A unit name, for example, "meter", "micrometer*mirometer", "hour". Stored as a text string.
3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string.
2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string.
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.
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.
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.
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.
hasQuality links an instance of a CBO quality.
quality_Of links a CBO quality to an object instance.
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.
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.
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).
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.
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.
An energy is a CBO:physical_object_quality is the energy of the object for which it is a quality.
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.
Volume is a geometrical_property describing the total volume of spaced occupied by the object at a particular instant in time.
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.
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.
Anisotropy is a geometrical_property describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:isotropy.
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.
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.
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.
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.
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.
Surface area is a CBO:geometrical_property describing the scalar value of the objects surface area at a particular instant in time.
Contact_surface_area is a CBO:geometrical_property describing the scalar value of two objects contact surface area at a particular instant in time.
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
Extent_geometrical is a CBO:geometrical_property that describes the basic granularity of the coordinate system.
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.
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.
Dimensionality is a CBO:geometrical_property that describes the number of independent spatial axis in a model or system.
Dimension_1D is a CBO:dimensionality quality for a system with one spatial dimension.
OPB:"One dimensional spatial coordinate system"
Dimension_1D is a CBO:dimensionality quality for a system with two spatial dimensions.
OPB:"Two dimensional spatial coordinate system"
Dimension_fractal is a CBO:dimensionality quality for a system with fractal dimensions. Probably does not belong in the class?
Dimension_1D is a CBO:dimensionality quality for a system with three spatial dimensions.
OPB:"Three dimensional spatial coordinate system"
Texture is a CBO:geometrical_property describing the characteristics of a surface texture.
Uniform_texture is a CBO:texture consisting of a positionally independent texture description.
Pattern_texture is a CBO:texture consisting of a positionally repetitive texture description.
Gradient_texture is a CBO:texture consisting of a texture description that varies smoothly across one or more dimensions.
Kinetic_property is a CBO:physical_object_quality describing a kinetic characteristic of an object.
Mass is a CBO:physical_object_quality describing the mass of the object.
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.
MeSH:G01.374, MeSH:"Mechanical Phenomena"
Yielding_threshold (Yield stress threshold, Y) is a CBO:mechanical_property describing the rheological yield stress of an object.
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)
MeSH:G01.374.590.605, MeSH:"Young's modulus", MeSH:"Elastic Modulus"
Pressure_mechanical is a CBO:mechanical_property describing the barometric pressure of an object or location in space.
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.
Tension_mechanical is a CBO:mechanical_property that describes the pulling force exerted on an entity (a stretching or distorting force).
Stiffness_mechanical is a CBO:mechanical_proerty that describes an elastic object's resistance to deformation by an applied force along a given direction.
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).
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.
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.
OPB:"Portion of electrical potential energy"
Electrical_current is a CBO:electrical_property ... (OPB) is the temporal derivative of an Ion amount.
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.
Age is a CBO:physical_oject_quality class that describes the chronological or generational age of a physical object.
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."
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."
Geometrical_entity is a CBO class for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions.
Boundary is a CBO:geometrical_entity that demarks the interface between to bona fide physical objects.
Cell_region is a CBL:geometrical_entity class that includes descriptors for various fiat regions. (A fiat region generally does not clear boundaries.)
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.
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.
Lateral_part is a CBO:cell_region that is between the CBO:basal_part and CBO:lateral_part.
Medial_part is a CBO:cell_region located near the center of the cell.
Organismal_region is a CBO:geometrical_entity class for regions of an animal.
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.
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.
OPB: ...is a period of time bounded by two temporal moments (that may be the same moment).
Material_type is a CBO class of qualities that describe objects as either solids, liquids (fluids), gels or solutes.
Fluid_material_type is a CBO:material_type (OPB) ...that is a material substance with fluid kinetic properties.
Solute_material_type is a CBO:material_type (OPB) ...that has both chemical and diffusional kinetic properties.
Solid_material_type is a CBO:material_type (OPB) ...that is a material substance with solid kinetic properties.
Gel_material_type is a CBO:material_type that is a material substance with fluid kinetic properties intermediate between a solid and a fluid.
System is a CBO class that describes and includes the qquniverseqq described by the model or experiment.
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.
A molecule is a CBO class OPB: ...that is a polyatomic entity.
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.
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.
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.
MeSH: The fluid of the body that is outside of CELLS. It is the external environment for the cells.
Cell_part is a CBO class including any constituent part of a cell.
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.
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.
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.
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.
FMA: Cell component which consists of cytosol and cytoplasmic organelles.
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.
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.
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.
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)
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.
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.
MeSH: D12.776.157.530, MeSH:"Membrane Transport Proteins"
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.
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.
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
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
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
Cell_kingdom_type is a CBO class describing the basic kingdom the cell belongs to. For example, qqprokaryoteqq or qqeucaryoteqq.
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.
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.
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.
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.
A fundamental_physical_process is a CBO:process (snap:process) that changes a quality or characteristic of an object.
Movement is a fundamental_physical_process resulting in the change in location or shape of a physical object.
Translation is a movement resulting in a change in the spatial location of an object.
Rotation is a movement resulting in a change in orientation of an object.
Diffusion is a movement arising from random motion, either thermal of motive (cf. motility), of an object.
Shape_change is a fundamental_physical_process resulting in the change in the shape, including extents, of an object.
Volume_change is a fundamental_physical_process resulting in a change, an increase or decrease, in the volume occupied by an object.
Expansion is a volume_change resulting in an increase in volume occupied by an object.
Contraction is a volume_change resulting in a decrease in volume occupied by an object.
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.
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.
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.
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.
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.
Cell_process is a CBO:process (snap:process) describing a process characteristic of a CBO:cell.
Existential_cell_processes is a cell_process that is assumed, without formal proof, to be a process of a cell.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
Necrosis is a cell_death caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin.
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.
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.
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.
Cell_differentiation is an existential_cell_process in which the type (CBO:phenotype) of a cell is changed.
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.
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.
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.
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.
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.
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.
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).
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).
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).
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).
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).
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.
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.
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.
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.
Cellular_mechanical_process is a cellular_property_process that results in a change in a mechanical property of a cell.
Cellular_kinetic_process is a cellular_property_process that changes a kinetic dependence.
Geometrical_cell_process is a cellular_property_process that results in a a change in the geometry of a cell.
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.
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.
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.
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).
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.
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.
Cell_rotation is a cell_movement resulting in a rotation of a cell about it center (center of mass or center of volume).
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.
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.
Cellular_electrical_process is a cell_environment_process that results in a change in an electrical quality of the cell.
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.
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.
Extracellular_matrix_process is a CBO:process involving a change in the qualities, or quantity of extracellular matrix and its components.
interstitial_matrix_process is an extracellular_matrix_process involving a change in the qualities, or quantity of interstitial matrix and its components.
interstitial_matrix_creation is an interstitial_matrix_process involving an increase in the quantity of the interstitial matrix and its components.
interstitial_matrix_deletion is an interstitial_matrix_process involving a decrease in the quantity of the interstitial matrix and its components.
interstitial_matrix_change is an interstitial_matrix_process involving a change in the components or characteristics of the interstitial matrix components.
Basement_lamina_process is an extracellular_matrix_process involving a change in the qualities, or quantity of a basement membrane or its components.
Basement_lamina_creation is a basement_lamina_process involving an increase in the quantity of the basement lamina and its components.
Basement_lamina_deletion is an basement_lamina_process involving a decrease in the quantity of the basement lamina and its components.
Basement_lamina_change is an basement_lamina_process involving a change in the components or characteristics of the basement lamina components.
Molecule_process is a CBO:Process that involves a molecule.
Molecule_creation is a molecule_process that results in the creation of a new molecule or an increase in a molecule's concentration.
Molecule_deletion is a molecule_process that results in the deletion of a molecule, or a decrease in a molecule's concentration.
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.
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.
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.
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.
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).
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.
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.
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.
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.
Molecular_targeting is an intraentity_transport in which a molecule is actively directed from one place in a cell to another.