffusion
type: Class
subclass of: MoleculeProcess
description: 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.
see also: subclass of: BFO:span:fiat_process_part
creator: jps
date: 24 Aug. 2011

MoleculeMoleculeAdhesion
type: Class
subclass of: MoleculeProcess
creator: jps
date: 24 Aug. 2011
description: 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.

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

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

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

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

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

OpenAlea
type: Class
subclass of: ComputationalPlatform
date: 23 Jul. 2012
description: 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
creator: jps

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

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

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

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

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

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

PhenotypicChange
type: Class
subclass of: FundamentalPhysicalProcess
creator: jps
date: 24 Aug. 2011
description: 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.

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

PhysicalObjectQuality
type: Class
subclass of: CBO_Object
date: 24 Aug. 2011
creator: jps
see also: subclass of: BFO:snap:quality
description: 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.

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

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

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

Pseudopodium
type: Class
subclass of: CellMembraneLocalStructure
date: 24 Aug. 2011
creator: jps
description: 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

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

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

RateFunction
type: Class
subclass of: CBO_Object
creator: jps
see also: subclass of: BFO:snap:quality
description: 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.
date: 24 Aug. 2011

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

SecondOrderRate
type: Class
subclass of: RateFunction
description: 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.
date: 24 Aug. 2011
creator: jps

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

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

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

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

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

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

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

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

SymmetricCellDivisionRandomCleavagePlane
type: Class
subclass of: Mitosis
creator: jps
description: 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.
date: 24 Aug. 2011

System
type: Class
subclass of: CBO_Object
description: 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.
date: 24 Aug. 2011
creator: jps
see also: subclass of: BFO:snap:object

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

SystemExtent
type: Class
subclass of: SystemQuality
creator: jps
description: 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.
date: 25 Jul. 2012

SystemExtentX
type: Class
subclass of: SystemExtent
date: 25 Jul. 2012
creator: jps
description: 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.

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

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

SystemPeriodic
type: Class
subclass of: SystemBoundary
disjoint with: SystemWall
description: 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.
date: 25 Jul. 2012
creator: jps

SystemPeriodicX
type: Class
subclass of: SystemPeriodic
date: 25 Jul. 2012
creator: jpos
description: 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.

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

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

SystemPixel2DistanceScale
type: Class
subclass of: SystemQuality
creator: jps
description: 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.
date: 25 Jul. 2012

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

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

SystemWallX
type: Class
subclass of: SystemWall
creator: jps
date: 25 Jul. 2012
description: 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.

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

SystemWallZ
type: Class
subclass of: SystemWall
creator: jps
date: 25 Jul. 2012
description: 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.

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

TemporalAge
type: Class
subclass of: Age
creator: jps
date: 24 Aug. 2011
description: 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.

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

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

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

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

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

TightJunction
type: Class
subclass of: CellMembranePart
description: 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)
creator: jps
date: 24 Aug. 2011

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

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

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

VTK_FileName
type: Class
subclass of: VTK_Quality
creator: JPS
description: 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.
date: 10/25/2012

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

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

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

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

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

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

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

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

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

YoungsModulus
type: Class
subclass of: MechanicalProperty
description: 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)
date: 24 Aug. 2011
creator: jps

ZerothOrderRate
type: Class
subclass of: RateFunction
creator: jps
date: 24 Aug. 2011
description: 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.

topObjectProperty
comment: Note that OWL DL does not support antiymetric properties so those have been removed from the OBO Relation defintiions for the properties.

IndependentContinuant
description: 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.