Ontology1298055835221.owl
type: Ontology
date: 5/19/2011
creator: J Sluka
version info: Version 0.9 (developmental version)
imports: relationship

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

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

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

Location_Value_Set_3D
type: DatatypeProperty
type: FunctionalProperty
comment: 3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string.

Location_Value_Set_2D
type: DatatypeProperty
type: FunctionalProperty
comment: 2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string.

Location_Value_Set_1D
type: DatatypeProperty
type: FunctionalProperty
comment: 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.

Location_Value_Set_nD
type: DatatypeProperty
type: FunctionalProperty
comment: 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.

Points_value_set_nD
type: DatatypeProperty
type: FunctionalProperty
comment: Data is a lst 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.

Parameter_value_set_nD
type: DatatypeProperty
type: FunctionalProperty
comment: Data is a lst 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.

has_Quality
type: ObjectProperty
def: hasQuality links an instance of a CBO quality.
comment: CBO Specific

quality_Of
type: ObjectProperty
def: quality_Of links a CBO quality to an object instance.
comment: CBO Specific

CBO
type: Class

CBO_Object
type: Class
subclass of: CBO
date: 18 May 2011
creator: jps

physical_entity_type
type: Class
subclass of: CBO_Object
comment: A physical_entity_type is a CBO:Class (BFO:snap:quality) class of physical objects. For example, a cell, a basement membrane of a diffusible molecule.
date: 18 May 2011
creator: jps

corpuscular_entity
type: Class
subclass of: physical_entity_type
comment: A corpuscular_entity is a physical_entity_type (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 corpuscular_entity is not divisible without a fundamental change in characteristics, qualities or identity. For example, an individual cell.
date: 18 May 2011
creator: jps

continuous_entity
type: Class
subclass of: physical_entity_type
comment: A continuous_entity is a physical_entity_type (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. Continuous_entities are spatially exclusive and do not overlap. Unlike a corpuscular_entity, a continuous_entity 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).
disjoint with: corpuscular_entity
date: 18 May 2011
creator: jps

diffuse_entity
type: Class
subclass of: physical_entity_type
comment: A diffuse_entity is a physical_entity_type (BFO:snap:object) that spans a particular extent at a particular time but not is spatially exclusive and may, and generally does, overlap with other physical_entity_types at a particular time. In addition, a diffuse_entity may be described as having a position dependent concentration or density function. Unlike a corpuscular_entity, a continuous_entity is geometrically divisible without a fundamental change in characteristics or identity. A corpuscualar_entity may be restricted to exist along with another physical_entity_type, such as the case of a cell membrane bound receptor (diffuse_entity) distributed on the cell membrane of a particular cell (a corpuscular_entity). For example, a portion of a chemical field distributed across the interstitial space of a region.
disjoint with: continuous_entity
date: 18 May 2011
creator: jps

physical_object_quality
type: Class
subclass of: CBO_Object
comment: A physical_object_quality is a CBO:Class (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the qualities of physical objects. BFO uses qqQualityqq, OPB uses qqPropertyqq. Foe example, quality is a characteristics of a physical object such as location, volume, energy, type etc.
date: 18 May 2011
creator: jps

energy
type: Class
subclass of: physical_object_quality
comment: An energy is a CBO:physical_object_quality is the energy of the object for which it is a quality.
date: 18 May 2011
creator: jps
see also: OPB:"energy amount"

geometrical_property
type: Class
subclass of: physical_object_quality
comment: geometrical_property 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.
disjoint with: energy
date: 18 May 2011
creator: jps

volume
type: Class
subclass of: geometrical_property
comment: Volume is a geometrical_property describing the total volume of spaced occupied by the object at a particular instant in time.
date: 18 May 2011
creator: jps
see also: OPB:"volume of volume region"

shape
type: Class
subclass of: geometrical_property
comment: Shape is a geometrical_property describing the spatial (2 or 3 dimensions) of a region of spaced occupied by an object at a particular instant in time.
disjoint with: volume
date: 18 May 2011
creator: jps
see also: OPB:"bounded volume shape"

body_shape
type: Class
subclass of: shape
comment: Body_shape is a geometrical_property describing the spatial (2 or 3 dimensions) shape of a region of spaced occupied by an object at a particular instant in time. Body_shape 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: 18 May 2011
creator: jps
see also: OPB:"bounded volume shape"

anisotropy
type: Class
subclass of: body_shape
comment: Anisotropy is a geometrical_property describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:isotropy.
date: 18 May 2011
creator: jps

directed_anisotropy
type: Class
subclass of: anisotropy
date: 18 May 2011
creator: jps

polarity_anisotropy
type: Class
subclass of: directed_anisotropy
date: 18 May 2011
creator: jps

undirected_anisotropy
type: Class
subclass of: anisotropy
date: 18 May 2011
creator: jps

elongation_anisotropy
type: Class
subclass of: undirected_anisotropy
date: 18 May 2011
creator: jps

isotropy
type: Class
subclass of: body_shape
comment: Isotropy is a geometrical_property describing the lack of a directionality of a directionally dependent quality of the object. This is the opposite of CBO:anisotropy.
date: 18 May 2011
creator: jps

protrusion
type: Class
subclass of: shape
comment: Protrusion is a geometrical_property describing an extension from an otherwise simpler CBO:body_shape description. For example, a transient pseudopodia or a persistent neuronal axon.
date: 18 May 2011
creator: jps

center_of_volume
type: Class
subclass of: geometrical_property
comment: The Center_of_volume is a CBO:position that describes the center of volume of a spatially extended object at a particular time. The center_of_volume inherits the CBO:dimensionality of the particular object or CBO:dimensionality of the CBO:system object. See also center_of_mass which may be, for practical purposes, identical.
date: 18 May 2011
creator: jps

center_of_mass
type: Class
subclass of: geometrical_property
comment: The Center_of_mass is a CBO:position that describes the center of mass of a spatially extended object at a particular time. The center_of_mass inherits the CBO:dimensionality of the particular object or CBO:dimensionality of the CBO:system object. See also center_of_volume which may be, for practical purposes, identical.
disjoint with: center_of_volume
date: 18 May 2011
creator: jps

orientation
type: Class
subclass of: geometrical_property
comment: Orientation is a CBO:geometrical_property 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.
disjoint with: center_of_mass
date: 18 May 2011
creator: jps

surface_area
type: Class
subclass of: geometrical_property
comment: Surface area is a CBO:geometrical_property describing the scalar value of the objects surface area at a particular instant in time.
disjoint with: orientation
date: 18 May 2011
creator: jps
see also: OPB:"Area of surface region"

contact_surface_area
type: Class
subclass of: geometrical_property
comment: Contact_surface_area is a CBO:geometrical_property describing the scalar value of two objects contact surface area at a particular instant in time.
disjoint with: surface_area
date: 18 May 2011
creator: jps

location
type: Class
subclass of: geometrical_property
comment: Location is a geometrical_property of a mathematical point. Depending on the CBO:dimensionality of the system this may have one, two or three dataProperty values. AKA: position
disjoint with: contact_surface_area
date: 18 May 2011
creator: jps

extent_geometrical
type: Class
subclass of: geometrical_property
comment: Extent_geometrical is a CBO:geometrical_property that describes the basic granularity of the coordinate system.
disjoint with: location
date: 18 May 2011
creator: jps

continuous_extent
type: Class
subclass of: extent_geometrical
comment: Continous_extent is an CBO:extent_geometrical for a position, location, or otherwise positionaly sensitive quantity in an infinitely finely grained coordinate system. Compare with discrete_extent.
date: 18 May 2011
creator: jps

discrete_extent
type: Class
subclass of: extent_geometrical
comment: Discrete_extent is an CBO:extent_geometrical for a position, location, or otherwise positionally sensitive quantity in a finitely grained coordinate system. Compare with continuous_extent.
disjoint with: continuous_extent
date: 18 May 2011
creator: jps

dimensionality
type: Class
subclass of: geometrical_property
comment: Dimensionality is a CBO:geometrical_property that describes the number of independent spatial axis in a model or system.
date: 18 May 2011
creator: jps
see also: OPB:"Spatial coordinate system"

dimension_1d
type: Class
subclass of: dimensionality
comment: Dimension_1D is a CBO:dimensionality quality for a system with one spatial dimension.
date: 18 May 2011
creator: jps
see also: OPB:"One dimensional spatial coordinate system"

dimension_2d
type: Class
subclass of: dimensionality
comment: Dimension_1D is a CBO:dimensionality quality for a system with two spatial dimensions.
disjoint with: dimension_1d
date: 18 May 2011
creator: jps
see also: OPB:"Two dimensional spatial coordinate system"

dimension_fractal
type: Class
subclass of: dimensionality
comment: Dimension_fractal is a CBO:dimensionality quality for a system with fractal dimensions. Probably does not belong in the class?
disjoint with: dimension_2d
date: 18 May 2011
creator: jps

dimension_3d
type: Class
subclass of: dimensionality
comment: Dimension_1D is a CBO:dimensionality quality for a system with three spatial dimensions.
disjoint with: dimension_fractal
date: 18 May 2011
creator: jps
see also: OPB:"Three dimensional spatial coordinate system"

texture
type: Class
subclass of: geometrical_property
comment: Texture is a CBO:geometrical_property describing the characteristics of a surface texture.
date: 18 May 2011
creator: jps

uniform_texture
type: Class
subclass of: texture
comment: Uniform_texture is a CBO:texture consisting of a positionally independent texture description.
date: 18 May 2011
creator: jps

pattern_texture
type: Class
subclass of: texture
comment: Pattern_texture is a CBO:texture consisting of a positionally repetitive texture description.
disjoint with: uniform_texture
date: 18 May 2011
creator: jps

gradient_texture
type: Class
subclass of: texture
comment: Gradient_texture is a CBO:texture consisting of a texture description that varies smoothly across one or more dimensions.
disjoint with: pattern_texture
date: 18 May 2011
creator: jps

kinetic_property
type: Class
subclass of: physical_object_quality
comment: Kinetic_property is a CBO:physical_object_quality describing a kinetic characteristic of an object.
date: 18 May 2011
creator: jps
see also: OPB:"Kinetic manifestation"

mass
type: Class
subclass of: physical_object_quality
comment: Mass is a CBO:physical_object_quality describing the mass of the object.
disjoint with: kinetic_property
date: 18 May 2011
creator: jps
see also: OPB:"Discrete solid mass"

mechanical_property
type: Class
subclass of: physical_object_quality
comment: Mechanical_property is a CBO:physical_object_quality class that includes a variety of parameters describing the physical behavior of objects. Mechanical_properties are intrinsic to the object.
disjoint with: mass
date: 18 May 2011
creator: jps
see also: MeSH:G01.374, MeSH:"Mechanical Phenomena"

yielding_threshold
type: Class
subclass of: mechanical_property
comment: Yielding_threshold (Yield stress threshold, Y) is a CBO:mechanical_property describing the rheological yield stress of an object.
date: 18 May 2011
creator: jps

youngs_modulus
type: Class
subclass of: mechanical_property
comment: Youngs_modulus (Young's modulus, tensile modulus) is a numerical CBO:physical_object_quality 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)
disjoint with: yielding_threshold
date: 18 May 2011
creator: jps
see also: MeSH:G01.374.590.605, MeSH:"Young's modulus", MeSH:"Elastic Modulus"

pressure_mechanical
type: Class
subclass of: mechanical_property
comment: Pressure_mechanical is a CBO:mechanical_property describing the barometric pressure of an object or location in space.
disjoint with: youngs_modulus
date: 18 May 2011
creator: jps
see also: MeSH:G01.374.715, MeSH:pressure

adhesive_property
type: Class
subclass of: mechanical_property
comment: Adhesive_property is a CBO:mechanical_property 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.
disjoint with: pressure_mechanical
date: 18 May 2011
creator: jps

tension_mechanical
type: Class
subclass of: mechanical_property
comment: Tension_mechanical is a CBO:mechanical_property that describes the pulling force exerted on an entity (a stretching or distorting force).
disjoint with: adhesive_property
date: 18 May 2011
creator: jps

stiffness_mechanical
type: Class
subclass of: mechanical_property
comment: Stiffness_mechanical is a CBO:mechanical_proerty that describes an elastic object's resistance to deformation by an applied force along a given direction.
disjoint with: tension_mechanical
date: 18 May 2011
creator: jps

poisson_ratio
type: Class
subclass of: mechanical_property
comment: Poisson_ratio is a CBO:mechanical_property 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).
disjoint with: stiffness_mechanical
date: 18 May 2011
creator: jps

chemical_property
type: Class
subclass of: physical_object_quality
comment: Chemical_property is a CBO:physical_object_quality class that includes a variety of parameters describing the physical behavior of chemicals Chemical_properties are intrinsic to the object.
date: 18 May 2011
creator: jps

chemical_localization
type: Class
subclass of: chemical_property
date: 18 May 2011
creator: jps

chemical_affinity
type: Class
subclass of: chemical_property
disjoint with: chemical_localization
date: 18 May 2011
creator: jps

chemical_pattern
type: Class
subclass of: chemical_property
disjoint with: chemical_affinity
date: 18 May 2011
creator: jps

chemical_pattern_gradient
type: Class
subclass of: chemical_pattern
date: 18 May 2011
creator: jps

chemical_density
type: Class
subclass of: chemical_property
date: 18 May 2011
creator: jps

electrical_property
type: Class
subclass of: physical_object_quality
comment: Electrical_property is a CBO:physical_object_quality class that includes a variety of parameters describing the electrical qualities of objects. Electrical_property are intrinsic to the object.
date: 18 May 2011
creator: jps
see also: OPB:"Electrical entity"

charge
type: Class
subclass of: electrical_property
date: 18 May 2011
creator: jps
see also: OPB:"Charge amount"

voltage
type: Class
subclass of: electrical_property
disjoint with: charge
date: 18 May 2011
creator: jps
see also: OPB:"Portion of electrical potential energy"

electrical_current
type: Class
subclass of: electrical_property
comment: Electrical_current is a CBO:electrical_property ... (OPB) is the temporal derivative of an Ion amount.
disjoint with: voltage
date: 18 May 2011
creator: jps
see also: OPB:"Electrical current"

electrical_capacity
type: Class
subclass of: electrical_property
disjoint with: electrical_current
date: 18 May 2011
creator: jps
see also: OPB:"Electrical capacitance"

electrical_resistance
type: Class
subclass of: electrical_property
disjoint with: electrical_capacity
date: 18 May 2011
creator: jps
see also: OPB:"Electrical resistance"

electrical_conductivity
type: Class
subclass of: electrical_property
disjoint with: electrical_resistance
date: 18 May 2011
creator: jps
see also: OPB:"Electrical conductivity"

movement_field
type: Class
subclass of: physical_object_quality
date: 18 May 2011
creator: jps

statistical_property
type: Class
subclass of: physical_object_quality
comment: Statistical_property is a CBO:physical_object_quality class that includes a variety of parameters describing the statistical qualities of objects. Statistical_property are intrinsic to the object.
disjoint with: movement_field
date: 18 May 2011
creator: jps

random
type: Class
subclass of: statistical_property
date: 18 May 2011
creator: jps

age
type: Class
subclass of: physical_object_quality
comment: Age is a CBO:physical_oject_quality class that describes the chronological or generational age of a physical object.
date: 18 May 2011
creator: jps

temporal_age
type: Class
subclass of: age
comment: Temporal_age 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."
date: 18 May 2011
creator: jps

generational_age
type: Class
subclass of: age
comment: Generational_age is a CBO:age that describes the number of generations that have passed for a particfular cell within its lineage. For example, a mesenchymal cell derived from a stem cell would have generational_age equal to one. When that mesenchymal cell divides both daughter cells would have generational ages 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."
disjoint with: temporal_age
date: 18 May 2011
creator: jps

geometrical_entity
type: Class
subclass of: CBO_Object
comment: Geometrical_entity is a CBO class for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions.
date: 18 May 2011
creator: jps

boundary
type: Class
subclass of: geometrical_entity
comment: Boundary is a CBO:geometrical_entity that demarks the interface between to bona fide physical objects.
date: 18 May 2011
creator: jps

cell_region
type: Class
subclass of: geometrical_entity
comment: Cell_region is a CBL:geometrical_entity class that includes descriptors for various fiat regions. (A fiat region generally does not clear boundaries.)
disjoint with: boundary
date: 18 May 2011
creator: jps

basal_part
type: Class
subclass of: cell_region
comment: Basal_part is a CBO:cell_region that includes the base of the cell where qqbaseqq 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.
date: 18 May 2011
creator: jps
see also: GO:0045178, FMA:72558

apical_part
type: Class
subclass of: cell_region
comment: Apical_part is a CBO:cell_region of a polarized cell is the region that is closests to the lumen. (Wikipedia)This is particularly evident in epithelial and endothelial cells, but also describes other polarized cells, such as neurons.
disjoint with: basal_part
date: 18 May 2011
creator: jps

lateral_part
type: Class
subclass of: cell_region
comment: Lateral_part is a CBO:cell_region that is between the CBO:basal_part and CBO:lateral_part.
disjoint with: apical_part
date: 18 May 2011
creator: jps

medial_part
type: Class
subclass of: cell_region
comment: Medial_part is a CBO:cell_region located near the center of the cell.
disjoint with: lateral_part
date: 18 May 2011
creator: jps

organismal_region
type: Class
subclass of: geometrical_entity
comment: Organismal_region is a CBO:geometrical_entity class for regions of an animal.
date: 18 May 2011
creator: jps

dorsal
type: Class
subclass of: organismal_region
comment: Dorsal is a CBO:organismal_region characteristic of the back of an object relative to the body it is contained in. For example dorsal fin.
date: 18 May 2011
creator: jps
see also: EFO:0001656, FMA:74535

ventral
type: Class
subclass of: organismal_region
comment: Ventral is a CBO:organismal_region 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.
disjoint with: dorsal
date: 18 May 2011
creator: jps

temporal_entity
type: Class
subclass of: CBO_Object
comment: OPB: ...is a moment or span of time.
date: 18 May 2011
creator: jps
see also: OPB:"temporal entity"

temporal_instant
type: Class
subclass of: temporal_entity
comment: OPB: ...is a point in time.
date: 18 May 2011
creator: jps
see also: OPB:"temporal instant"

temporal_interval
type: Class
subclass of: temporal_entity
comment: OPB: ...is a period of time bounded by two temporal moments (that may be the same moment).
disjoint with: temporal_instant
date: 18 May 2011
creator: jps
see also: OPB:"temporal interval"

material_type
type: Class
subclass of: CBO_Object
comment: Material_type is a CBO class of qualities that describe objects as either solids, liquids (fluids), gels or solutes.
date: 18 May 2011
creator: jps

fluid_material_type
type: Class
subclass of: material_type
comment: Fluid_material_type is a CBO:material_type (OPB) ...that is a material substance with fluid kinetic properties.
date: 18 May 2011
creator: jps
see also: OPB:"Portion of fluid"

solute_material_type
type: Class
subclass of: material_type
comment: Solute_material_type is a CBO:material_type (OPB) ...that has both chemical and diffusional kinetic properties.
disjoint with: fluid_material_type
date: 18 May 2011
creator: jps
see also: OPB:"Portion of molecules"

solid_material_type
type: Class
subclass of: material_type
comment: Solid_material_type is a CBO:material_type (OPB) ...that is a material substance with solid kinetic properties.
disjoint with: solute_material_type
date: 18 May 2011
creator: jps
see also: OPB:"Portion of solid substance"

gel_material_type
type: Class
subclass of: material_type
comment: Gel_material_type is a CBO:material_type that is a material substance with fluid kinetic properties intermediate between a solid and a fluid.
disjoint with: solid_material_type
date: 18 May 2011
creator: jps

system
type: Class
subclass of: CBO_Object
comment: System is a CBO class that describes and includes the qquniverseqq described by the model or experiment.
date: 18 May 2011
creator: jps

cell
type: Class
subclass of: CBO_Object
comment: Cell is a CBO 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.
disjoint with: system
date: 18 May 2011
creator: jps
see also: GO:0005623, CL:0000000, FMA:68646

molecule
type: Class
subclass of: CBO_Object
comment: A molecule is a CBO class OPB: ...that is a polyatomic entity.
disjoint with: cell
date: 18 May 2011
creator: jps

extracellular_matrix
type: Class
subclass of: CBO_Object
comment: Extracellular_matrix is a CBO class that includes all physical entites that are discrete (though possible of considerable extent) that are distinct from cell and media. The extracellular matrix provides support and restricts movement of objects.
disjoint with: molecule
date: 18 May 2011
creator: jps
see also: GO:0031012, FMA:9672

interstitial_matrix
type: Class
subclass of: extracellular_matrix
comment: 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: 18 May 2011
creator: jps

basement_membrane
type: Class
subclass of: extracellular_matrix
comment: 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.
disjoint with: interstitial_matrix
date: 18 May 2011
creator: jps

molecular_field
type: Class
subclass of: CBO_Object
date: 18 May 2011
creator: jps

extracellular_fluid
type: Class
subclass of: CBO_Object
comment: MeSH: The fluid of the body that is outside of CELLS. It is the external environment for the cells.
disjoint with: molecular_field
date: 18 May 2011
creator: jps

cell_part
type: Class
subclass of: CBO_Object
comment: Cell_part is a CBO class including any constituent part of a cell.
disjoint with: extracellular_fluid
date: 18 May 2011
creator: jps

nucleus
type: Class
subclass of: cell_part
comment: 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.
date: 18 May 2011
creator: jps
see also: GO:0005634, FMA:63840

cell_border
type: Class
subclass of: cell_part
comment: Cell_border is a CBO:cell-part consiting of the outer boundary of the cell, that is, the surface that delineates the cell from the surrondings. Depending on the species and phyla the cell_boarder may be either a CBO:cell_membrane or aCBO: cell_wall.
disjoint with: nucleus
date: 18 May 2011
creator: jps

cell_membrane
type: Class
subclass of: cell_border
comment: Cell_membrane is a CBO:cell_border consiting of (MeSH) The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
date: 18 May 2011
creator: jps
see also: GO:0005886, FMA:63841

cell_wall
type: Class
subclass of: cell_border
comment: Cell_wall is a CBO:cell_border 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.
disjoint with: cell_membrane
date: 18 May 2011
creator: jps
see also: GO:0005618, MeSH:A11.284.183

cytoplasm
type: Class
subclass of: cell_part
comment: FMA: Cell component which consists of cytosol and cytoplasmic organelles.
date: 18 May 2011
creator: jps

cell_membrane_part
type: Class
subclass of: CBO_Object
comment: Cell_membrane_part is a CBO class that includes the various proteinaceous parts commonly found on a cell membrane. Not 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.
date: 18 May 2011
creator: jps

membrane_receptor
type: Class
subclass of: cell_membrane_part
comment: Membrane_receptor is a CBO:cell_membrane_part that is a protein embeded in the cell membrane 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: 18 May 2011
creator: jps

adhesion_molecule
type: Class
subclass of: cell_membrane_part
comment: Adhesion_molecule is a CBO:cell_membrane_part 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.
disjoint with: membrane_receptor
date: 18 May 2011
creator: jps

tight_junction
type: Class
subclass of: cell_membrane_part
comment: 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)
disjoint with: adhesion_molecule
date: 18 May 2011
creator: jps
see also: GO:0005923, MeSH:A11.284.149.165.420.820

gap_junction
type: Class
subclass of: cell_membrane_part
comment: Gap_junction is a CBO:cell_membrane_part that acts as a connection between, and adhesion mediator, between two cells. In addition, the gap allows for the trancefer 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.
disjoint with: tight_junction
date: 18 May 2011
creator: jps
see also: GO:0005921, MeSH:A11.284.149.165.420.471, FMA:67423

pump
type: Class
subclass of: cell_membrane_part
comment: A Pump is a CBO:cell_membrane_part that is a membrane bound protein that transfers ions and molecules arcoss 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.
disjoint with: gap_junction
date: 18 May 2011
creator: jps
see also: MeSH: D12.776.157.530, MeSH:"Membrane Transport Proteins"

ion_channel
type: Class
subclass of: cell_membrane_part
comment: An ion_channel is a CBO:cell_membrane_part 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.
disjoint with: pump
date: 18 May 2011
creator: jps
see also: GO:0022831, MeSH:D12.776.157.530.400

cell_membrane_local_structure
type: Class
subclass of: CBO_Object
comment: A cell_membrane_local_structure is a CBO class that includes the various topological patterns found, often transiently, on cell walls. For example, filopodia. MeSH: Specialized structures of the cell that extend the cell membrane and project out from the cell surface. GO: A prolongation or process extending from a cell, e.g. a flagellum or axon.
date: 18 May 2011
creator: jps
see also: GO:0042995, MeSH:A11.284.18

filopodium
type: Class
subclass of: cell_membrane_local_structure
comment: A filopdium is a CBO:cell_membrane_local_structure 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
date: 18 May 2011
creator: jps
see also: GO:0030175, MeSH:A11.284.180.700

brush_border
type: Class
subclass of: cell_membrane_local_structure
comment: A brush_border is a CBL:cell_membrane_local_structure characteriszed 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, qqStriated Borderqq
disjoint with: filopodium
date: 18 May 2011
creator: jps
see also: GO:0005903, FMA:70977, MeSH:A11.284.180.565

pseudopodium
type: Class
subclass of: cell_membrane_local_structure
comment: A pseudopodium is a CBO:cell_membrane_local_structure cahracterized 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
disjoint with: brush_border
date: 18 May 2011
creator: jps
see also: GO:0031143, MeSH:A11.284.180.700

cell_kingdom_type
type: Class
subclass of: CBO_Object
comment: Cell_kingdom_type is a CBO class describing the basic kingdom the cell belongs to. For example, qqprokaryoteqq or qqeucaryoteqq.
date: 18 May 2011
creator: jps

prokaryote_cell
type: Class
subclass of: cell_kingdom_type
comment: A prokaryote is a CBO:cell_kingdom_type for prokaryote cells which generally do not contain a distinct nucleous and other distinct cellular organelles. Examples include bacteria.
date: 18 May 2011
creator: jps

eukaryote_cell
type: Class
subclass of: cell_kingdom_type
comment: A eukaryote is a CBO:cell_kingdom_type for eukaryotic cells which generally contain a distinct nucleous and other distinct organelles. MeSH: These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
disjoint with: prokaryote_cell
date: 18 May 2011
creator: jps
see also: CL:0000255, MeSH:B01

anuclear_cell
type: Class
subclass of: cell_kingdom_type
comment: Cell without nuclei, e.g., platelets and erythrocytes. Not to be confused with non-nuclear prokaryotic cells. FMA: Cell that consists of cytoplasm surrounded by a plasma membrane. Examples: erythrocyte, corneocyte, lens fiber.
disjoint with: eukaryote_cell
date: 18 May 2011
creator: jps
see also: CL:0000225, FMA:68647

virus_cell
type: Class
subclass of: cell_kingdom_type
comment: A virus_cell is a CBO:cell_kingdom_type for viruses, qqcellsqq which contain only DNA or RNA and which can only reproduce inside a host cell. MeSH: Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. NCI: The complete particle usually contains only DNA or RNA, not both, and is usually covered by a protein shell or capsid that protects the nucleic acid. They range in size from 15 um up to several hundred um. Classification of viruses depends upon characteristics of virions as well as upon mode of transmission, host range, symptomatology, and other factors.
disjoint with: anuclear_cell
date: 18 May 2011
creator: jps

CBO_Process
type: Class
subclass of: CBO
date: 18 May 2011
creator: jps

fundamental_physical_process
type: Class
subclass of: CBO_Process
comment: A fundamental_physical_process is a CBO:process (snap:process) that changes a quality or characteristic of an object.
date: 18 May 2011
creator: jps

movement
type: Class
subclass of: fundamental_physical_process
comment: Movement is a fundamental_physical_process resulting in the change in location or shape of a physical object.
date: 18 May 2011
creator: jps

translation
type: Class
subclass of: movement
comment: Translation is a movement resulting in a change in the spatial location of an object.
date: 18 May 2011
creator: jps

rotation
type: Class
subclass of: movement
comment: Rotation is a movement resulting in a change in orientation of an object.
disjoint with: translation
date: 18 May 2011
creator: jps

diffusion
type: Class
subclass of: movement
comment: Diffusion is a movement arising from random motion, either thermal of motive (cf. motility), of an object.
disjoint with: rotation
date: 18 May 2011
creator: jps

shape_change
type: Class
subclass of: fundamental_physical_process
comment: Shape_change is a fundamental_physical_process resulting in the change in the shape, including extents, of an object.
date: 18 May 2011
creator: jps

volume_change
type: Class
subclass of: fundamental_physical_process
comment: Volume_change is a fundamental_physical_process resulting in a change, an increase or decrease, in the volume occupied by an object.
disjoint with: shape_change
date: 18 May 2011
creator: jps

expansion
type: Class
subclass of: volume_change
comment: Expansion is a volume_change resulting in an increase in volume occupied by an object.
date: 18 May 2011
creator: jps

contraction
type: Class
subclass of: volume_change
comment: Contraction is a volume_change resulting in a decrease in volume occupied by an object.
disjoint with: expansion
date: 18 May 2011
creator: jps

creation
type: Class
subclass of: fundamental_physical_process
comment: Creation is a fundamental_physical_process resulting in the creation of a new object. Often this will involve an increase in count of an object.
date: 18 May 2011
creator: jps

deletion
type: Class
subclass of: fundamental_physical_process
comment: Deletion is a fundamental_physical_process resulting in the deletion of a new object. Often this will involve an decrease in count of an object.
disjoint with: creation
date: 18 May 2011
creator: jps

phenotypic_change
type: Class
subclass of: fundamental_physical_process
comment: Phenotypic_change is a fundamental_physical_process resulting in the change of type of an object. Phenotypic_change applies to both the normally defined phenotypic change of a cell and also includes molecular changes such as ionization.
disjoint with: deletion
date: 18 May 2011
creator: jps

barrier_crossing
type: Class
subclass of: fundamental_physical_process
comment: Barrier_crossing is a fundamental_physical_process 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:cell_import and CBO:cell_export.
disjoint with: phenotypic_change
date: 18 May 2011
creator: jps

structural_process
type: Class
subclass of: CBO_Process
comment: Structural_process 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.
date: 18 May 2011
creator: jps

cell_process
type: Class
subclass of: CBO_Process
comment: Cell_process is a CBO:process (snap:process) describing a process characteristic of a CBO:cell.
disjoint with: structural_process
date: 18 May 2011
creator: jps

existential_cell_processes
type: Class
subclass of: cell_process
comment: Existential_cell_processes is a cell_process that is assumed, without formal proof, to be a process of a cell.
date: 18 May 2011
creator: jps

cell_growth
type: Class
subclass of: existential_cell_processes
comment: Cell_growth is a cell_process that changes the volume of a cell. Cell_growth includes both an increase and a decrease in the cell's volume. (Similar to, but here specific to a CBO:cell) to CBO:volume_change. This definition differs from that in GO:0016049 qqThe process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.qq
date: 18 May 2011
creator: jps

cell_division
type: Class
subclass of: existential_cell_processes
comment: Cell_division is a existential_cell_process involving the creation of two new cells (qqdaughtersqq) from a single qqparentqq cell. GO: The process resulting in the physical partitioning and separation of a cell into daughter cells.
disjoint with: cell_growth
date: 18 May 2011
creator: jps

fission
type: Class
subclass of: cell_division
comment: Fission is a existential_cell_process of bacterial cells resulting in the creation of two qqdaughterqq cells from a single qqparentqq cell. Fission is specific to bacterial cells.
date: 18 May 2011
creator: jps

mitosis
type: Class
subclass of: cell_division
comment: Mitosis is a cell_division resulting in the creation of two qqdaughterqq cells from a single qqparentqq 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.
disjoint with: fission
date: 18 May 2011
creator: jps

symmetric_cell_division__random_cleavage_plane
type: Class
subclass of: mitosis
comment: Symmetric_cell_division__random_cleavage_plane is a mitosis characterized by the creation of two identical qqdaughterqq cells from a single qqparentqq cell. In addition, the cleavage plane of the division process is randomly oriented with respect to both the environment and the characteristics of the qqparentqq cell.
date: 18 May 2011
creator: jps

symmetric_cell_division__oriented_cleavage_plane
type: Class
subclass of: mitosis
comment: Symmetric_cell_division__oriented_cleavage_plane is a mitosis characterized by the creation of two identical qqdaughterqq cells from a single qqparentqq cell. In addition, the cleavage plane of the division process is oriented with respect to either the environment or the characteristics of the qqparentqq cell.
disjoint with: symmetric_cell_division__random_cleavage_plane
date: 18 May 2011
creator: jps

asymmetric_cell_division__random_cleavage_plane
type: Class
subclass of: mitosis
comment: Asymmetric_cell_division__random_cleavage_plane is a mitosis characterized by the creation of two non-identical qqdaughterqq cells from a single qqparentqq cell. In addition, the cleavage plane of the division process is oriented randomly with respect to both the environment and the characteristics of the qqparentqq 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.
disjoint with: symmetric_cell_division__oriented_cleavage_plane
date: 18 May 2011
creator: jps

asymmetric_cell_division__oriented_cleavage_plane
type: Class
subclass of: mitosis
comment: Asymmetric_cell_division__oriented_cleavage_plane is a mitosis characterized by the creation of two non-identical qqdaughterqq cells from a single qqparentqq cell. In addition, the cleavage plane of the division process is oriented with respect to either the environment or the characteristics of the qqparentqq 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.
disjoint with: asymmetric_cell_division__random_cleavage_plane
date: 18 May 2011
creator: jps

meiosis
type: Class
subclass of: cell_division
comment: Meiosis is a cell_division 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.
date: 18 May 2011
creator: jps

cell_death
type: Class
subclass of: existential_cell_processes
comment: Cell_death is an existential_cell_process 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: 18 May 2011
creator: jps

necrosis
type: Class
subclass of: cell_death
comment: Necrosis is a cell_death caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin.
date: 18 May 2011
creator: jps

apoptosis
type: Class
subclass of: cell_death
comment: Apoptosis is a cell_death 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.
disjoint with: necrosis
date: 18 May 2011
creator: jps

autophagic_death
type: Class
subclass of: cell_death
comment: Autophagic_death is a cell_death 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.
disjoint with: apoptosis
date: 18 May 2011
creator: jps

cell_fusion
type: Class
subclass of: existential_cell_processes
comment: Cell_fusion is an existential_cell_process 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: 18 May 2011
creator: jps

cell_differentiation
type: Class
subclass of: existential_cell_processes
comment: Cell_differentiation is an existential_cell_process in which the type (CBO:phenotype) of a cell is changed.
disjoint with: cell_fusion
date: 18 May 2011
creator: jps

cell_environment_process
type: Class
subclass of: cell_process
comment: Cell_environment_process is an existential_cell_process involving the interaction between a cell and a component of the environment, where qqenvironmentqq includes other cells. For example, adhesion of a cell to a basement membrane.
date: 18 May 2011
creator: jps

cell_adhesion
type: Class
subclass of: cell_environment_process
comment: Cell_adhesion is a cell_environment_process involving the adhesive interaction between a cell and some other physical object (another cell, basement membrane etc.). Note that qqadhesionqq is a distinct process from qqcontactqq (see CBO:cell_contact) but that qqadhesionqq requires qqcontactqq.
date: 18 May 2011
creator: jps

cell_cell_adhesion
type: Class
subclass of: cell_adhesion
comment: Cell_cell_adhesion is a cell_adhesion involving the adhesive interaction between two cells. Note that qqadhesionqq is a distinct process from qqcontactqq (see CBO:cell_contact) but that qqadhesionqq requires qqcontactqq.
date: 18 May 2011
creator: jps

cell_noncell_adhesion
type: Class
subclass of: cell_adhesion
comment: Cell_noncell_adhesion is a cell_adhesion involving the adhesive interaction between a cell and another physical object where the second object is not itself a cell. Note that qqadhesionqq is a distinct process from qqcontactqq (see CBO:cell_contact) but that qqadhesionqq requires qqcontactqq.
disjoint with: cell_cell_adhesion
date: 18 May 2011
creator: jps

cell_interstitial_matrix_adhesion
type: Class
subclass of: cell_noncell_adhesion
comment: Cell_interstitial_matrix_adhesion is a cell_noncell_adhesion involving the adhesive interaction between a cell and the interstitial matrix. Note that qqadhesionqq is a distinct process from qqcontactqq (see CBO:cell_contact) but that qqadhesionqq requires qqcontactqq.
date: 18 May 2011
creator: jps

cell_basement_membrane_adhesion
type: Class
subclass of: cell_noncell_adhesion
comment: Cell_basement_membrane_adhesion is a cell_noncell_adhesion involving the adhesive interaction between a cell and a basement membrane. Note that qqadhesionqq is a distinct process from qqcontactqq (see CBO:cell_contact) but that qqadhesionqq requires qqcontactqq.
disjoint with: cell_interstitial_matrix_adhesion
date: 18 May 2011
creator: jps

cell_contact
type: Class
subclass of: cell_environment_process
comment: Cell_contact is a cell_environment_process involving the direct physical contact between a cell and some other physical object (another cell, basement membrane etc.). Note that qqcontactqq is a distinct process from qqadhesionqq (see CBO:cell_adhesion).
date: 18 May 2011
creator: jps

cell_cell_contact
type: Class
subclass of: cell_contact
comment: Cell_cell_contact is a cell_contact involving the direct physical contact between two cells. Note that qqcontactqq is a distinct process from qqadhesionqq (see CBO:cell_adhesion).
date: 18 May 2011
creator: jps

cell_noncell_contact
type: Class
subclass of: cell_contact
comment: Cell_noncell_contact is a cell_contact involving direct physical contact between a cell and another physical object where the second object is not itself a cell. Note that qqcontactqq is a distinct process from qqadhesionqq (see CBO:cell_adhesion).
disjoint with: cell_cell_contact
date: 18 May 2011
creator: jps

cell_basement_lamina_contact
type: Class
subclass of: cell_noncell_contact
comment: Cell_basement_lamina_contact is a cell_noncell_contact involving the direct contact between a cell and a basement membrane. Note that qqcontactqq is a distinct process from qqadhesionqq (see CBO:cell_adhesion).
date: 18 May 2011
creator: jps

cell_interstitial_matrix_contact
type: Class
subclass of: cell_noncell_contact
comment: Cell_interstitial_matrix_contact is a cell_noncell_contact involving the direct contact between a cell and a component of the interstitial matrix. Note that qqcontactqq is a distinct process from qqadhesionqq (see CBO:cell_adhesion).
disjoint with: cell_basement_lamina_contact
date: 18 May 2011
creator: jps

cell_related_transport
type: Class
subclass of: cell_environment_process
comment: Cell_related_transport is a cell_environment_process involving movement of an entity across the cell's membrane. The moving entity becomes qqcontainedqq in the cell but is not qqpartOfqq the cell. Cell_related_transport includes active and selective processes. For passive (e.g., diffusive) transport see CBO:barrier_crossing.
date: 18 May 2011
creator: jps

cell_import
type: Class
subclass of: cell_related_transport
comment: Cell_import is a cell_related_transport 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:barrier_crossing.
date: 18 May 2011
creator: jps

cell_export
type: Class
subclass of: cell_related_transport
comment: Cell_export is a cell_related_transport 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:barrier_crossing.
disjoint with: cell_import
date: 18 May 2011
creator: jps

cellular_property_process
type: Class
subclass of: cell_process
comment: Cellular_property_process is a cell_process that results in a change in a property of a cell. For example, cell_movement changes the property of location.
date: 18 May 2011
creator: jps

cellular_mechanical_process
type: Class
subclass of: cellular_property_process
comment: Cellular_mechanical_process is a cellular_property_process that results in a change in a mechanical property of a cell.
date: 18 May 2011
creator: jps

cellular_kinetic_process
type: Class
subclass of: cellular_property_process
comment: Cellular_kinetic_process is a cellular_property_process that changes a kinetic dependence.
disjoint with: cellular_mechanical_process
date: 18 May 2011
creator: jps

geometrical_cell_process
type: Class
subclass of: cellular_property_process
comment: Geometrical_cell_process is a cellular_property_process that results in a a change in the geometry of a cell.
disjoint with: cellular_kinetic_process
date: 18 May 2011
creator: jps

cell_movement
type: Class
subclass of: geometrical_cell_process
comment: Cell_movement is a geometrical_cell_process that results in a change in the location or orientation of a cell. Note that this definition is incompatible with GO:0006928 qqcell movementqq.
date: 18 May 2011
creator: jps

cell_displacement
type: Class
subclass of: cell_movement
comment: Cell_displacement is a cell_movement that results in a change in the location, defined by the center of mass or center of volume, of a cell.
date: 18 May 2011
creator: jps

cell_advection
type: Class
subclass of: cell_movement
comment: Cell_advection is a cell_movement 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.
disjoint with: cell_displacement
date: 18 May 2011
creator: jps

chemotaxis
type: Class
subclass of: cell_movement
comment: Chemotaxis is a cell_movement 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).
disjoint with: cell_advection
date: 18 May 2011
creator: jps
see also: GO:0006935, GO:0060326

haptotaxis
type: Class
subclass of: cell_movement
comment: Haptotaxis is a cell_movement 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.
disjoint with: chemotaxis
date: 18 May 2011
creator: jps

cell_motility
type: Class
subclass of: cell_movement
comment: Cell_motility is a cell_movement involving an energy dependent self-propelled displacement of the 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.
disjoint with: haptotaxis
date: 18 May 2011
creator: jps

cell_rotation
type: Class
subclass of: cell_movement
comment: Cell_rotation is a cell_movement resulting in a rotation of a cell about it center (center of mass or center of volume).
disjoint with: cell_motility
date: 18 May 2011
creator: jps

cell_volume_change
type: Class
subclass of: geometrical_cell_process
comment: deprecated
date: 18 May 2011
creator: jps

cell_shape_change
type: Class
subclass of: geometrical_cell_process
comment: Cell_shape_change is a geometrical_cell_process that results in a change in shape of the bounding surface of the cell defined by the cell wall or cell membrane.
disjoint with: cell_volume_change
date: 18 May 2011
creator: jps

cell_orientation_change
type: Class
subclass of: geometrical_cell_process
comment: Cell_orientation_change is a geometrical_cell_process 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.
disjoint with: cell_shape_change
date: 18 May 2011
creator: jps

cellular_electrical_process
type: Class
subclass of: cell_environment_process
comment: Cellular_electrical_process is a cell_environment_process that results in a change in an electrical quality of the cell.
date: 18 May 2011
creator: jps

cellular_chemical_process
type: Class
subclass of: cell_environment_process
comment: Cellular_chemical_process is a cell_environment_process in which an environmental (local) chemical (or chemical gradient) changes a process or quality of a cell.
disjoint with: cellular_electrical_process
date: 18 May 2011
creator: jps

cell_cell_process
type: Class
subclass of: cell_process
comment: Cell_cell_process is a cell_process in which the interaction between two cells leads to a change in characteristic or behavior of one or both of the cells.
date: 18 May 2011
creator: jps

extracellular_matrix_process
type: Class
subclass of: CBO_Process
comment: Extracellular_matrix_process is a CBO:process involving a change in the qualities, or quantity of extracellular matrix and its components.
date: 18 May 2011
creator: jps

interstitial_matrix_process
type: Class
subclass of: extracellular_matrix_process
comment: interstitial_matrix_process is an extracellular_matrix_process involving a change in the qualities, or quantity of interstitial matrix and its components.
date: 18 May 2011
creator: jps

interstitial_matrix_creation
type: Class
subclass of: interstitial_matrix_process
comment: interstitial_matrix_creation is an interstitial_matrix_process involving an increase in the quantity of the interstitial matrix and its components.
date: 18 May 2011
creator: jps

interstitial_matrix_deletion
type: Class
subclass of: interstitial_matrix_process
comment: interstitial_matrix_deletion is an interstitial_matrix_process involving a decrease in the quantity of the interstitial matrix and its components.
disjoint with: interstitial_matrix_creation
date: 18 May 2011
creator: jps

interstitial_matrix_change
type: Class
subclass of: interstitial_matrix_process
comment: interstitial_matrix_change is an interstitial_matrix_process involving a change in the components or characteristics of the interstitial matrix components.
disjoint with: interstitial_matrix_deletion
date: 18 May 2011
creator: jps

basement_lamina_process
type: Class
subclass of: extracellular_matrix_process
comment: Basement_lamina_process is an extracellular_matrix_process involving a change in the qualities, or quantity of a basement membrane or its components.
date: 18 May 2011
creator: jps

basement_lamina_creation
type: Class
subclass of: basement_lamina_process
comment: Basement_lamina_creation is a basement_lamina_process involving an increase in the quantity of the basement lamina and its components.
date: 18 May 2011
creator: jps

basement_lamina_deletion
type: Class
subclass of: basement_lamina_process
comment: Basement_lamina_deletion is an basement_lamina_process involving a decrease in the quantity of the basement lamina and its components.
disjoint with: basement_lamina_creation
date: 18 May 2011
creator: jps

basement_lamina_change
type: Class
subclass of: basement_lamina_process
comment: Basement_lamina_change is an basement_lamina_process involving a change in the components or characteristics of the basement lamina components.
disjoint with: basement_lamina_deletion
date: 18 May 2011
creator: jps

molecule_process
type: Class
subclass of: CBO_Process
comment: Molecule_process is a CBO:Process that involves a molecule.
date: 18 May 2011
creator: jps

molecule_creation
type: Class
subclass of: molecule_process
comment: Molecule_creation is a molecule_process that results in the creation of a new molecule or an increase in a molecule's concentration.
date: 18 May 2011
creator: jps

molecule_deletion
type: Class
subclass of: molecule_process
comment: Molecule_deletion is a molecule_process that results in the deletion of a molecule, or a decrease in a molecule's concentration.
disjoint with: molecule_creation
date: 18 May 2011
creator: jps

molecule_change
type: Class
subclass of: molecule_process
comment: Molecule_change is a molecule_process that results in a qqphenotypicqq change in the molecule. For example, changes in the ionization state of an acid.
disjoint with: molecule_deletion
date: 18 May 2011
creator: jps

molecule_diffusion
type: Class
subclass of: molecule_process
comment: Molecule_diffusion is a molecule_process 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:molecule_barrier_crossing.
disjoint with: molecule_change
date: 18 May 2011
creator: jps

molecule_barrier_crossing
type: Class
subclass of: molecule_process
comment: Molecule_barrier_crossing is a molecule_process describing the transfer of a molecule across a bona fide boundary such as a basement membrane or a cell wall.
disjoint with: molecule_diffusion
date: 18 May 2011
creator: jps

molecule_molecule_adhesion
type: Class
subclass of: molecule_process
comment: Molecule_molecule_adhesion is a molecule_process 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.
disjoint with: molecule_barrier_crossing
date: 18 May 2011
creator: jps

transport
type: Class
subclass of: CBO_Process
comment: 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:cell_import and CBO:cell_export) and for molecules (CBO:molecule_barrier_crossing).
date: 18 May 2011
creator: jps

interentity_transport
type: Class
subclass of: transport
comment: Interentity_transport is a transport of an object across a bona fide boundary. For example, from within a bone to the space outside the bone.
date: 18 May 2011
creator: jps

interentity_import
type: Class
subclass of: interentity_transport
comment: Interentity_import is a interentity_transport 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.
date: 18 May 2011
creator: jps

interentity_export
type: Class
subclass of: interentity_transport
comment: Interentity_export is a interentity_transport 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.
disjoint with: interentity_import
date: 18 May 2011
creator: jps

intraentity_transport
type: Class
subclass of: transport
comment: Intraentity_transport is a transport of an entity from one place within a containing object to another place within the same object. For example, movement of a mRNA from the nucleus to the cytosol.
date: 18 May 2011
creator: jps

molecular_targeting
type: Class
subclass of: intraentity_transport
comment: Molecular_targeting is an intraentity_transport in which a molecule is actively directed from one place in a cell to another.
date: 18 May 2011
creator: jps