1.3 The cell Behavior Ontology (CBO) is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors. Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA. The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinformatics. 2014 Apr 22. pii: btu210. [Epub ahead of print] PubMed PMID: 24755304. http://bioinformatics.oxfordjournals.org/content/early/2014/05/18/bioinformatics.btu210.long 1.0.2 Version 1.0.0 is the initial release of the Cell Behavior Ontology (CBO). Version 1.0.1 added Journal citation for the Cell Behavior Ontology (CBO). Version 1.0.2 corrected a few annotations that had "snap:process" that should be "span:process". Version 1.0.3 corrected/changed class "SpacialExclusive" to "SpatialExclusive" and property "has_Quality" to "has_quality". OBO_REL http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry" 1.0.3 The cell Behavior Ontology (CBO) is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors. J Sluka, Biocomplexity Insitute, Indiana University 4 Aug 2016 release version 1.0.3 jps jps 1/24/2012 has_Quality links an instance of a CBO quality to a class or individual. has_Quality links an instance of a CBO quality to a class or individual. has_Quality OBO_REL_adjacent_to OBO_REL_adjacents_to OBO_REL_adjacented_to true OBO_REL:0000012 Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity" [PMID:15892874] adjacent_to OBO_REL_agent_in OBO_REL_agents_in OBO_REL_agented_in OBO_REL:has_agent OBO_REL:0000022 agent_in OBO_REL_contained_in OBO_REL_containeds_in OBO_REL_containeded_in OBO_REL:contains OBO_REL:0000010 Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): "C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)" [PMID:15892874] contained_in OBO_REL_contains OBO_REL_containses OBO_REL_containsed OBO_REL:contained_in OBO_REL:0000011 contains OBO_REL_derived_into OBO_REL_deriveds_into OBO_REL_deriveded_into OBO_REL:derives_from OBO_REL:0000016 derived_into OBO_REL_derives_from OBO_REL_deriveses_from OBO_REL_derivesed_from OBO_REL:derived_into OBO_REL:0000015 Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'." [PMID:15892874] "derived_from" [] derives_from OBO_REL_has_agent OBO_REL_has_agents OBO_REL_has_agented OBO_REL:agent_in OBO_REL:0000021 "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [PMID:15892874] has_agent OBO_REL_has_improper_part OBO_REL_has_improper_parts OBO_REL_has_improper_parted OBO_REL:improper_part_of OBO_REL:0000024 See reasons for obsoletion of improper_part_of true has_improper_part OBO_REL_has_integral_part OBO_REL_has_integral_parts OBO_REL_has_integral_parted OBO_REL:integral_part_of true OBO_REL:0000005 has_integral_part OBO_REL_has_part OBO_REL_has_parts OBO_REL_has_parted OBO_REL:part_of true OBO_REL:0000003 has_part OBO_REL_has_participant OBO_REL_has_participants OBO_REL_has_participanted OBO_REL:participates_in OBO_REL:0000019 Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t" [PMID:15892874] has_participant OBO_REL_has_proper_part OBO_REL_has_proper_parts OBO_REL_has_proper_parted OBO_REL:proper_part_of OBO_REL:0000007 has_proper_part OBO_REL_improper_part_of OBO_REL_improper_part_ofs OBO_REL_improper_part_ofed OBO_REL:has_improper_part OBO_REL:0000025 OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf] "As for part_of, with the additional constraint that subject and object may be identical" [PMID:15892874] true improper_part_of OBO_REL_instance_of OBO_REL_instance_ofs OBO_REL_instance_ofed OBO_REL:0000023 true The instance_of relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for completeness "A relation between an instance and a class. For components: a primitive relation between a component instance and a class which it instantiates at a specific time. For processes: a primitive relation, between a process instance and a class which it instantiates, holding independently of time" [PMID:15892874] instance_of OBO_REL_integral_part_of OBO_REL_integral_part_ofs OBO_REL_integral_part_ofed OBO_REL:has_integral_part true OBO_REL:0000004 "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [PMID:15892874] integral_part_of OBO_REL_is_a OBO_REL_is_as OBO_REL_is_aed true OBO_REL:0000001 true The is_a relationship is considered axiomatic by the obo file format specification. In the representation of obo in OWL, where obo terms are represented as OWL classes, is_a is mapped on to the subClassOf axiom "For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'." [PMID:15892874] "is_subtype_of" [] owl:subClassOf is_a OBO_REL_located_in OBO_REL_locateds_in OBO_REL_locateded_in OBO_REL:location_of OBO_REL:0000008 Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)" [PMID:15892874] located_in OBO_REL_location_of OBO_REL_location_ofs OBO_REL_location_ofed OBO_REL:located_in OBO_REL:0000009 location_of OBO_REL_part_of OBO_REL_part_ofs OBO_REL_part_ofed OBO_REL:has_part true OBO_REL:0000002 Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [PMID:15892874] part_of OBO_REL_participates_in OBO_REL_participateses_in OBO_REL_participatesed_in OBO_REL:has_participant OBO_REL:0000020 participates_in OBO_REL_preceded_by OBO_REL_preceded_bies OBO_REL_preceded_bied OBO_REL:precedes OBO_REL:0000017 An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [PMID:15892874] preceded_by OBO_REL_precedes OBO_REL_precedeses OBO_REL_precedesed OBO_REL:preceded_by OBO_REL:0000018 precedes OBO_REL_proper_part_of OBO_REL_proper_part_ofs OBO_REL_proper_part_ofed OBO_REL:has_proper_part OBO_REL:0000006 "As for part_of, with the additional constraint that subject and object are distinct" [PMID:15892874] proper_part_of OBO_REL_transformation_of OBO_REL_transformation_ofs OBO_REL_transformation_ofed OBO_REL:0000013 When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes. "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874] transformation_of 1 value (included for completeness, probably best to just use hasFloatValue or hasIntValue). For example, the 1D length of an object of "3.2". Stored as a text string. Value is assumed to be X in a square coordinate system. hasExtentValueSet1D 2 Comma separated values (CSV). For example, the extent of a 2D region (area) "5,10". Stored as a text string. Values are assumed to be X,Y in a square coordinate system. hasExtentValueSet2D 3 Comma separated values (CSV). For example, the extent of a 3D region (volume) "5,5,10". Stored as a text string. Values are assumed to be X,Y,Z in a square coordinate system. hasExtentValueSet3D A single floating point number. hasFloatValue A single floating point number representing the target value of a quality or function. hasFloatValueTarget A single integer number. hasIntValue A single integer number representing the target value of a quality or function. hasIntValueTarget 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. hasLocationValueSet1D 2 Comma separated values (CSV). For example, the location of a point "3.2,-34.1". Stored as a text string. hasLocationValueSet2D 3 Comma separated values (CSV). For example, the location of a point "3.2,2.4,-34.1". Stored as a text string. hasLocationValueSet3D 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. hasLocationValueSetND Data is a list of n-tupes (one n-tuple/line) listing values of various kinds. For example, the list of interaction energies between a set of cell types. Comma separated values (CSV) with [CR] end of row markers. The dimensions (number of rows and columns) is not explicitly stated. Stored as a text string. hasParameterValueSetND Data is a list of n-tupes (one n-tuple/line) listing the coordinates of the elements within a set. For example, the list of x,y,z coordinates of a cell in a grid-based coordinate system. Comma separated values (CSV) with [CR] end of row markers. The dimensions (number of rows and columns) is not explicitly stated. Stored as a text string. hasPointsValueSetND A unit name, for example, "meter", "micrometer*micrometer", "hour". Stored as a text string. hasUnit jps 11/9/2012 hasVTKfieldID is a CBO data property that links a field prototype to the character string name used in the VTK files. For example, an oxygen field in the simulaitno will probably be named described inthe VTK file as a field called "oxygen". hasVTKfieldID JPS 10/25/2012 hasVTKtypeID is a CBO data property that links a cell prototype (or other physical entitiy prototype) to the integer ID used in the VTK files. Often, in models that include medium as a CBO:Fill, the value of hasVTKtypeID will be 0 (zero). Note that a VTK "cell" has both a type ID (hasVTKtypeID) and an ID. The type ID identifies the class of cell, the ID identifies the individual cell. Many cells can have the same type ID, no two cells can have the same ID. Both types of IDs are unsigned integers. jps 24 Aug. 2011 An AcceptanceFunction is a CBO:EnergyFunction describing the acceptance and rejection criteria for a change in the system. A simple AcceptanceFunction might state that all changes to the system which result in a lowering of the systems energy are accepted but all other changes are rejected. AcceptanceFunction jps 24 Aug. 2011 An AdhesionEnergy is a CBO:EnergyQuality representing the energy associated with the contact between two physical objects. AdhesionEnergy jps 24 Aug. 2011 AdhesionMolecule is a CBO:CellMembranePart that is a protein that mediates the adhesion between the Cell and other Cells or components of the extracellular space. MeSH: Surface ligands, usually glycoproteins, that mediate Cell-to-Cell adhesion. Their functions include the assembly and interconnection of various vertebrate Systems, as well as maintenance of tissue integration, wound healing, morphogenic movements, cellular migrations, and metastasis. urn:miriam:obo.fma:67214 AdhesionMolecule jps 24 Aug. 2011 AdhesiveProperty is a CBO:MechanicalProperty that describes an aspect of one of the objects involved in an adhesive force between two entities. For example, the adhesion properties of one Cell in the adhesion between a pair of Cells in contact, or between a Cell and a basement membrane. AdhesiveProperty jps 29 Oct. 2012 Advection is a Movement that is caused by a carrying medium (such as blood) that results in a change in location. Advection CellAdvection jps 24 Aug. 2011 Age is a CBO:PhysicalObjectQuality class that describes the chronological or generational Age of a physical object. Age jps 24 Aug. 2011 Anisotropy is a GeometricalProperty describing the directionality of a directionally dependent quality of the object. This is the opposite of CBO:Isotropy. Anisotropy jps 24 Aug. 2011 ApicalPart is a CBO:CellRegion of a polarized Cell is the region that is closest to the lumen. (Wikipedia)This is particularly evident in epithelial and endothelial cells, but also describes other polarized cells, such as neurons. ApicalPart jps 24 Aug. 2011 Apoptosis is a CellDeath characterized by an orderly, and triggered process of cell death. GO: A form of programmed cell death that begins when a cell receives internal or external signals that trigger the activity of proteolytic caspases, proceeds through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopods, reduction of cellular Volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing (but maintenance of its integrity until the final stages of the process), and ends with the death of the cell. PATO:0000638 urn:miriam:obo.go:0006915 Apoptosis jps 24 Aug. 2011 A AreaEnergy is a CBO:EnergyQuality representing the energy associated with a given area entity. AreaEnergy jps 24 Aug. 2011 AsymmetricCellDivisionOrientedCleavagePlane is a Mitosis characterized by the Creation of two non-identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is oriented with respect to either the environment or the characteristics of the parent cell. GO: The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity. AsymmetricCellDivisionOrientedCleavagePlane jps 24 Aug. 2011 AsymmetricCellDivisionRandomCleavagePlane is a Mitosis characterized by the Creation of two non-identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is oriented randomly with respect to both the environment and the characteristics of the parent cell. GO: The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity. AsymmetricCellDivisionRandomCleavagePlane jps 24 Aug. 2011 AutophagicDeath is a CellDeath characterized by the auto degradation of cellular components. GO: A form of programmed cell death that is accompanied by macroautophagy, which is characterized by the sequestration of cytoplasmic material within autophagosomes for bulk degradation by lysosomes. Autophagic cell death is characterized by lack of chromatin condensation, massive vacuolization of the cytoplasm, and accumulation of (double-membrane) autophagic vacuoles, with little or no uptake by phagocytic cells. urn:miriam:obo.go:0048102 AutophagicDeath jps 24 Aug. 2011 BarrierCrossing is a FundamentalPhysicalProcess involving the transfer of an object across a bona fide boundary. For example, diiffusive transfer of a small molecule, such as molecular oxygen, across a cell membrane. For active Transport see CBO:CellImport and CBO:CellExport. BarrierCrossing jps 24 Aug. 2011 BasalPart is a CBO:CellRegion that includes the base of the Cell where the base is generally defined relative to an extraCellular membrane. GO: The region of a Cell situated near the base. For example, in a polarized epithelial Cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue. urn:miriam:obo.fma:72558 urn:miriam:obo.go:0045178 BasalPart jps 24 Aug. 2011 BasementLaminaChange is an BasementLaminaProcess involving a change in the components or characteristics of the basement lamina components. BasementLaminaChange jps 24 Aug. 2011 BasementLaminaCreation is a BasementLaminaProcess involving an increase in the quantity of the basement lamina and its components. BasementLaminaCreation jps 24 Aug. 2011 BasementLaminaDeletion is a BasementLaminaProcess involving a decrease in the quantity of the basement lamina and its components. BasementLaminaDeletion jps 24 Aug. 2011 BasementLaminaProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of a basement membrane or its components. BasementLaminaProcess jps 24 Aug. 2011 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. urn:miriam:obo.go:0005605 BasementMembrane jps 11/8/2012 BioEntityType is a CBO_Object for biological concepts such as Cell and ECM. BioEntityType subclass of: BFO:snap:object jps 24 Aug. 2011 BodyShape is a GeometricalProperty describing the spatial (2 or 3 dimensions) Shape of a region of spaced occupied by an object at a particular instant in time. BodyShape may be defined as a locus of point in 3 (or 2) dimensional space, or as a predefined common Shape such as a sphere or cube. urn:miriam:opb:'bounded Volume Shape' BodyShape jps 24 Aug. 2011 A BoltzmannFactor is a CBO:EnergyFunction:AcceptanceFunction describing an acceptance criteria that uses a Boltzmann factor. A Boltzmann function accepts all system changes that result in a lowering of the systems total energy. In addition, changes that result in an increase in the systems energy are accepted based on a probability function. The probability function is generally described as being based on the temperature of the system (though the temperature may not be directly related to a physical temepertature.) The form of the Boltzmann factor is: Accept if deltaE is less than zero, where deltaE is the change in energy of the system calculated as the new energy minus the previous energy. If deltaE is greater than zero then accept the change if e^(-1/(k*T*deltaE)) is greater than a randomly choosen number between zero and one. k is Boltzmann's constant (in MKS units 1.38x10^-23 m^2 kg/(s^2 K) ) and T is the Boltzmann temperature (T is greater than zero). BoltzmannFactor jps 24 Aug. 2011 Boundary is a CBO:GeometricalEntity that demarks the interface between two bona fide physical objects. Boundary subclass of: BFO:snap:object_Boundary jps 24 Aug. 2011 A BrushBorder is a CBO:CellMembraneLocalStructure characterized by a highly convoluted Cell surface. GO: Dense covering of microvilli on the apical surface of epithelial Cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the Cell. MeSH: Minute projections of Cell membranes which greatly increase the surface area of the Cell. AKA: Microvilli, Striated Border urn:miriam:obo.fma:70977 urn:miriam:obo.go:0005903 BrushBorder jps 24 Aug. 2011 CBO_Object is the top level CBO class for physical objects and object qualities. CBO_Object is BFO:continuant (endurant). CBO_Object subclass of: BFO:continuant jps 24 Aug. 2011 CBO_Process is the top level CBO class for processes. CBO_Process is BFO:occurant (processual). CBO_Process subclass of: BFO:occurrent jps 23 Jul. 2012 CHASTERcenter is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.cs.ox.ac.uk/chaste/sysbio_index.html CHASTEcenter jps 24 Aug. 2011 Cell is a CBO:BioEntityType class for the basic unit of an organism. A Cell includes at least the plasma membrane and the cytosol. GO: The basic structural and functional unit of all organisms. urn:miriam:obo.clo:0000000 urn:miriam:obo.fma:68646 urn:miriam:obo.go:0005623 Cell jps 24 Aug. 2011 CellAdhesion is a CellEnvironmentProcess involving the adhesive interaction between a cell and some other physical object (another cell, basement membrane etc.). Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact. PATO:0001531 urn:miriam:obo.go:0007155 CellAdhesion jps 24 Aug. 2011 CellAdvection is a CellMovement that is caused by a carrying medium (such as blood) that results in a change in location, defined by the center of mass or center of Volume, of a cell. CellAdvection jps 24 Aug. 2011 CellBasementLaminaContact is a CellNonCellContact involving the direct contact between a cell and a basement membrane. Note that contact is a distinct process from adhesion (see CBO:CellAdhesion). CellBasementLaminaContact jps 24 Aug. 2011 CellBasementMembraneAdhesion is a CellNonCellAdhesion involving the adhesive interaction between a cell and a basement membrane. Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact. CellBasementMembraneAdhesion jps 24 Aug. 2011 CellBorder is a CBO:CellPart consisting of the outer Boundary of the Cell, that is, the surface that delineates the Cell from the surroundings. Depending on the species and phyla the CellBorder may be either a CBO:CellMembrane or a CBO: CellWall. CellBorder jps 24 Aug. 2011 CellCellAdhesion is a CellAdhesion involving the adhesive interaction between two cells. Note that adhesion is a distinct process from contact (see CBO:CellContact) but that adhesion requires contact. PATO:0001531 urn:miriam:obo.go:0016337 CellCellAdhesion jps 24 Aug. 2011 CellCellContact is a CellContact involving the direct physical contact between two cells. Note that contact is distinct from adhesion (see CBO:CellAdhesion). CellCellContact jps 24 Aug. 2011 CellCellProcess is a CellProcess in which the interaction between two cells leads to a change in characteristic or behavior of one or both of the cells. CellCellProcess jps 24 Aug. 2011 CellContact is a CellEnvironmentProcess involving the direct physical contact between a cell and some other physical object (another cell, basement membrane etc.). Note that contact is distinct from adhesion (see CBO:CellAdhesion). CellContact subclass of: BFO:span:fiat_process_part jps 24 Aug. 2011 CellDeath is an existential_CellProcess in involving the death of a cell. The cell count in the system is decreased by one and there may or may not be cellular fragments left behind. urn:miriam:obo.go:0008219 CellDeath jps 24 Aug. 2011 CellDifferentiation is an existential_CellProcess in which the type (CBO:Phenotype) of a cell is changed. CellDifferentiation jps 24 Aug. 2011 CellDisplacement is a CellMovement that results in a change in the location, defined by the center of mass or center of Volume, of a cell. CellDisplacement jps 24 Aug. 2011 CellDivision is an ExistentialCellProcess involving the Creation of two new cells (daughters) from a single parent cell. GO: The process resulting in the physical partitioning and separation of a cell into daughter cells. urn:miriam:obo.go:0051301 CellDivision jps 24 Aug. 2011 CellEnvironmentProcess is an ExistentialCellProcess involving the interaction between a cell and a component of the environment, where the environment includes other cells. For example, adhesion of a cell to a basement membrane. CellEnvironmentProcess jps 24 Aug. 2011 CellExport is a CellRelatedTransport involving Movement of an entity across the cell membrane from the inside of the cell to the outside of the cell. For passive (e.g., diffusive) Transport see CBO:BarrierCrossing. CellExport jps 24 Aug. 2011 CellFusion is an existential_CellProcess involving the merging of two or more cells into a single giant cell containing multiple nuclei. GO: The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. urn:miriam:obo.go:0000768 CellFusion jps 24 Aug. 2011 CellGrowth is a CellProcess that changes the Volume of a cell. CellGrowth includes both an increase and a decrease in the cell's Volume. (Similar to, but here specific to a CBO:Cell) to CBO:VolumeChange. This definition differs from that in GO:0016049 The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. PATO:0001489 urn:miriam:obo.go:0016049 CellGrowth subclass of: BFO:span:fiat_process_part jps 24 Aug. 2011 CellImport is a CellRelatedTransport involving Movement of an entity across the cell membrane from the outside of the cell to the inside of the cell. For passive (e.g., diffusive) Transport see CBO:BarrierCrossing. CellImport jps 24 Aug. 2011 CellInterstitialMatrixAdhesion is a CellNonCellAdhesion involving the adhesive interaction between a cell and the interstitial matrix. Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact. CellInterstitialMatrixAdhesion jps 24 Aug. 2011 CellInterstitialMatrixContact is a CellNonCellContact involving the direct contact between a cell and a component of the interstitial matrix. Note that contact is a distinct process from adhesion (see CBO:CellAdhesion). CellInterstitialMatrixContact jps 24 Aug. 2011 CellMembrane is a CBO:CellBorder consisting of (MeSH) the lipid- and protein-containing, selectively permeable membrane that surrounds the Cytoplasm in prokaryotic and eukaryotic Cells. urn:miriam:obo.fma:63841 urn:miriam:obo.go:0005886 CellMembrane jps 24 Aug. 2011 A CellMembraneLocalStructure is a CBO_Object that includes the various topological patterns found, often transiently, on Cell walls. For example, filopodia. MeSH: Specialized structures of the Cell that extend the Cell membrane and project out from the Cell surface. GO: A prolongation or process extending from a Cell, e.g. a flagellum or axon. urn:miriam:obo.go:0042995 CellMembraneLocalStructure subclass of: BFO:snap:specifically_dependent_continuant jps 24 Aug. 2011 CellMembranePart is a CBO:CellPart class that includes the various proteinaceous parts commonly found on a Cell membrane. Note that this class does not include topological features such as axons or filopodia. GO: plasma membrane part; Any constituent part of the plasma membrane, the membrane surrounding a Cell that separates the Cell from its external environment. urn:miriam:obo.go:0044459 CellMembranePart subclass of: BFO:snap:specifically_dependent_continuant jps 24 Aug. 2011 CellMotility is a CellMovement involving an Energy dependent self-propelled displacement of a cell's center of mass or center of volume. GO: Any process involved in the controlled self-propelled Movement of a cell that results in translocation of the cell from one place to another. urn:miriam:obo.go:0048870 CellMotility jps 24 Aug. 2011 CellMovement is a GeometricalCellProcess that results in a change in the location or orientation of a cell. Note that this definition is incompatible with GO:0006928 cell Movement. CellMovement jps 24 Aug. 2011 CellNonCellAdhesion is a CellAdhesion involving the adhesive interaction between a cell and another physical object where the second object is not itself a cell. Note that adhesion is distinct from contact (see CBO:CellContact) but that adhesion requires contact. urn:miriam:obo.go:0031589 CellNonCellAdhesion jps 24 Aug. 2011 CellNonCellContact is a CellContact involving direct physical contact between a cell and another physical object where the second object is not itself a cell. Note that contact is a distinct process from adhesion (see CBO:CellAdhesion). CellNonCellContact jps 24 Aug. 2011 CellOrientationChange is a GeometricalCellProcess that changes the relationship between the cell's internal axis and the environments axis. For example, a change in the alignment between a cell's apical-basal axis and the organismal animal-vegetal axis. CellOrientationChange jps 24 Aug. 2011 CellPart is a CBO_Object including any constituent part of a Cell. urn:miriam:obo.fma:61764 CellPart subclass of: BFO:snap:specifically_dependent_continuant jps 24 Aug. 2011 CellProcess is a CBO_Process (span:process) describing a process characteristic of a CBO:Cell. CellProcess subclass of: BFO:span:process jps 24 Aug. 2011 CellRegion is a CBL:GeometricalEntity class that includes descriptors for various fiat regions. (A fiat region generally does not have clear boundaries.) CellRegion subclass of: BFO:snap:fiat_object_part jps 24 Aug. 2011 CellRelatedTransport is a CellEnvironmentProcess involving Movement of an entity across the cell's membrane. The moving entity becomes contained in the cell but is not partOf the cell. CellRelatedTransport includes active and selective processes. For passive (e.g., diffusive) Transport see CBO:BarrierCrossing. urn:miriam:obo.go:0006810 CellRelatedTransport jps 24 Aug. 2011 CellRotation is a CellMovement resulting in a Rotation of a cell about it center (center of mass or center of Volume). urn:miriam:obo.pato:0001599 CellRotation jps 24 Aug. 2011 CellShapeChange is a GeometricalCellProcess that results in a change in Shape of the bounding surface of the cell defined by the cell wall or cell membrane. CellShapeChange jps 24 Aug. 2011 A CellState is aCBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the biological state of a cell at a particular time. CellState includes concepts such as "quiescent", "growing", "necrotic" (dying) etc. CellState subclass of: BFO:snap:quality jps 24 Aug. 2011 deprecated CellVolumeChange jps 24 Aug. 2011 CellWall is a CBO:CellBorder consisting of (MeSH) the outermost layer of a Cell in most PLANTS; BACTERIA; FUNGI; and ALGAE. The Cell wall is usually a rigid structure that lies external to the Cell MEMBRANE, and provides a protective barrier against physical or chemical agents. (GO) The rigid or semi-rigid envelope lying outside the Cell membrane of plant, fungal, and most prokaryotic Cells, maintaining their Shape and protecting them from osmotic lysis. In plants it is made of Cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan. It is unclear if CellWall is a CellPart of if CellWall should be classified as a type of extracellular matrix. Is a particular portion of CellWall "owned" by a single cell or is it "owned" and maintained by the two or more cells on either side? urn:miriam:obo.go:0005618 CellWall jps 24 Aug. 2011 CellularChemicalProcess is a CellEnvironmentProcess in which an environmental (local) chemical (or chemical gradient) changes a process or quality of a cell. CellularChemicalProcess jps 24 Aug. 2011 CellularElectricalProcess is a CellEnvironmentProcess that results in a change in an electrical quality of the cell. CellularElectricalProcess jps 24 Aug. 2011 CellularKineticProcess is a CellularPropertyProcess that changes a kinetic dependence. CellularKineticProcess jps 24 Aug. 2011 CellularMechanicalProcess is a CellularPropertyProcess that results in a change in a mechanical property of a cell. CellularMechanicalProcess jps 24 Aug. 2011 CellularPropertyProcess is a CellProcess that results in a change in a property of a cell. For example, CellMovement changes the property of location. CellularPropertyProcess jps 23 Jul. 2012 CenterModelPlatform is a CBO:ComputationalPlatformQuality class for computational platforms which describe a cell (or other CBO:CorpuscularEntity) primarily as the center point of an object. The extent of the object are described by other characteristics and often the complete extent of an object can only be described by reference to other (adjacent) objects. Unlike DiscreteModelPlatform a CenterModelPlatform does not impose a regular grid on the location of objects and does not contain pixels/voxels. CenterModelPlatform jps 24 Aug. 2011 The CenterOfMass is a CBO:position that describes the center of Mass of a spatially extended object at a particular time. The CenterOfMass inherits the CBO:Dimensionality of the particular object or CBO:Dimensionality of the CBO:System object. See also CenterOfVolume which may be, for practical purposes, identical. CenterOfMass jps 24 Aug. 2011 The CenterOfVolume is a CBO:position that describes the center of Volume of a spatially extended object at a particular time. The CenterOfVolume inherits the CBO:Dimensionality of the particular object or CBO:Dimensionality of the CBO:System object. See also CenterOfMass which may be, for practical purposes, identical. CenterOfVolume jps 24 Aug. 2011 Charge is a CBO:ElectricalProperty describing the overall electrical charge of an entitiy. PATO: A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. urn:miriam:obo:pato:0002193 urn:miriam:opb:'Charge amount' Charge jps 24 Aug. 2011 ChemicalAffinity is a ChemicalProperty that describes an affinity (atraction, repulsion) between a molecule and another object. ChemicalAffinity jps 24 Aug. 2011 ChemicalDensity is a ChemicalProperty that describes the concentration (mass or number of molecules) per unit volume. ChemicalDensity jps 24 Aug. 2011 ChemicalLocalization is a ChemicalProperty that describes a tendency for the chemical species to localize in a particular region (e.g., cell membrane). ChemicalLocalization jps 24 Aug. 2011 ChemicalPattern is a ChemicalProperty that describes a tendency for the chemical species to organize or partition in a particular pattern. ChemicalPattern jps 24 Aug. 2011 ChemicalPatternGradient is a ChemicalPattern that describes a tendency for the chemical species to organize or partition in a particular pattern that includes a gradient in concentration. ChemicalPatternGradient jps 24 Aug. 2011 ChemicalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the physical behavior of chemicals ChemicalProperty(ies) are intrinsic to the object. ChemicalProperty jps 24 Aug. 2011 Chemotaxis is a CellMovement in which an Energy dependent process gives a directed Movement of the cell relative to an external gradient. GO: The directed Movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive Chemotaxis) or towards a lower concentration (negative Chemotaxis). urn:miriam:obo.go:0006935 urn:miriam:obo.go:0060326 Chemotaxis jps 23 Jul. 2012 Compucell3D is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. See www.Compucell3D.org Compucell3D jps 23 Jul. 2012 ComputationalPlatform is a SystemQuality class describing a particular computational platform. ComputationalPlatform jps 27 Jul. 2012 ComputationalPlatformQuality is a CBO class describing qualities of computational platforms for preforming multicell modeling. ComputationalPlatformQuality jps 24 Aug. 2011 ContactSurfaceArea is a CBO:GeometricalProperty describing the scalar value of two objects contact surface area at a particular instant in time. ContactSurfaceArea jps 23 Jul. 2012 DiscreteModelPlatform is a CBO:ComputationalPlatformQuality class for computational platforms which describe a cell (or other CBO:CorpuscularEntity) in a discretized coordinate system (a regular grid) of voxels or pixels. Unlike DiscreteModelPlatform a DiscreteModelPlatform jps 24 Aug. 2011 A ContinuousEntity is a PhysicalEntityType (BFO:snap:object) that has a particular extent at a particular time but which also may extend beyond the limits of the view or model. ContinuousEntities are spatially exclusive and do not overlap. Unlike a CorpuscularEntity, a ContinuousEntity is geometrically divisible without a fundamental change in characteristics, qualities or identity. For example, a portion of a basement membrane, Cell wall, or medium (e.g., water). ContinuousEntity jps 24 Aug. 2011 ContinousExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionaly sensitive quantity in an infinitely finely grained coordinate System. Compare with DiscreteExtent. ContinuousExtent jps 24 Aug. 2011 Contraction is a VolumeChange resulting in a decrease in Volume occupied by an object. Contraction jps 24 Aug. 2011 A CorpuscularEntity is a PhysicalEntityType (BFO:snap:object) that has a particular Location and Volume at a particular time. CorpuscularEntities are spatially exclusive and do not overlap. Furthermore, a CorpuscularEntity is not divisible without a fundamental change in characteristics, qualities or identity. For example, an individual Cell. CorpuscularEntity jps 24 Aug. 2011 Creation is a FundamentalPhysicalProcess resulting in the Creation of a new object. Often this will involve an increase in count of an object. Creation jps 24 Aug. 2011 FMA: Cell component which consists of cytosol and Cytoplasmic organelles. Cytoplasm jps 24 Aug. 2011 Deletion is a FundamentalPhysicalProcess resulting in the Deletion of an object. Often this will involve a decrease in count of an object. Deletion jps 24 Aug. 2011 A DiffuseEntity is a PhysicalEntityType (BFO:snap:object) that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a DiffuseEntity may be described as having a position dependent concentration or density function. Unlike a CorpuscularEntity, a ContinuousEntity is geometrically divisible without a fundamental change in characteristics or identity. A DiffuseEntity may be restricted to exist along with another PhysicalEntityType, such as the case of a cell membrane bound receptor (DiffuseEntity) distributed on the cell membrane of a particular cell (a CorpuscularEntity). For example, a portion of a chemical field distributed across the interstitial space of a region. DiffuseEntity jps 24 Aug. 2011 Diffusion is a Movement arising from random motion, either thermal or motive (cf. motility), of an object. Diffusion jps 24 Aug. 2011 Dimension1d is a CBO:Dimensionality quality for a System with one spatial dimension. urn:miriam:opb:'One dimensional spatial coordinate System' Dimension1d jps 24 Aug. 2011 Dimension2d is a CBO:Dimensionality quality for a System with two spatial dimensions. urn:miriam:opb:'Two dimensional spatial coordinate System' Dimension2d jps 24 Aug. 2011 Dimension3d is a CBO:Dimensionality quality for a System with three spatial dimensions. urn:miriam:opb:'Three dimensional spatial coordinate System' Dimension3d jps 24 Aug. 2011 Dimensionality is a CBO:GeometricalProperty that describes the number of independent spatial axis in a model or System. urn:miriam:opb:'Spatial coordinate System' Dimensionality jps 24 Aug. 2011 DiscreteExtent is a CBO:ExtentGeometrical for a position, Location, or otherwise positionally sensitive quantity in a finitely grained coordinate System. Compare with ContinuousExtent. DiscreteExtent jps 24 Aug. 2011 A Divisible quality is a CBO:PhysicalObjectQuality for objects which can be divided, conceptually or for ease of representation, without a fundamental change in the character or qualites of the object. For example, the fluid (medium, CBO:ExtraCellularFluid) surronding a cell. Physical objects with the Divisible quality can often be treated as portionsOf, the individual protions behave as does the bulk object with only changes in, for example, the location, extent and identifier for the portionOfs. Divisible jps 24 Aug. 2011 Dorsal is a CBO:OrganismalRegion characteristic of the back of an object relative to the body it is contained in. For example Dorsal fin. urn:miriam:obo.fma:74535 Dorsal jps 24 Aug. 2011 ElectricalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the electrical qualities of objects. ElectricalProperty are intrinsic to the object. urn:miriam:opb:'Electrical entity' ElectricalProperty jps 8/1/2012 A ElectromechanicalField is a CBO:Field class for the description of electric and mechanical fields that span a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a ElectromechanicalField may be described as having a position dependent concentration or density function. Unlike a CBO:Cell, a ElectromechanicalField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) A ElectromechanicalField may be restricted to a particular region or part of a physical object (CBO:PhysicalEntityType:CorpuscularEntity or CBO:PhysicalEntityType:ContinousEntity), such as the case of a transmembrane electrical field. ElectromechanicalField jps 24 Aug. 2011 An Energy is a CBO:PhysicalObjectQuality is the Energy of the object for which it is a quality. urn:miriam:opb:'Energy amount' Energy jps 24 Aug. 2011 An EnergyFunction is a CBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the mathematical form used to define a particular EnergyQuality. Energy subclass of: BFO:snap:quality jps 24 Aug. 2011 A EnergyQuality is a CBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the energy qualities of physical objects. For example, the energy of a particular cell, at a particular cell in a particular environment. EnergyQuality subclass of: BFO:snap:quality jps 24 Aug. 2011 ExistentialCellProcesses is a CellProcess that is assumed, without formal proof, to be a process of a cell. ExistentialCellProcesses jps 24 Aug. 2011 Expansion is a VolumeChange resulting in an increase in Volume occupied by an object. Expansion jps 24 Aug. 2011 ExtentGeometrical is a CBO:GeometricalProperty that describes the basic granularity of the coordinate System. ExtentGeometrical jps 24 Aug. 2011 ExtracellularFluid is a CBO:BioEntityType for the fluids that exist outsides of cells. MeSH: The fluid of the body that is outside of Cells. It is the external environment for the Cells. ExtraCellularFluid jps 24 Aug. 2011 ExtraCellularMatrix is a CBO:BioEntityType that includes all physical entities that are discrete (though possible of considerable extent) that are distinct from Cell and media. The ExtraCellularMatrix provides support and restricts movement of objects. urn:miriam:obo.fma:9672 urn:miriam:obo.go:0031012 ExtraCellularMatrix jps 24 Aug. 2011 ExtracellularMatrixProcess is a CBO_Process involving a change in the qualities, or quantity of extracellular matrix and its components. ExtracellularMatrixProcess subclass of: BFO:span:process jps 19 Jul. 2012 A Field is a CBO_Object for the description of entities that span a particular extent at a particular time but are not spatially exclusive and may, and generally do, overlap with other PhysicalEntityTypes at a particular time. In addition, a Field may be described as having a position dependent concentration, density or value function. Unlike a CBO:Cell, a Field is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) A Field may be restricted to a particular region or part of a physical object (CBO:PhysicalEntityType:CorpuscularEntity or CBO:PhysicalEntityType:ContinousEntity), such as the case of an electromagnetic field. Or, a portion of a chemical field distributed across the interstitial space of a region. subclass of: BFO:snap:object jps 11/8/2012 FieldProcess is a CBO_Process (span:process) describing a process characteristic of a CBO:Field. FieldProcess subclass of: BFO:span:process jps 11/8/2012 A FieldQuality is a CBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the qualities of field objects. BFO uses QUALITY, OPB uses PROPERTY. For example, quality is a characteristic of a physical object such as Location, Volume, Energy, type etc. FieldQuality subclass of: BFO:snap:quality jps 24 Aug. 2011 A Fill quality is a CBO:PhysicalObjectQuality for objects that can be understood to fill all available space. An object with the Fill quality also has the SpatialExclusive quality. Examples include the medium (CBO:ExtraCellularFluid) or the air inside the lungs. Fill jps 24 Aug. 2011 A Filopodium is a CBO:CellMembraneLocalStructure and is a thin, stiff Protrusion extended by the leading edge of a motile Cell such as a crawling fibroblast or amoeba, or an axonal growth cone. GO: Thin, stiff Protrusion extended by the leading edge of a motile Cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward. MeSH: A dynamic actin-rich extension of the surface of an animal Cell used for locomotion or prehension of food. AKA: Axopodia, Filopodia, Lamellipodia, Lobopodia, Pseudopodium, Reticulopodia urn:miriam:obo.go:0030175 Filopodium jps 24 Aug. 2011 A FirstOrderRate is a CBO:RateFunction describing the mathematical form used to define a first order rate of change of a quality with respect to time. For quality n; dn/dt=k*n, where k is the rate constant. FirstOrderRate jps 24 Aug. 2011 Fission is an ExistentialCellProcess of bacterial cells resulting in the Creation of two daughter cells from a single parent cell. Fission is specific to bacterial cells. Fission jps 24 Aug. 2011 A FundamentalPhysicalProcess is a CBO_Process (span:Process) that changes a quality or characteristic of an object. urn:miriam:dummy:1 urn:miriam:dummy:2 urn:miriam:dummy:3 FundamentalPhysicalProcess subclass of: BFO:span:process jps 24 Aug. 2011 GapJunction is a CBO:CellMembranePart that acts as a connection between, and adhesion mediator, between two Cells. In addition, the gap allows for the transfer of small Molecules (hence information) between two adjacent Cells. MeSH: Connections between Cells which allow passage of small Molecules and electric current. Gap junctions were first described anatomically as regions of close apposition between Cells with a narrow (1-2 nm) gap between Cell membranes. The variety in the properties of gap junctions is reflected in the number of CONNEXINS, the family of proteins which form the junctions. urn:miriam:obo.fma:67423 urn:miriam:obo.go:0005921 GapJunction jps 24 Aug. 2011 GenerationalAge is a CBO:Age that describes the number of generations that have passed for a particular Cell within its lineage. For example, a mesenchymal Cell derived from a stem cell would have GenerationalAge equal to one. When that mesenchymal cell divides both daughter cells would have GenerationalAge of 2. GO:0001302 replicative cell aging, namespace: biological_process def: The process associated with progression of the Cell from its inception to the end of its lifespan that occurs as the Cell continues cycles of growth and division. urn:miriam:obo.go:0001302 GenerationalAge jps 24 Aug. 2011 GeometricalCellProcess is a CellularPropertyProcess that results in a change in the geometry of a cell. GeometricalCellProcess jps 24 Aug. 2011 GeometricalEntity is a CBO_Object for sub-regions and boundaries of objects. The regions, and boundaries, may be fiat or bona fide regions. GeometricalEntity subclass of: BFO:snap:independent_continuant jps 24 Aug. 2011 GeometricalProperty are CBO:physical_object_qualities that define the geometrical qualities of an object at a particular time. This includes the Shape, extents, position etc. of an abject. GeometricalProperty jps 24 Aug. 2011 GradientTexture is a CBO:Texture consisting of a Texture description that varies smoothly across one or more dimensions. GradientTexture jps 24 Aug. 2011 A Hamiltonian is a CBO:PhysicalObjectQuality is the total energy associated with a physical object. The Hamiltonian is the algebraic sum of the energies associated with the physical object. Hamiltonian jps 24 Aug. 2011 Haptotaxis is a CellMovement in which an Energy dependent process gives a directed Movement of the cell relative to an external matrix such as interstitial fibrils or a basement membrane. Haptotaxis jps 24 Aug. 2011 A HarmonicEnergy function is a CBO:EnergyFunction describing the mathematical form used to define a harmonic relationship used to calculate a particular energyQuality. The equation is of the form E = k(target value - current value)^2, where k is a scaling canstant and target value and current value are qualities of a particular physical object. This HarmonicEnergy function is Hooke's Law in the energy domain. HarmonicEnergy jps 24 Aug. 2011 InterentityExport is an InterentityTransport of an object across a bona fide boundary in which the Transporting entity is moving out of another object. For example, from inside of a bone to the outside of the bone. InterentityExport jps 24 Aug. 2011 InterentityImport is an InterentityTransport of an object across a bona fide boundary in which the Transporting entity is moving into (containedIn) another object. For example, from the space outside of a bone to within the bone. InterentityImport jps 24 Aug. 2011 InterentityTransport is a Transport of an object across a bona fide boundary. For example, from within a bone to the space outside the bone. InterentityTransport subclass of: BFO:span:process jps 24 Aug. 2011 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. urn:miriam:obo.go:0005614 InterstitialMatrix jps 24 Aug. 2011 InterstitialMatrixChange is an InterstitialMatrixProcess involving a change in the components or characteristics of the interstitial matrix components. InterstitialMatrixChange jps 24 Aug. 2011 InterstitialMatrixCreation is an InterstitialMatrixProcess involving an increase in the quantity of the interstitial matrix and its components. InterstitialMatrixCreation jps 24 Aug. 2011 InterstitialMatrixDeletion is an InterstitialMatrixProcess involving a decrease in the quantity of the interstitial matrix and its components. InterstitialMatrixDeletion jps 24 Aug. 2011 InterstitialMatrixProcess is an ExtracellularMatrixProcess involving a change in the qualities, or quantity of interstitial matrix and its components. InterstitialMatrixProcess jps 24 Aug. 2011 IntraentityTransport is a Transport of an entity from one place within a containing object to another place within the same object. For example, Movement of an mRNA from the nucleus to the cytosol. IntraentityTransport jps 24 Aug. 2011 An IonChannel is a CBO:CellMembranePart that is a membrane bound protein that transfers ions across the Cell membrane against the natural diffusion gradient direction or transfers an ion across a membrane that would normally be impervious to the ion. MeSH: Membrane proteins whose primary function is to facilitate the transport of Molecules across a biological membrane. Included in this broad category are proteins involved in active transport ( BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS. GO: Enables the transport of a solute across a membrane via a narrow pore channel that opens in response to a particular stimulus. urn:miriam:obo.go:0022831 IonChannel jps 24 Aug. 2011 IsApoptotic is a CBO:CellState describing a biological state of apoptotic (programmed) dying of a cell at a particular time. This is a boolean (true/false) concept. IsApoptotic jps 24 Aug. 2011 IsDebris is a CBO:CellState describing a biologicaly dead cell at a particular time. IsDebris is used to represent the material left over after a cell dies. This is a boolean (true/false) concept. IsDebris jps 24 Aug. 2011 IsGrowing is a CBO:CellState describing a biological state of a cell that is growing at a particular time. This is a boolean (true/false) concept. IsGrowing jps 24 Aug. 2011 IsHypoxic is a CBO:CellState describing a biological state of oxygen deprivation of a cell at a particular time. This is a boolean (true/false) concept. Also known as anoxic or anoxia. IsHypoxic jps 24 Aug. 2011 IsNerotic is a CBO:CellState describing a biological state of dying of a cell at a particular time. This is a boolean (true/false) concept. See also IsApoptotic. IsNecrotic jps 24 Aug. 2011 IsQuiescent is a CBO:CellState describing a biological state of resting (minimal growth or other characteristic cellular processing) of a cell at a particular time. This is a boolean (true/false) concept. IsQuiescent jps 24 Aug. 2011 Isotropy is a GeometricalProperty describing the lack of a directionality of a directionally dependent quality of the object. This is the opposite of CBO:Anisotropy. Isotropy jps 24 Aug. 2011 KineticProperty is a CBO:PhysicalObjectQuality describing a kinetic characteristic of an object. urn:miriam:opb:'Kinetic manifestation' KineticProperty jps 24 Aug. 2011 A LJ_6_12Energy function is a CBO:EnergyFunction describing the mathematical form used to define a Leonard-Jones energy potential used to calculate a particular energyQuality. The equation is of the form E = e((rm/r)^12 - 2(rm/r)^6), where e is the depth of the potential well, rm is the value of the quality at which the potential is a mimimum and r is the current value of the quality. LJ_6_12Energy jps 24 Aug. 2011 LateralPart is a CBO:CellRegion that is between the CBO:BasalPart and CBO:LateralPart. LateralPart jps 24 Aug. 2011 A LinearEnergy function is a CBO:EnergyFunction describing the mathematical form used to define a linear relationship used to calculate a particular energyQuality. The equation is of the form E = mX + b, where m is a scaling constant, X is the value quality of a particular physical object and b is an offset. A LinearEnergy fucntion is often used to describe the energy of adhesions between, for example, two cells. For cell-cell adhesion m might represent the cell type(s) specific adhesion energy and X the contact area between the two cells. LinearEnergy jps 24 Aug. 2011 Location is a GeometricalProperty of a mathematical point. Depending on the CBO:Dimensionality of the System this may have one, two or three dataProperty values. AKA: position Location jps 24 Aug. 2011 Mass is a CBO:PhysicalObjectQuality describing the Mass of the object. PATO:0000125 urn:miriam:opb:'Discrete solid Mass' Mass jps 24 Aug. 2011 MechanicalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the physical behavior of objects. MechanicalProperty(ies) are intrinsic to the object. MechanicalProperty jps 24 Aug. 2011 MedialPart is a CBO:CellRegion located near the center of the Cell. MedialPart jps 24 Aug. 2011 Meiosis is a CellDivision specific to meiotic cells. GO: A cell cycle process comprising the steps by which a cell progresses through the nuclear division phase of a meiotic cell cycle, the specialized nuclear and cell division in which a single diploid cell undergoes two nuclear divisions following a single round of DNA replication in order to produce four daughter cells that contain half the number of chromosomes as the diploid cell. Meiotic division occurs during the formation of gametes from diploid organisms and at the beginning of haplophase in those organisms that alternate between diploid and haploid generations. urn:miriam:obo.go:0007126 Meiosis jps 24 Aug. 2011 MembraneReceptor is a CBO:CellMembranePart that is a protein embedded in the CellMembrane that interacts with extracellular Molecules. Binding (or occupancy) of the receptor results in a signal to the Cell. A protein Molecule (or assembly of proteins) that is permanently attached or firmly anchored in the plasma membrane via its hydrophobic domains interacting with the membrane phospholipids which can transfer information from the Cell exterior to its interior. MembraneReceptor jps 24 Aug. 2011 A MinimizationAcceptanceFunction is a CBO:EnergyFunction:AcceptanceFunction describing an acceptance criteria that requires that the energy of the new state is less than the energy of the previous state. MinimizationAcceptanceFunction jps 24 Aug. 2011 Mitosis is a CellDivision resulting in the Creation of two daughter cells from a single parent cell. Mitosis is specific to eukaryotic cells. GO: A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, Mitosis produces two daughter nuclei whose chromosome complement is identical to that of the parent cell. urn:miriam:obo.go:0007067 Mitosis jps 24 Aug. 2011 A MolecularField is a CBO:Field class for the description of moleules (or sets of molecules) that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a MolecularField may be described as having a position dependent concentration or density function. Unlike a CBO:Cell, a MolecularField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) A MolecularField may be restricted to a particular region or part of a physical object (CBO:PhysicalEntityType:CorpuscularEntity or CBO:PhysicalEntityType:ContinousEntity), such as the case of a cell membrane bound receptor molecule distributed on the cell membrane of a particular cell (a CorpuscularEntity). Or, a portion of a chemical field distributed across the interstitial space of a region. MolecularField subclass of: BFO:snap:object jps 24 Aug. 2011 MolecularTargeting is an IntraentityTransport in which a molecule is actively directed from one place in a cell to another. urn:miriam:obo.go:0006605 MolecularTargeting jps 24 Aug. 2011 Molecule is a CBO:BioEntityType class OPB: ...that is a polyatomic entity. urn:miriam:opb:'Molecule' Molecule jps 24 Aug. 2011 MoleculeBarrierCrossing is a MoleculeProcess describing the transfer of a molecule across a bona fide boundary such as a basement membrane or a cell wall. MoleculeBarrierCrossing jps 24 Aug. 2011 MoleculeChange is a MoleculeProcess that results in a phenotypic change in the molecule. For example, changes in the ionization state of an acid. MoleculeChange jps 24 Aug. 2011 MoleculeCreation is a MoleculeProcess that results in the Creation of a new molecule or an increase in a molecule's concentration. MoleculeCreation jps 24 Aug. 2011 MoleculeDeletion is a MoleculeProcess that results in the Deletion of a molecule, or a decrease in a molecule's concentration. MoleculeDeletion jps 24 Aug. 2011 MoleculeDiffusion is a MoleculeProcess in which a molecule passively diffuses through the medium, a cell cytosol of the interstitial space. For Diffusion across a bone fide boundary see CBO:MoleculeBarrierCrossing. MoleculeDiffusion subclass of: BFO:span:fiat_process_part jps 24 Aug. 2011 MoleculeMoleculeAdhesion is a MoleculeProcess that describes the interaction Energy (or interaction equilibrium) between a pair of molecules. The molecules may be of the same or different types. One or both of the molecules may be associated with another object. For example, the adhesive interaction between a pair of cellular adhesion molecules each located (embedded, bound) to the cell membranes of different cells. MoleculeMoleculeAdhesion jps 24 Aug. 2011 MoleculeProcess is a CBO_Process that involves a molecule. MoleculeProcess subclass of: BFO:span:process jps 24 Aug. 2011 Movement is a FundamentalPhysicalProcess resulting in the change in location or Shape of a physical object. Movement subclass of: BFO:span:fiat_process_part jps 24 Aug. 2011 MovementField is a CBO:PhysicalObjectProperty describing the movement of a physical object or aggregate of physical objects. For example, blood flow through a blood vessel is a MovementField capable of carrying physical objects such as cells. MovementField jps 24 Aug. 2011 Necrosis is a CellDeath caused by a lack of nutrient, physical process (such as heat or mechanical disruption) or toxin. PATO:0000647 Necrosis jps 24 Aug. 2011 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. urn:miriam:obo.fma:63840 urn:miriam:obo.go:0005634 Nucleus jps 23 Jul. 2012 OpenAlea is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. OpenALea is targeted to plant modeling. See http://openalea.gforge.inria.fr/dokuwiki/doku.php?id=openalea OpenAlea jps 23 Jul. 2012 OpenSourceModelPlatform is a CBO:ComputationalPlatformQuality class for compuational platforms which are open source. OpenSourceModelPlatform jps 24 Aug. 2011 OrganismalRegion is a CBO:GeometricalEntity class for regions of an animal. OrganismalRegion subclass of: BFO:snap:fiat_object_part jps 24 Aug. 2011 Orientation is a CBO:GeometricalProperty describing the directionality of a quality of an object. The directionality of the Orientation may be described in terms of the CBO:System axis or Isotropy of the objects local environment or by the Isotropy of the object itself. Orientation jps 23 Jul. 2012 OtherComputationalPlatform is a CBO:ComputationalPlatform class describing a particular compuational platform for preforming multicell modeling. This is a "cover-all" class for platforms which do not have a specific name. OtherComputationalPlatform jps 23 Jul. 2012 OtherPublicationReference is a CBO:ComputationalPlatformQuality class for computational platforms referenced only by a literature citation. OtherPublicationReference jps 24 Aug. 2011 PatternTexture is a CBO:Texture consisting of a positionally repetitive Texture description. PatternTexture jps 24 Aug. 2011 PhenotypicChange is a FundamentalPhysicalProcess resulting in the change of type of an object. PhenotypicChange applies to both the normally defined phenotypic change of a cell and also includes molecular changes such as ionization. PhenotypicChange jps 24 Aug. 2011 A PhysicalEntityType is a CBO_Object class of physical objects. For example, a Cell, a basement membrane of a diffusible Molecule. urn:miriam:dummy:1 urn:miriam:dummy:2 urn:miriam:dummy:3 PhysicalEntityType subclass of: BFO:snap:quality jps 24 Aug. 2011 A PhysicalObjectQuality is a CBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) of the qualities of physical objects. BFO uses QUALITY, OPB uses PROPERTY. For example, quality is a characteristic of a physical object such as Location, Volume, Energy, type etc. PhysicalObjectQuality subclass of: BFO:snap:quality jps 24 Aug. 2011 PoissonRatio is a CBO:MechanicalProperty that describes the ratio, when an object is stretched, of the contraction or transverse strain (perpendicular to the applied load), to the extension or axial strain (in the direction of the applied load). PoissonRatio jps 24 Aug. 2011 PressureMechanical is a CBO:MechanicalProperty describing the barometric pressure of an object or Location in space. PressureMechanical jps 24 Aug. 2011 Protrusion is a GeometricalProperty describing an extension from an otherwise simpler CBO:BodyShape description. For example, a transient pseudopodia or a persistent neuronal axon. Protrusion jps 24 Aug. 2011 A Pseudopodium is a CBO:CellMembraneLocalStructure characterized by a transient extension of the Cell wall. MeSH: A dynamic actin-rich extension of the surface of an animal Cell used for locomotion or prehension of food. GO: A temporary Protrusion or retractile process of a Cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding. AKA: pseudopodia urn:miriam:obo.go:0031143 Pseudopodium jps 24 Aug. 2011 A Pump is a CBO:CellMembranePart that is a membrane bound protein that transfers ions and Molecules across the Cell membrane against the natural diffusion gradient direction. MeSH: Membrane proteins whose primary function is to facilitate the transport of Molecules across a biological membrane. Included in this broad category are proteins involved in active transport ( BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS. MeSH: D12.776.157.530 MeSH:'Membrane Transport Proteins' Pump jps 24 Aug. 2011 Random is a CBO:StatisticalProperty class that describes a quality of randomness to an object or process. Random jps 24 Aug. 2011 An RateFunction is a CBO_Object (BFO:snap:continuant:dependent_continuant:specifically_dependent_continuant:quality) describing the mathematical form used to define a changes in a particular Quality as a function of time. RateFunction subclass of: BFO:snap:quality jps 24 Aug. 2011 Rotation is a Movement resulting in a change in orientation of an object. Rotation jps 24 Aug. 2011 A SecondOrderRate is a CBO:RateFunction describing the mathematical form used to define a second order rate of change of a quality with respect to time. For quality n (and m); dn/dt=k*n^2, or dn/dt=k*n*m, where k is the rate constant. SecondOrderRate jps 24 Aug. 2011 Shape is a GeometricalProperty describing the spatial (2 or 3 dimensions) of a region of spaced occupied by an object at a particular instant in time. PATO:0000052 urn:miriam:opb:'bounded Volume Shape' Shape jps 24 Aug. 2011 ShapeChange is a FundamentalPhysicalProcess resulting in the change in the Shape, including extents, of an object. ShapeChange subclass of: BFO:span:fiat_process_part jps 24 Aug. 2011 A SpatialExclusive quality is a CBO:PhysicalObjectQuality for objects that can be the only occupier of a particular point or region of space for the set of all objects with the SpatialExclusive quality. For example, CBO:Cell and medium (CBO:ExtracellularFluid) generally will individually have the SpatialExclusive quality and hence individual cells and medium cannot occupy the same region of space at the same time. Objects without the SpatialExclusive quality, for example a chemical field (CBO:DiffuseEntity, CBO:SoluteMaterialType), can overlay objects with the SpatialExclusive quality. That is fields and solutes do not generally have the SpatialExclusive quality. SpacialExclusive jps 24 Aug. 2011 StatisticalProperty is a CBO:PhysicalObjectQuality class that includes a variety of parameters describing the statistical qualities of objects. StatisticalProperty are intrinsic to the object. StatisticalProperty jps 24 Aug. 2011 StiffnessMechanical is a CBO:MechanicalProperty that describes an elastic object's resistance to deformation by an applied force along a given direction. StiffnessMechanical jps 24 Aug. 2011 StructuralProcess is a CBO_Process (span:process) that results does not result in a change in the identity of the Object, but the Object does change in its DATA structure. StructuralProcess subclass of: BFO:span:process jps 24 Aug. 2011 SurfaceArea is a CBO:GeometricalProperty describing the scalar value of the object's surface area at a particular instant in time. urn:miriam:opb:'Area of surface region' SurfaceArea jps 24 Aug. 2011 SymmetricCellDivisionOrientedCleavagePlane is a Mitosis characterized by the Creation of two identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is oriented with respect to either the environment or the characteristics of the parent cell. SymmetricCellDivisionOrientedCleavagePlane jps 24 Aug. 2011 SymmetricCellDivisionRandomCleavagePlane is a Mitosis characterized by the Creation of two identical daughter cells from a single parent cell. In addition, the cleavage plane of the division process is randomly oriented with respect to both the environment and the characteristics of the parent cell. SymmetricCellDivisionRandomCleavagePlane jps 24 Aug. 2011 System is a CBO_Object that describes and includes the universe described by the model or experiment. In general cell instances and fields are "contained_In" (inverse of "contains") a CBO:System as opposed to "part_Of" a CBO:System since cells, fields, etc. may come and go during a simulation. System subclass of: BFO:snap:object jps 25 Jul. 2012 SystemBoundary is a SystemQuality that describes the edges (boundary) of a computational model. SystemBoundary jps 25 Jul. 2012 SystemExtent classes are SystemQualties the describe the extent of the model in two or three dimensions. SystemExtent can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents. SystemExtent jps 25 Jul. 2012 SystemExtentX is a are SystemExtent the describe the extent of the model in the X dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents. SystemExtentX jps 25 Jul. 2012 SystemExtentY is a are SystemExtent the describe the extent of the model in the Y dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents. SystemExtentY jps 25 Jul. 2012 SystemExtentZ is a are SystemExtent the describe the extent of the model in the Y dimension. SystemExtent classes can be expressed as a distance (e.g., 100uM) or in pixel or voxel extents. SystemExtentZ jps 25 Jul. 2012 SystemPeriodic is a SystemBoundary that describes the edges (boundary) of a computational model as being a periodic edge. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side. SystemPeriodic jpos 25 Jul. 2012 SystemPeriodicX is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the X-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side. SystemPeriodicX jps 25 Jul. 2012 SystemPeriodicY is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the Y-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side. SystemPeriodicY jps 25 Jul. 2012 SystemPeriodicZ is a SystemPeriodic that describes the edges (boundary) of a computational model as being a periodic edge (or face) that is perpendicular to the Z-axis. Objects that extend beyond a periodic edge are assumed to wrap around the model to the other side. SystemPeriodicZ jps 25 Jul. 2012 SystemPixel2DistanceScale is a SystemQualties that describes the relationship between the size of a voxel (or pixel) and a length measurement. In general, SystemPixel2Distance will point to a floating point number that, when multiplied by a number of pixels will return a distance. For example, a SystemPixel2DistanceScale=2um/pix indicates that each pixel is 2 micrometers wide. SystemPixel2DistanceScale jps 24 Jul. 2012 SystemQualities is CBO_Object class that describes the computational platform (suite of code or a standalone computational tool) and instantiation of a particular model. SystemQuality subclass of: BFO:snap:quality jps 25 Jul. 2012 SystemWall is a SystemBoundary that describes the edges (boundary) of a computational model as being an impenetrable wall. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall. SystemWall jps 25 Jul. 2012 SystemWallX is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the X-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall. SystemWallX jps 25 Jul. 2012 SystemWallY is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the Y-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall. SystemWallY jps 25 Jul. 2012 SystemWallZ is a SystemWall that describes the edges (boundary) of a computational model as being an impenetrable wall that is perpendicular to the Z-axis. Objects are not allowed to penetrate or extend beyond a SystemWall though they may interact with a SystemWall. SystemWallZ jps 19 Jul. 2012 A TemperatureField is a CBO:Field class for the description of the temperature that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a TemperatureField may be described as having a position dependent intensity function. Unlike a CBO:Cell, a TemperatureField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) A TemperatureField is a CBO:Field class for the description of the temperature that spans a particular extent at a particular time but is not spatially exclusive and may, and generally does, overlap with other PhysicalEntityTypes at a particular time. In addition, a TemperatureField may be described as having a position dependent intensity function. Unlike a CBO:Cell, a TemperatureField is geometrically divisible without a fundamental change in characteristics or identity. (Division down to the scale of an individual molecule is outside the distance scale covered by the CBO.) TemperatureField jps 24 Aug. 2011 TemporalAge is a CBO:Age that describes the time interval between the time of the objects creation and the current time. PATO: A time quality inhering in a bearer by virtue of how long the bearer has existed. urn:miriam:obo.pato:0000011 TemporalAge jps 24 Aug. 2011 TemporalEntity is a CBO_Processt that OPB: ...is a moment or span of time. urn:miriam:opb:'temporal entity' TemporalEntity subclass of: BFO:span:connected_temporal_region jps 24 Aug. 2011 OPB: ...is a point in time. urn:miriam:opb:'temporal instant' TemporalInstant subclass of: BFO:snap:TemporalInstant jps 24 Aug. 2011 OPB: ...is a period of time bounded by two temporal moments (that may be the same moment). urn:miriam:opb:'temporal interval' TemporalInterval subclass of: BFO:snap:TemporalInterval jps 24 Aug. 2011 TensionMechanical is a CBO:MechanicalProperty that describes the pulling force exerted on an entity (a stretching or distorting force). TensionMechanical jps 24 Aug. 2011 Texture is a CBO:GeometricalProperty describing the characteristics of a surface Texture. Texture jps 24 Aug. 2011 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) urn:miriam:obo.go:0005923 TightJunction jps 24 Aug. 2011 Translation is a Movement resulting in a change in the spatial location of an object. Translation jps 24 Aug. 2011 Transport is a CBO_Process describing the general case of Movement of an object across space, a fiat boundary or a bona fide boundary. For example, Transport of oxygen from the outside of an animal to the inside of the animal. Note that there are specific terms elsewhere for Transport across cell boundaries (CBO:CellImport and CBO:CellExport) and for molecules (CBO:MoleculeBarrierCrossing). TransportProcess jps 24 Aug. 2011 UniformTexture is a CBO:Texture consisting of a positionally independent Texture description. UniformTexture JPS 10/25/2012 VTK_FileName is a CBO:SystemQuality:VTK_Quality giving a full file name (which may or may not by a URI, IRI, or fully qualified path+filename to the local file system) for a snapshot VTK file giving the cells, cell extents, cell types, fields etc of the model at a particular point in simulated time. Recommended file name structure: ModelName_TimeStamp_runID_time.vtk where; "ModelName" is the same string used for the CBO_System instant that encompasses the entire model. This should also be the name of the OWL ontology for the model. "TimeStamp" is the wall clock time that the simulation that created the VTK was started. Resommended format of YYYYMMDDhhmmss. "runID" is an additional qualifier to differentiate multiple runs of the same model that may have been started at the same wall clock time. Often this may be assumed to be "1". "time" is the simulated time for this particular snapshot of the system. It is recomended that the "time" be a zero filled string, for example 000000010, for the file created after the simulated time of 10*VTK_FileTimeStep in the simulation. VTK_FileName JPS 10/25/2012 VTK_FileRoot is a CBO:SystemQuality:VTK_Quality giving the root name for the VTK files associated with the particular model. VTK_FileRoot JPS 10/25/2012 VTK_FileTimeStep is a CBO:SystemQuality:VTK_Quality that carries the time scale for the VTK files. The value of the VTK_FileTimeStep instance, when multiplied by it's units and then by the numeric part of the VTK_FileName gives the simulated time offset from the start of the simulated time. For example; VTK_fts instanceOf VTK_FileTimeStep VTK_fts hasFloatValue 100 VTK_fts hasUnit UO:milliseconds and the VTK file name "MySim_20121024112233_1_000250.vtk is understood to represent the simulated time of (100)(250)milliseconds = 25 seconds Often the instance of VTK_FileTimeStep will have a numeric value of 1 and most of the time information will be carried by the units (seconds, minutes, days, ...) and the numeric part of the VTK file name (000250 in the example above). VTK_FileTimeStep jps 10/25/2012 VTK_InitialCondition is a CBO:SystemQuality:VTK_Quality that points at a VTK file giving the initial configuration of the model. Typically this configuration represents time=0 in the model. VTK_InitialCondition JPS 10/29/2012 VTK_Quality is a CBO:SystemQuality that includes classes for specificying the name, ilneage and time of a VTK snap(shot) of the simulation. VTK_Quality jps 24 Aug. 2011 Ventral is a CBO:OrganismalRegion characteristic of the front of an object relative to the body it is contained in. EFO: Ventral is a geometric modifier describing parts pertaining to the front or anterior of any structure for example Ventral striatum. Ventral jps 24 Aug. 2011 Volume is a GeometricalProperty describing the total Volume of spaced occupied by the object at a particular instant in time. PATO:0000918 urn:miriam:opb:'Volume of Volume region' Volume jps 24 Aug. 2011 VolumeChange is a FundamentalPhysicalProcess resulting in a change, an increase or decrease, in the Volume occupied by an object. VolumeChange subclass of: BFO:span:fiat_process_part jps 24 Aug. 2011 A VolumeEnergy is a CBO:EnergyQuality representing the energy associated with a given volume entity. VolumeEnergy jps 24 Aug. 2011 YieldingThreshold (Yield stress threshold, Y) is a CBO:MechanicalProperty describing the rheological yield stress of an object. YieldingThreshold jps 24 Aug. 2011 YoungsModulus (Young's modulus, tensile modulus) is a numerical CBO:PhysicalObjectQuality indicating the measure of stiffness in a material. It is defined by the ratio of stress in a unit area of substance to the resulting deformation (strain). This allows the behavior of a material under load (such as bone) to be calculated. (From Mesh) YoungsModulus jps 24 Aug. 2011 A ZerothOrderRate is a CBO:RateFunction describing the mathematical form used to define a constant rate of change of a quality with respect to time. For quality n; dn/dt=k, where k is a constant. ZerothOrderRate CBO_Process is the top level CBO class for processes and process qualities. CBO_Object is BFO:continuant (endurant). CBO_Process is euivalent to BFO:occurrent. Note that OWL DL does not support antiymetric properties so those have been removed from the OBO Relation defintiions for the properties.