]>
wikipedia
synonym
IUPACclass
hasPropertyAttribute
...that relates a property to a property attribute
hasPartOfProcess
hasDimension
...that relates a property to the dimension of the property
hasSpatialCoordinate
...that relates a property to the spatial coordinate system in which an instance of the property is defined
hasMathForm
...that relates a property to the mathematical form of an instance of the property
occursDuring
...that relates an occurrence of a process to the temporal interval during which it occurs
hasParticipant
...that relates an instance of a dynamical entity to an instance of the occurrence of a process in which the dynamical enity participates
participatesIn
...that relates an instance of the occurrence of a process to an instance of a dynamical entity that participates in the process
occurenceOf
...that relates an occurrence to the process class of which it is an instance
subProcessOf
hasSubProcess
hasPropertyPlayer
hasPosPropertyPlayer
hasPart
successorOf
successorTo
partOf
hasNegPropertyPlayer
deferred object prop
hasPropertyAttribute deferred
hasPropertyValue
hasTemporalPartOfProcess
hasStructuralPartOfProcess
hasSourceParticipant
...in which the participant is the source of the quantity that flows during the process
hasSinkParticipant
...in which the participant is the sink or destinatlon of the quantity that flows during the process
is_conserved
...that is an attribute of a physical quantity that can neither be created or destroyed.
hasMediatorParticipant
..in which the entity is the location or mechanism that mediates the process but is unchanged in the process
hasProcessDependency
...that attributes a process dependency to a process
hasProcessDependency
isDependencyForProcess
hasDependencyPlayerProperty
hasThermodynamicPlayer
hasDynamicalPlayer
hasConstitutivePlayer
...that is a algebraic relation that relates the values of dynamical properties in a constitutive dependency
hasFlowPlayer
hasAmountPlayer
hasMomentumPlayer
hasForcePlayer
hasKineticEnergyPlayer
hasPotentialEnergyPlayer
hasEnergyFlowPlayer
hasFlowSource
hasFlowSink
hasForceSource
...that tends to accelerate or move an entity toward the origin of its spatial location
hasForceSink
...that tends to accelerate or move an entity away from the origin of its spatial location
hasResistanceProportionality
hasCapacitanceProportionality
hasInductanceProportionality
hasConstitutiveProportionality
...that is a proportionality factor
hasConstitutiveFunction
...that is an non-proportional mathematical function
propertyOf
...that relates an instance of a property to an instance of the physical entity in which the property inheres
hasThermodynamicEntity
...that relates an instance of a thermodynamic to the instance of a dynamical entity in which the thermodynamic inheres.
hasProperty
...that relates an instance of a physical entity to an instance of a property that inheres in the entity
hasPhysicalDomain
...that relates a physical property to the domain of the entity of which it is a property
hasSpatialScope
...that relates a property to the spatial scope for which an instance of the property is defined
hasBoundary
boundaryOf
isThermodynamicEntityOf
...that relates an instance of a dynamical entity to an instance of a thermodynamic entity that inheres in the dynamical entity.
synonym
displayName
discussion
Information entropy amount
Dynamical rate property
Rate properties represent the FORCE DIFFERENTIAL or the RATE OF FLOW of material, charge, energy, or information across a boundary separating one physical entity from another via some pathway. Examples:
1) fluid flow rate through a tube or vessel (dimensions of volume/time)
2) charge flow rate of an electrical current through an ion channel or wire (dimensions of charge/time or current)
3) chemical flux through a reaction kinetic pathway (dimensions of amount/time typially moles/sec or concentration/time)
Thus, as differentials or flow rates, rate properties must be distinguished in terms of source, sink, and (perhaps) mediating pathway
In some representations, rate properties are commonly termed "through variables" in that they are measures of the rate of flow through some process. In the PhysSys ontology and in Karnopp, etal, rate properties are simply termed "flows" (f) which conflates the flow of stuff with its rate measure; see:
1. Borst, P., H. Akkermans, and J. Top: Engineering ontologies. Int. J. Human–Computer Studies 1997. 46:365-406.
2. Karnopp, D., D.L. Margolis, and R.C. Rosenberg, System dynamics: a unified approach. 2nd ed. A Wiley-Interscience Publication1990, New York: Wiley.
A dynamical property that is the temporal differential of a dynamical state property.
Heat conduction dependency
1
Imaginary numerical form
Complex numerical form
Magnetic flux linkage
1
Chemical conductance
1
Solid conductance
1
Spatial differential dependency
Portion of potential energy
A portion of energy attributed to a quantitative difference in the values of state properties of two entities.
Fluid conductance
1
Heat conductance
1
Portion of kinetic energy
A portion of energy attributed to the motion of material or electrical charge.
Magnetic field
A potential energy field are produced by moving electric charges and/or the intrinsic magnetic moments of elementary particles that exerts force on moving electrical charges and magnetic dipoles.
Electrical conductance
1
Boltzmann constant
...that is the proportionality of the energy of a particle per rise in absolute temperature; equal to the Gas constant divided by Avogadro's constant.
Boltzmann constant
Diffusion kinetic domain
Dynamical domain for which physical entities are portions of particles and processes are the tranport of particles from one spatial location to another.
Partial gas pressure
Electromagnetic constant
Portion of entropy
A themodynamic entity that is a portion of thermodynamic entropy
Portion of energy
A themodynamic entity that is a portion of energy inhering in a dynamical entity
Portion of fluid kinetic energy
A portion of kinetic energy attributed to the motion of a portion of fluid.
Portion of solid kinetic energy
A portion of kinetic energy attributed to the motion of a solid.
Portion of fluid potential energy
Portion of elastic potential energy
Portion of chemical potential energy
Portion of thermal potential energy
Portion of diffusion potential energy
Portion of electrical potential energy
Portion of magnetic potential energy
Portion of magnetic inductive energy
A portion of kinetic energy attributed to an electrical current.
Temporal origin
...that is designated as the origin of a temporal coordinate system
Translational momentum
Translational momentum
Mechanical force
1
...that accelerates or deforms solid entities; measured as ratio of ratio the acceleration of the entity divided by its mass (Newton's Law) or as the deformation of the entity divided by its stiffness (Hooke's Law)
Electromagnetic field
A potential energy field that is the combination of an electrostatic field and a magnetic field.
Chemical capacitance
1
Total energy amount
Conductance
...is the derivative of flow versus force in a resistive dependency; the reciprocal of kinetic resistance property
Discrete scope
A physical property has discrete scope if its value applies to the entire spatial region of a physical entity.
Accumulation of material
...is the law that states that the net rate of material traversing the Boundary of a Physical entity is exactly equal to the gain or loss of material within the Boundary.
...that is the amount of material
Continuum scope
A physical property has continuum scope if it's values vary smoothly throughout a spatial region occupied by the physical entity that has the physical property.
Event rate
A property of tracjectory that is the number of events occuring during a temporal interval of an event trajectory divided by the duration of the temporal interval.
frequency
event frequency
Electrical resistivity
1
Bending displacement
Constitutive proportionality
A constitutive dependency property that is a proportionality factor in a mathematical expression by which values of dynamical property players are proportional to each other; i.e., having a linear relationship that intersects the origin; a characteristic of "ideal" dynamical elements
ideal property
By rights, a conductance (or its inverse, resistance) is a constitutive property of an electrochemical flow process (see: OPB:Electrical conductance). However, we classify ionic conductances as dynamical amounts because they are, ultimately, determined by the aggregates of the molecular conformational states of the ionic channels mediating the electropotential ion transport. Thus, these classes are suitable for representing the conductance ion channels at a moment in time, as well as the conductance of ion channel as characterized for standard conditions and by which the channel is named (e.g., "250 pS Ca-dependent K-channel")
Constitutive proportionalities apply only to those constitutive dependencies that can be expressed by which the dependent property is proportional to the independent property. Any other algebraic form of the dependency may have specifially-defined parameters (e.g., offsets, rate parameters). Given the creativity and license of modelers for creating the best fit to constitutive dependencies, the parameters of such non-proportional dependencies must be annotated by some local mechanism that does not depend on OPB classifications.
Constitutive proportionalities are approximations to dependencies for which a first-order, linear approximation is sufficient for the purposes of analysis. Piecewise linear approximations may apply over a limited range of dynamical property values. In general, various algebraic functions may be required using one or more parameters to fit observed dependency relationships. Given the range of possible constitutive dependencies, OPB defers representing such possibilities on a case-by-case basis for specific use-cases.
Non-proportionality constants include coefficients and parameters required to characterize linear and nonlinear dependencies that are not simple proportionalities. Some may constitutive dependencies may include dynamic modeling schemes with internal dynamic states (e.g., the "gating variable" of Hodgkin-Huxley ion gating equations). We will treat such properties as "internal" to the constitutive dependency, shielded from other entities in the system and known solely as hypothetical constructs derived as constitutively observed dynamic phenomena. Thus, HH gating variables will be classified as properties of constitutive dependencies which are also subclasses of Dynamical property without, however, declaring a Dynamical entity of which it is a property.
Important to realize that MM params, HH params, etc. are all derived and asserted by virtue of curve-fits to the directly observed attributes of a system; number of gating particles and their respective states is entirely inferential by best fits and, so, are no more physically real than any other coefficient or parameter.
Chemical amount
1
A material amount that is the temporal integral of a chemical flow
Chemical amount
Polar coordinate system 2D
2D-Polar coordinate system
Length dependency
Geometric form
...that is the mathematical structure of a property value.
Cardinality dimension
...that is the number of entities in a set of entities
N
number of entities
count
Unitary dimension
...that is a dimension that is equivalent to an integer = 1.
1
Fluid momentum
1
...is the temporal integral of a Fluid pressure; also the Fluid flow times the mass density of a Portion of fluid
Pressure momentum
Fluid volumetric elastance
1
Chemical elastance
1
Mechanical velocity
1
Flow rate property that is the temporal derivative of a solid displacement
Thermodynamical property
1
A physical property that is an attribute of an instance of dynamical entity or an occurrence of a dynamical process whose value is the amount of the portion of thermodynamic energy inhering in the entity or is is the rate at which energy is flowing during an occurrence of a dynamical process.
Solid elastance
1
Shear capacitance
Kinetic energy amount
Potential energy amount
Real numerical form
Electrical elastance
1
Particle diffusive elastance
Faraday constant
...is the amount of electric charge per mole of electrons;
Faraday constant
Chemical potential flow dependency
1
...that is the dependence of a chemical flow rate on the differential of the chemical potentials of reactants (e.g., substrates, products) in a chemical reaction.
...that is the dependence of chemical flow rate on the differential of the chemical potentials of the reacting participants
Heat elastance
Gravitational field
Gravitational field
Potential energy field in which material entities exert an attractive force on each other that proportional to the product of their masses and inversely to the square of the distance separating them.
Spatial coordinate basis
...that is a spatial coordinate system.
Transformer modulus
1
...is the nondimensional ratio of the magnitudes of kinetic property that are players in a transformer dependency
Thermodynamic entropy amount
Mass volumetric density
...that is the ratio of the amount of material in a 3-dimensional spatial region to the volume of that region.
Fluid inertia
1
fluid inductance
...that is the mass of a portion of fluid that is a participant in an "ideal" fluid inductance process
fluid inertance
Fluid viscosity
1
Time dimension
Time
defined as "time", a BASE dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162. See:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC61354/pdf/0060151.pdf
and as 'time', a BASE dimension in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", See:
http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
t
Accumulation of momentum
...that is the accumulation of momentum due to net of forces acting on a spatially discrete material dynamical entity
Shear force
Shear force
Tensile force
Tensile force
Inertance
...is the derivative momentum versus force in an inductive dependency
Amount property
A dynamical state property that is the temporal integral of a flow rate
Bending velocity
Standard gravity constant
... is the nominal acceleration due to gravity at the Earth's surface at sea level; http://en.wikipedia.org/wiki/Standard gravity
Cartesian coordinate system 2D
2D-Cartesian coordinate system
Physical property
Physical properties classes are categorized according to the analytical domain in which they have meaning. For example, OPB:Dynamical properties apply to the domain of dynamical systems for which the concepts of thermodynamics have meaning, whereas OPB:Spatial properties apply to spatial and geometrical concepts that have no thermodynamic meaning.
The representations of OPB:Information content and OPB:Statistical properties are deferred pending appropriate use-case needs.
A physical attribute of an instance of a physical entity, an occurrence of a physical process, or a physical dependency that has a quantitative value that is measurable by a physical device or method, or is computable from such values.
http://goldbook.iupac.org/list_goldbook_quantities_defs_A.html
Electrical resistance
1
Fluid volume
1
Fluid volume
An amount property that is the temporal integral of a fluid flow
Temporal instant
...is a point in time
Fluid flow resistance
1
Angular momentum
Angular momentum
Temperature dimension
T
thermodynamic temperature
defined as "temperature", a BASE dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162.
and as 'thermodynamic temperature', a BASE dimension in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", see: http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
temperature
Property dimension
OPB:Physical dimension subclasses are a set of base dimensions as identified by either:
IUPAC (International Union of Pure and Applied Chemistry) in their "Green Book" [1] as summarized in: "Concise Summary of Quantities, Units and Symbols in Physical Chemistry" [2]. IUPAC "base quantities" are:
length, time, mass, electric current, thermodynamic temperature, luminosity, amount of substance.
UCUM (Unified Code for Units of Measure [3]) defines an alternative (but ultimately, equivalent) set of base "quantity kinds" [4] as:
length, time, mass, charge, temperature, luminous intensity, angle.
In either system, a coherent set of "working" property dimensions can be derived for for other physical properties as products of base dimensions raised to integer (both positive and negative) powers (e.g., velocity = length•time-1, pressure = force•length-2, volume = length+3).
Resources:
[1] http://www.iupac.org/home/publications/e-resources/nomenclature-and-terminology/quantities-units-and-symbols-in-physical-chemistry-green-book.html
[2] http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf
[3] http://unitsofmeasure.org/trac/
[4] http://jamia.oxfordjournals.org/content/jaminfo/6/2/151.full.pdf
See also:
Schadow, G. and C.J. McDonald. The Unified Code for Units of Measure.; Available from: http://aurora.regenstrief.org/UCUM/ucum.html
...is a fundamental coordinate of a physical property upon which its units of measure are based
Chemical resistance
1
Solid capacitance
1
solid complliance
mechanical compliance
Solid momentum
1
Solid momentum
...is the temporal integral of a Solid force; also the Solid-velocity times the mass of a solid Material physical entity
Cardinality of set
A statistical property that is the number of individuals in a set
Electrical flow dependency
1
...that is the dependence of the flow rate of electrical charges (electrical current) on a electrical potential differential.
Fluid flow dependency
1
Mechancal velocity dependency
1
Diffusion-gradient rate dependency
1
...that is the dependence of a particle flow rate on the differential of the amounts of portions of one kind of particles across a flow boundary separating the portion
Ficks law
Fick's law of diffusion
Solid viscous resistance
1
Bending capacitance
Mass dimension
defined as "mass", a BASE dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162.
and as 'mass', a BASE dimension in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", see: http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
m
Mass lineal density
...that is the ratio of the amount of material in a 2-dimensional spatial region to the volume of that region.
Tensile capacitance
Solid mechanic domain
Dynamical domain in which the physical entity is a discrete structure.
Heat transfer resistance
1
Heat flow rate
1
Flow rate property that is the temporal derivative of an amount of heat.
heat flux
Charge dimension
ionic charge
defined as 'charge' dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162.
and as 'electric charge', a dimension DERIVED from 'electric current' in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", see: http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
electrical charge
Q
Statistical property of value distribution
...that is a
Electrochemical domain
Dynamical domain in which the physical entity is a portions of ions.
Newtonian gravitational constant
...that is the constant of proportionality that relates the gravitational force between two Material physical entities as the product of the masses of the entities divided by the distance between the entities; <http://en.wikipedia.org/wiki/Gravitational constant>
Newtonian gravitational constant
Electric constant
formerly dielectric constant
Elastance
...is the derivative of force versus displacement in a capacitive dependency; reciprocal of capacitance property
Resistance
...is the derivative of force versus flow in a resistive dependency; reciprocal of kinetic conductance property
Variance
Diffusion resistance
1
Torsional capacitance
Angle dimension
defined as 'angle' BASE dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162. See:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC61354/pdf/0060151.pdf
and as 'plane angle', a DERIVED dimension per:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", in http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
plane angle
ang
theta
Chemical flow rate
1
Flow rate property that is the temporal derivative of the amount of chemical
Dynamical domain
Physical domain that applies to a single class of dynamical entity.
Chemical bond
Chemical bonds are represented in a cursory fashion pending use-cases involving molecular dynamic analyses and modeling for which more detailed annotations will be required.
In the interim, a bond is an abstraction that represents ONLY the energetics of an attractive interaction between entities; i.e., the bond is manifested as a minimum energy state (usually as a function of entity-entity distance). Thus, a bond can be defined irrespective of the physical mechanism that mediates the bond such as electron-sharing or the extracellular matrix between cells.
A potential energy field that is an attractive interaction between atoms that allows the formation of chemical substances that contain two or more atoms
Translational velocity
Mass areal density
...that is the ratio of the amount of material in a 1-dimensional spatial region to the volume of that region.
Process event trajectory
...that is a temporally-ordered series of process events that occur during a process
Material dynamical entity
A dyanamical entity that is composed of matter; i.e., atoms
Per BFO2.0: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part.
Capacitive storage process
...that is a Capacitive dependency
Temporal duration
duration
Temporal property that is the amount of time between two temporal instants that are boundaries of a temporal interval
time span
Translational displacement
Translational displacement
Thermodynamic domain
Physcal domain that applies to a portion of thermodynamic energy.
Potential energy field
An energy field that is the distribution of potential energy due to the separation of material, charge, or magnetic monopoles
Constitutive transactor coefficient
...that is the proportionality between two dynamical properties in a transactor dependency
Temperature
1
A force property that drives the flow of heat energy from one portion of heat to another.
Area
area
surface area
A spatial base amount that is the two-dimensional extent of a surface region.
Fluid flow rate
1
volume flow rate
VolumetricFlowRate - Volume of fluid passing a point in a system per unit of time.
http://www.unitsofmeasurement.org/apidocs/index.html
volume flow
Flow rate property that is the temporal derivative of a fluid volume
One dimensional spatial coordinate basis
...that is comprised of a single spatial dimension
Correlation coefficient
A statistical property that is a measure of the statistical correlation between computed and/or measured property values.
Charge flow rate
1
Flow rate property that is the temporal derivative of an amount of portion of electrical charge.
current
charge flow
electrical current
Luminosity dimension
defined as "luminous intensity", a BASE dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162.
and as 'luminous intensity', a BASE dimension in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", see: http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
lum
luminous intensity
Solid displacement
1
...is the temporal integral of a Solid velocity
Volumetric capacitance
1
volumetric compliance
fluid compliance
vascular compliance
compliance
Shear displacement
Shear displacement
Heat capacitance
1
Chemical concentration
The molar amount of a portion of molecules normalized to the spatial amount of the spatial region occupied by the molecules
Energy flow process
A rate process that proceeds according to a resistive dependency and dissipates energy as heat
Property value attribute
...that characterizes the spatial attributes, mathematical form, or unit of measure of the value of a physical property
Portion of fluid
A portion of material that has fluid kinetic properties.
Shear velocity
Cartesian 3D-coordinate system
Initial instant
...that is the first temporal instant in a temporal interval
Terminal instant
...that is the last temporal instant in a temporal interval
Geometrical dependency
...that is a dependency between spatial properties according to the science of geometry.
Magnetic constant
Magnetic constant
Chemical potential
1
that is the dynamical force differential that drives chemical kinetic reactions according to a force-driven dependency
"...gradients of Gibbs free energy represent the thermodynamic driving force for constant temperature and pressure (isothermal and isobaric) systems...typical of laoratory conditions and a reasonable approximation for most biological systems."
Isobaric, isothermal systems are also refered to "NPT" systems where N is the number of particles (participants), P, the pressure, and T, the temperature are held constant.
Beard, D.A. and H. Qian, Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge Texts in Biomedical Engineering. 2008: Cambridge University Press. p. 9
Gibbs free energy
G
Fluid kinetic domain
Dynamical domain in which the physical entity is a portion fluid
Point location dependency
Coupled flow dependency
1
A constitutive flow dependency in which the flow rates of two role-players are coupled to the respective forces of the role players according to the quantitative relationships: E1 = nE2, and nF1 = F2, where E and F are force and flow properties, respectively, of entities 1 and 2, and is a positive scalar transformer ratio..
The archetypical example of a transformer is the electrical tranformer of which there are no physiological examples. Here we generalize this class of dependencies to include transformations across dynamical domains according to subclass definitions and examples.
Statistical property
1
As with Informational properties, statistical properties are sketched in as placeholders for further development as use-cases require.
A physical property that is a property derived using the methods of descriptive statistics to characterize the distribution of the values physical properties of a set of physical entities
Temporal property
1
A physical property that is a measure of the occurrence of events within a temporal coordinate system.
Temporal location
A temporal property that is the amount of time between the origin of a temporal coordinate and a temporal Instant
Property value mathematical form
--- outsource this class to existing ontology??
...that is the mathematical form of an encoded datum or variable
Gas constant
...that is the proportionality of the energy of a substance per mole per rise in absolute temperature; the same as Boltzmann's constant times Avogadro's constant.
Gas constant
Charge amount
1
Electrical charge
An amount property that is the temporal integral of an electrical current
Mass
1
...that is the proportionality between momentum and velocity for a material entity; i.e., m = p/v given p = mv = ∫f dt; a definition of mass
solid inductance
Real-imaginary form
Gravitational constant
Constitutive state property of substance
...that is a physical property of matter or space whose value is invariant with respect to time
Chemical molar amount
1
Amount of a chemical that is the total amount of a portion of a chemical within a spatial region normalized to the molecular weight of the chemical.
Accumulation of charge
...that is the amount or number of electrical charges
...is the law that states that the net rate of electrical charge traversing the Boundary of a Physical entity is exactly equal to the gain or loss of electrical charge within the Boundary.
Alternatively, ...in which the amount of charge that inheres in a physical entity is invariant as the entity participates in a physical process
Vector form
...is a physical property whose value is expressed as a combination of a scalar and a spatial orientation in a spatial coordinate system.
Constitutive coupling proportionality
...that is a scalar proportionality of a constitutive coupling dependency between properties of two physical entities
constitutive property
Chemical kinetic domain
Dynamical domain for which physical entities are portions of moleculesand processes are chemical reactions by which of one kind of molecule is transformed into a different kind of molecule
Tensor form
...is a physical property whose value is a multidimensional array of scalars whose values are invariant under spatial coordinate transformation.
Statistical domain
Physical domain that applies to a set of physical analytical entities.
Portion of electrical charge
An Immaterial dynamical entity that is a set of quantal charges whose net charge is quantifiable by a continuous scalar quantity or an integer.
A portion of electrical charge represents the immaterial electrical charge itself and not the electron which is the material entity that bears the charge. Thus, electrical charges and electrical current flows can be calculated with out consideration for flow of the material entities that bear the charge.
Electrical capacitance
1
Temporal coordinate basis
...that is a temporal coordinate system.
Length dimension
defined as BASE dimension 'length' per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162.
and as 'length', a BASE dimension in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", see: http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
spatial displacement
span
L
displacement
Mean value
Mass density
Mass density
Cylindrical coordinate system
Cylindrical coordinate system
Avagadro constant
1
...that is the number particles, usually, atoms or molecules in one mole of a chemical entity.
Avogadro constant
Particle amount
1
Particle amount
An amount property that is the temporal integral of a Particle flow
Physical domain
A attribute of a physical analytical entity that characterizes its properties, dependencies, energies, and process participation that apply to a kind of physical analysis such as fluid dynamics, statistical analysis, or thermodynamics.
Note that a single physical entity may be modeled and analyzed in more than a single physical domain. For example, a molecule may participate in undergo (1) chemical transformation (chemical kinetic domain), (2) diffusion (diffusion kinetic domain), (3) structural deformation (solid mechanical domain), and, even (4) change of informational entropy (due to reorganization; information domain). Thus domains try to capture what aspects of an entity are of interest and abstraction in a given analysis.
Discrete intensive scope
...that is measured or applies to the entirety of a physical entity but is independent of the spatial extent or mass of the entity;
Force-driven flow dependency
Ohms law
Resistive flow dependencies represent the flow of stuff and the attendent flow of energy where the flows are driven by a force differential between sources and sinks for the flows. Subclasses apply to flows in other biophysical domains for which forces are defined.
All resistive dependencies relate a force (or force differential) to a flow-rate property which is a generalization on Ohm's law discovered by Georg Ohm in the mid-1820's using recently discovered galvanometers. Ohm's law refers strictly to cases where the force-flow relation is, at least approximately, linear. Non-linear dependencies abound both in the fields of engineering (e.g., electrical diodes) and biology (e.g., turbulent fluid flow, membrane channel mediated ion flow)
Ohm's law
A constitutive flow dependency in which a flow rate between depends on the the differential of forces between dependency role players.
Discrete extensive scope
A physical property has discrete extensive if it's value applies to the entire spatial region occupied by a physical entity and is the spatial integral of a property and is proportional to the spatial extent or mass of the entity.
Heat kinetic domain
Dynamical domain in which the physical entity is a portion of heat
Continuum point scope
A physical property has continuum point scope if it has the value at an arbitrarily small spatial region surrounding a spatial point within a spatial region; an intensive property.
Angular displacement
Inductive storage process
...that is an Inductive dependency
Momentum property
A dynamical state property that is the temporal integral of a force
Continuum field scope
A physical property has continuum field scope if it is the spatially distributed values of the property throughout a spatial region; the spatial distribution of an intensive property.
Angular velocity
Heat amount
1
Heat amount
A amount property that is the temporal integral of a heat flow
Area dependency
...that is the dependency of the area of a two-dimensional spatial region on the locus of points that bound the region.
Discrete mechanical structure
A discrete material structure that has solid dynamical properties and can participate in processes in the mechanical domain.
Spherical coordinate system
Spherical coordinate system
Spatial base amount
1
An amount property that is the spatial extent, location, or shape of a spatial entity.
Electrical potential
1
A force property that drives charge flow from one portion of charge to another. Measured as the difference in electric potential between two points or the difference in electric potential energy per unit charge between two points.
voltage
Fluid pressure
1
A force property that drives a fluid flow.
Temporal entity
A primitive physical processural entity that is a moment or span of time.
Capacitance
...is the derivative of displacement versus force in a capacitive dependency; reciprocal of elastance property
compliance
Thermodynamic entity
A physical entity that is the capacity of a dynamical entity to perform work and is a bearer of thermodynamic properties.
Electrostatic field
A potential energy field produced by electrically charged objects that attracts of repels other electrically charged objects.
Volume
volume
A spatial base amount that is the quantity of space enclosed in a bounded volume region
Temporal interval
...is a contiguouspan of time bounded by two temporal moments (that may be the same moment).
Physics analytical entity
The OPB is an ontology of the abstractions created by the sciences of classical physics and thermodynamics particularly as formulated for analytical purposes by the engineering concepts of system dynamics. Aside from its dependence on classical physics, the OPB does not purport to be a philosophically-based representation of physical "reality". We are motivated by utilitarian goal of facilitating and expediting the annotation and cross-referencing of physics-based analytical models in the broad realm of biomedicine.
The OPB does not include quantum or relativistic physics, nor is it intended to recapitulate the axiomatic basis of physics as a theoretical framework. Whereas the foundational theory of the OPB encompasses both discrete systems analysis (using ordinary differential equations; ODEs) and continuum systems analysis (using partial differential equations; PDEs), the first version of the OPB is targeted solely to discrete systems analysis.
In curating the OPB, we have strived to represent biological and biophysical knowledge of biological function using the formal tools and concepts of computational ontology as expressed in description logic (DL), web ontology language (OWL), and "upper ontologies" such as General Formal Ontology (GFO) and Basic Formal Ontology (BFO).
A physics analytical entity is a formal abstraction of the real world created for the science of classical physics for purposes of describing and analyzing real physical continuants and processes, their respective attributes, and dependencies by which their attributes are related.
Particle diffusion coefficient
1
mass diffusivity
partiicle diffusivity
Physiochemical constant
Particle flow rate
1
Flow rate property that is the temporal derivative of the amount of particles in a portion of particles.
Constitutive proportionality of substance
...that is a measureable at a point within a portion of material and is independent of the spatial extent of the portion
Spatial scale domain
...in which the physical entity is a spatial entity
Three dimensional spatial coordinate basis
...that is comprised of three orthogonal spatial dimensions
Two dimensional spatial coordinate basis
...that is comprised of two orthogonal spatial dimensions
Volume dependency
Volume dependency
Potential field dependency
Gravitational potential dependency
Electrostatic potential dependency
Entropy property
Energy amount
...that is a measure of the amount of energy in a portion of energy
Energy flow rate
...that is the temporal rate of change of the an energy amount or, equivalently, the temporal rate at which energy passes across a spatial boundary, or from one disecrete entity to another.
Entropy flow rate
...that is the temporal rate of change of the a entropy amount or, equivalently, the temporal rate at which entropy passes across a spatial boundary, or from one disecrete entity to another.
Entropy amount
...that is a measure of the amount of entropy in a portion of entropy
Dynamical property
http://en.wikipedia.org/wiki/Dynamical_system
A physical property that is an attribute of an energy-bearing physical entity, a dynamical process or a constitutive dynamical dependency whose value determines the amount or rate of change of the amount of thermodynamic energy inhering in the entity or the rate of energy transfer during a dynamical process.
OPB:Dynamical properties are attributes of dynamical systems whose values determine the thermodynamic content, forces, and flows of the system's participants and processes. The categorization of properties parallels that of OPB:Physical processes and OPB:Dynamical dependency, follows the development seen in:
1. Borst, P., H. Akkermans, and J. Top: Engineering ontologies. Int. J. Human–Computer Studies 1997. 46:365-406.
2. Karnopp, D., D.L. Margolis, and R.C. Rosenberg, System dynamics: a unified approach. 2nd ed. A Wiley-Interscience Publication1990, New York: Wiley.
Dynamical state property
Dynamical state properties are the CONSERVED amount or the CONSERVED momentum within the boundary of a physical entity. State property values are changed during a span of time according to the temporal integration of flow rates or forces according, respectively, to Stokes's law.
Differentials of state property values between physical entity process participants are the drivers for flows between entities as expressed in the constitutive dependencies according to the (linear, proportional) laws of Ohm, Hooke, and Newton.
--------
State properties are termed "across" or "cross" variables to express the idea that the value differential exists across the path to which a rate property applies. In PhysSys ontology [1] and Karnopp [2], they are classified as "forces" variables (f).
1. Borst, P., H. Akkermans, and J. Top: Engineering ontologies. Int. J. Human–Computer Studies 1997. 46:365-406.
2. Karnopp, D., D.L. Margolis, and R.C. Rosenberg, System dynamics: a unified approach. 2nd ed. A Wiley-Interscience Publication1990, New York: Wiley.
http://en.wikipedia.org/wiki/State_variable
A dynamical property that is the temporal integral of a dynamical rate property
Flow rate property
Dynamical rate property that is the temporal differential of an amount property
Force property
A dynamical rate property that is a temporal differential of a momentum property
Chemical molar flow rate
molar flow
molar flow rate
Chemical flow rate measured in concentration per unit time; moles/s
Chemical concentration flow rate
chemical flux
Chemical flow rate property measured in chemical concentration per unit time.
chemical concentration flux
Diffusion potential
1
A dynamical force property that drives the flow of particles from one portion of particles to another.
Transactor dependency
Transactor dependencies do not obey conservation laws (e.g., for mass or energy) and occur in models as simplifications of direct and indirect effects on model variables (i.e., property values) whose mechanisms are either unknown, partially understood, or too complex to be represented for the purposes of the model.
For example, the cardiovascular baroreceptor reflex is a neural signalling pathway by which pressure sensors in the aorta send afferent nerve impulses to brainstem nuclei where the signal is integrated with other neural inputs to produce an efferent autonomic nerve signal that adjust both heart rate and contractility. Not only are the details of this reflex arc poorly understood, the details are largely unimportant for most cardiovascular modeling purposes. Hence, a single transactor rate dependency is often used to say, show the dependence of contractility (a force) on aortic blood pressure.
A dynamical dependency that is a vectorial (i.e., directed) mathematical relationship of a property value of one physical entity on the value of a dynamical property of another physical entity irrespective of thermodynamic dependencies.
Spatial integral dependency
Particle concentration
Particle count
Rotational inertia
Accumulation of space
...that is the amount of space occupied by an entity
Accumulation of amount
per Wikipedia:Stokes' theorem --
In differential geometry, Stokes' theorem (also called the generalized Stokes' theorem) is a statement about the integration of differential forms on manifolds, which both simplifies and generalizes several theorems from vector calculus.
or for Wikipedia:Conservation of mass --
The law of conservation of mass, also known as the principle of mass/matter conservation, states that the mass of an isolated system (closed to all matter and energy) will remain constant over time. This principle is equivalent to the conservation of energy, in the sense when energy or mass is enclosed in a system and none is allowed in or out, its quantity cannot otherwise change (hence, its quantity is "conserved"). The mass of an isolated system cannot be changed as a result of processes acting inside the system. The law implies that mass cannot be created or destroyed, although it may be rearranged in space and changed into different types of particles; and that for any chemical process in a closed system, the mass of the reactants must equal the mass of the products
...that is the accumulation of a conserved quantity due to net of inflows and outflows of the quantity across the boundary of a spatially discrete dynamical entity and is represented mathematicallly as the temporal integral of conserved flows across a dynamical boundary; see Stokes theorem.
Solid entity translation
Lineal mechanical inductive dependency
Rotational mechanical inductive dependency
Shape model
A spatial entity that is a geometrical object that is a primitive set of geometrical shapes such as circle, sphere, cube.
Shape models provide a set of geometrical abstractions commonly used by physiologists to represent anatomical participants in biological processes.
Some Shape models have more than one topological part (e.g., a wall part and a lumenal part). Each part can be "filled" by a portion of material (e.g., cardiac muscle, blood, air) whose Dynamical properties may be equated with Shape model properties; for example the Lumenal volume of shape lumen could be equated with the Fluid volume of the portion of fluid occupying the shape lumen.
The set of Shape model classes is quite sparse and are not intended to be exhaustive. For example where a cardiac ventricle and its contained blood have a very complex geometry which has been modeled as a thick-walled sphere of cardiac muscle enclosing a portion of blood. To pursue more complex geometries (e.g., thick-walled ellipsoid, thick-walled hemiellipsoid) exposes a representative slippery slope that is, rightfully, the domain of spatial and geometrical ontologies devoted to such tasks. Our current goal is to represent commonly used, simple geometrical abstractions -- the 80% solution for available modeling use-cases.
IMPORTANT: An OPB:Shape model is NOT an OPB:Spatial region. Rather, a shape model is a geometrical abstraction that simply defines a set of mathematical dependencies between Spatial shape amount properties. For example, the surface area a rectangular plate is the product of its major and minor spans. The extent to which such geometrical dependencies are to be represented as OPB:Dependency classes is yet to be determined.
Summation of flow rates
...which holds for flow rate properties
Electrical domain
Dynamical domain for which physical entities are portions of electrical charges and/or electrical fields, and processes are transport of charge from one portion to another, or from one location to another in an electrical field.
Energy field
An immaterial dynamical entity that is a portion of energy distributed over a spatial region
Kinetic energy field
An energy field that is the distribution of kinetic energy due to the motion of material entities or electromagnetic fields
Dynamical entity
Dynamical entities are classes of physical analytical abstractions used by physicists to represent specific physical entities as they participate in physical processes within a particular domain.
Examples: cylindrical bone, spherical cell cytoplasm, etc.
These classes DO NOT, however, represent instances of biological entities themselves but, rather, are idealization that express the abstractions, idealizations, and simplifying assumptions used by physicists for computational inferences. Thus, a your femur is an instance of FMA:Femur, but it is analyzed as an OPB:Mechanical solid which is attributed with solid mechanical properties and can participate solid mechanical processes such as translation, rotation, flexion.
Thus, in a simulation model, a femur is annotated as both and independently, an instance of the FMA:Femur class (i.e., as a "real" biological entity) and as an instance of OPB:Mechanical solid, an analytical construct as imagined by a the modeler.
Physical entity that is a bearer of energy, has dynamical properties, and can be a participant in dynamical processes.
Charge flow process
electrical current
ion current
Energy property
Rate junctional dependency
A distributor is a junction that represents the convergence, in a circuit, of conductors for which the sum of currents at a moment in time but be identically zero. Otherwise known as Kirchoff's current law. The junction or distributor has no capacity to store or absorb.
Summation of forces
...which holds for force properties
Existential event
...that is the appearance, disappearance, or transformation of an process participant a consequence of a physical process
Magnetism
Constitutive storage dependency
A dynamical state dependency by which a change in potential energy of a physical entity depends the temporal integral of a product a force acting on the entity and the conjugate flow property of the entity
Time
Structural event
...that is a structural fluent.
...that is a discrete change in a structural relation between participants in a process that is a consequence of an occurrence of the process
Constitutive flow dependency
A dynamical rate dependency in which a flow rate between process participants depends on the amount or force properties of the participants.
Lagrangian dependency
An energy state dependency that is the difference the kinetic energy and the potential energy of a dynamical entity.
Constitutive storage proportionality
Solid potential energy amount
Fluid potential energy amount
Chemical potential energy amount
Fluid kinetic energy amount
Solid kinetic energy amount
Immaterial dynamical entity
A dynamical entity that is immaterial; i.e., not composed of atoms
Conservation dependency
Per Wikipedia: In physics, a conservation law states that a particular measurable property of an isolated physical system does not change as the system evolves.
A dynamical state dependency whereby the summation of the amounts of a conserved quantity contained in the entity is invariant if the flow rates of the conserved quantity across the entity's boundary are identically zero.
Lineal normal tensile stress
A Tensile stress that is the amount of force normal to a spatial line region normalized to the length of the line region.
surface tension
Surface tension has the dimension of force per unit length, or of energy per unit area. The two are equivalent—but when referring to energy per unit of area, people use the term surface energy—which is a more general term in the sense that it applies also to solids and not just liquids.
Surface tension, usually represented by the symbol γ, is measured in forces per unit length. Its SI unit is newton per meter but the cgs unit of dyne per cm is also used. (http://en.wikipedia.org/wiki/Surface_tension)
Entity dependency network
PhysioMap
A physical network that represents dynamical entities as nodes interlinked by dynamical processes in which the entities participate.
Property dependency network
A physical network in which nodes represent the values of physical properties interlinked by dynamical dependencies in which properties are role players.
Physical dimension
that are the dimensions of physical properties
xObsolete
Atomic anion
Process state trajectory
...that is the temporal history of the state of a participant during the occurrence of a physical process
Dynamical state trajectory
...that is the temporally-ordered locus of values of a physical property of a participant during the occurrence of a physical process
Physical process
A physical processural entity that is a flow, or the control of a flow, of energy and/or information amongst physical continuants that are participants in the physical process.
Property value coordinate basis
...that is the specification of the coordinate system in which a property and its value are defined.
Property value
subclasses are kinds of values as encoded in a particular dataset or analytical expression. For example, a blood pressure is_a variable evaluated at an instant (a Variable value) while the maximum blood pressure in a data set is a Maximum_of_set_of_property_values.
...that is the value of a physical property as determined by physics-based measures and/or computations on such measures.
Threshold-crossing event
Minimal value event
...that is a minimal value during an interval of a property value trajectory
Maximal value event
...that is a maximal value during an interval of a property value trajectory
Structural state trajectory
...that is the temporal history of the structural relations of a participant during the occurrence of a physical process
Existential state trajectory
...that is the temporally ordered of the entity-type a participant during the occurrence of a physical process
Mechanical stress
A mechanical force property that is the amount of force per unit of spatial extent.
Structural state
A physical continuant state that is an aggregate of structural relationships of a physical continuant to its parts and to physical continuants of which it is a part.
Property state
A physical continuant state that is an aggregate of the values of the physical properties of an instance of a physical continuant.
OPB:Dynamical state is intended to represent the global state of a physical entity as it exists at a moment in time which includes: 1) thermodynamic state including potential and kinetic energy components, 2) its spatial state as referenced to a coordinate system or to other physical entities with which it participates in physical processes, 3) its structural relations (e.g., parthood, adjacency, connection, etc.) with its own parts and the "wholes" of which it is a part, and other process participants, 4) its information content (e.g., information content of a DNA sequence), and 5) its ontological type or class as determined by st1-3.
Standard value for unit of measure
...that is the value of a property that is the basis for normalization to a unit of measure for a property
Physical process event
Occurrences of the class <physical process event> are discrete change in a process participant that occurs at an instant in time. Events serve to demarcate and define temporal boundaries (as in BFO:Process boundary) of the process occurrences. For example, the peak of the R-wave in an ECG could be taken to demarcate the beginning of ventricular systole.
A physical process manifestation that is a temporally discrete change to a physical entity as a consequence of its participation in the process.
Property of ion channel flux dependency
Span
A spatial base amount that is the quantity of spatial distance between two points in space.
Discrete chemical structure
reactant
As discrete structures, OPB:Chemical substance classes are intended to represent single discrete atomic or molecular scale structures for purposes of analyzing the molecular dynamic processes by which they interact and deform. Chemical reactions involving innumerable (e.g., molar quantities) atoms and molecules are modeled using the OPB:Portions of chemical reactant class.
A discrete material structure that whose parts cannot be separated without breaking chemical bonds and can participate in processes in the chemical domain process.
molecular species
substrate
chemical substrate
chemical product
chemical reactant
compound
Mechanical joint
A material dynamical entity by which two discrete dynamical structures are constrained rotational motion relative to each other.
Portion of solid potential energy
Plane angle
Portion of gravitational potential energy
Entity fusion event
...that is the transformation of more than one physical entity into a single entity
Entity fission event
...that is the transformation of one physical entity into more than one entity
Atomic cation
Entity appearance event
...that is the appearance of a physical entity of a classifiable type
Entity disappearance event
...that is the disappearance of a physical entity as a classifiable type
Property value spatial scope
...that distinguishes between values that apply to discrete properties, those that are spatial integrals over the dynamical entities to which they apply from continuum properties whose values are functions of spatial location within the bounds of a dynamical entity
Pressure differential
Absolute pressure
Property value spatial reference frame
...for continuum flows and displacements, the relationship between a portion of moving/displacing material and the spatial coordinate system in which the movement/displacement occurs
Eulerian reference frame
...within which spatially distributed rate properties of within an entity are defined at fixed points relative to an external reference frame.
Lagrangian reference frame
...within which rate properties of an entity define a trajectory of the entity relative to an external reference frame.
Algebraic form
...that is the algebraic relationship of a property value to another value of a property of the same class.
(from Dybkaer, R., An Ontology on Property - For Physical, Chemical and Biological Systems. e-published by IUPAC (International Union of Pure and Applied Chemistry), 2009 see: http://ontology.iupac.org/index.html.)
Differential form
...that can be subtracted from, but not divided by, another property value of the same class.
Following: "differential unitary quantity value" from Dybkaer, R., An Ontology on Property - For Physical, Chemical and Biological Systems. e-published by IUPAC (International Union of Pure and Applied Chemistry), 2009 see: http://ontology.iupac.org/index.html.
Ratiometric form
...that is a property value that is divided another property value of the same class.
Following: "rational unitary quantity value" from Dybkaer, R., An Ontology on Property - For Physical, Chemical and Biological Systems. e-published by IUPAC (International Union of Pure and Applied Chemistry), 2009 see: http://ontology.iupac.org/index.html.
Ordinal form
Following: "ordinal quantity value" from Dybkaer, R., An Ontology on Property - For Physical, Chemical and Biological Systems. e-published by IUPAC (International Union of Pure and Applied Chemistry), 2009 see: http://ontology.iupac.org/index.html.
...that is a property value that can only be ranked as having a magnitude that is lesser than, equal to, or greater than another property value of the same class.
Tensile stress
A mechanical stress that is the amount of force normal to a spatial line or surface region normalized to the spatial extent of the region.
Maximum value
Thermodynamic state
A physical continuant state that is an aggregate of the amounts of thermodynamic energy and entropy that are attributes of a physical continuant.
Charged particulate
ionic species
A particle that bears a net electrical charge and whose diffusive movement is subject to imposed electrical potential gradients
ion
Surface normal tensile stress
A tensile stress that is the amount of force normal to a surface region normalized to the area of the surface region.
Change containment event
Change parthood event
Attribute of physical property
Physical property entity that is the value, dimension, or value attribute of a physical property
Change adjacency event
Change connectivity event
Change location event
Entity transformation event
...that is the transformation of a single physical entity from one emtoty-type to another
Property event
...that occurs when the value of a physical property has a defined value
Material amount
An amount property that is the mass of matter that inhers in a material dynamical entity
synonyms: mass, inertia, inertial mass
Portion of chemical reactant
...that is an uncountably large set of chemical reactants.
Portion of particles
A portion of material that is comprised of an uncountably large set of particles that have diffusion kinetic properties and participate in diffusion processes.
Diffusion conductance
1
Threshold value
Information content
Uncharged particulate
A particle that bears no net electrical charge.
Fluid-mechanical process
...that converts fluid energy into solid energy by virtue of a change in fluid volume displacing a solid entity, or vice versa.
Examples: atrial filling during diastole, bladder filling
Excedes threshold event
Physical continuant
Physics analytical entity that represents the material, energy, and/or information content of material or immaterial, space-occupying continuants.
Portion of uncharged particles
A portion of particles that bear no net electrical charge
Quantal positive charge
A quantum electrical charge that is the charge of a positron
Physical state
A physical attribute of one or more physical continuants at a moment in time that is an aggregate of property values, structural relations, and/or entity type.
The class 'Physical continuant state' is intended to represent the physics concept of the "state" of a system which comprehends all physical state variables e.g., locations, energies, dynamic properties) as well as a description of the structural composition of physical entities that comprise the entity or system.
As such it closely related to class term "phenotype" as defined in biomedical phenotype ontologies (e.g., PATO: Phenotype And Trait Ontology, HPO: Human Phenotype Ontology). However, 'state' in OPB excludes psychological, genomic, evolutionary and other biological attributes except as measureable and quantifiable in terms of physical measures.. Thus, for the biomedical domain, OPB uses "Physical state" to comprehend the concepts of "state" and "fluent" as follows:
"Physical state" should also be synonymous with the concept of "fluent" (as in the situation calculus, the Process Specification Language, and OBO:Process Ontology) which is a changeable aspect of a system.
Quantal negative charge
A quantum electrical charge that is the charge of an electron
Solid entity deformation
Dynamical process dependency
A physical dependency entity relates values of dynamical properties that are attributes of entities participating in a physical process.
Shear stress
A mechanical stress that is the amount of force acting in the plane of a spatial region normalized to the spatial extent of the region.
Accumulation of linear momentum
...for the amount of linear momentum
Accumulation of angular momentum
...for the amount of angular momentum
Spatiotemporal coordinate basis
...that is a spatial coordinate system and a temporal coordinate system.
Thermal conductivity
Magnetic domain
Dynamical domain in which the physical entity is a magnetic field.
Thermal diffusivity
Minimum value
Continuum relative value
Mean value
Property unit of measure
...that is defined value of a physical property by which measured values of the same property are scaled.
Statistical value
...that is a statistical measure of a set of physical property values
Mean of set of property values
Maximum of set of property values
Cardinality of set of property values
Minimum of set of property values
Variance of set of property values
Lineal particle diffusion coefficient
Areal particle diffusion coefficient
Atomic weight
Molecular weight
Boundary dependency
Stoke's law
Stokes law
A dynamical state dependency of a change in an state property value is the temporal integral, over a span of time, of a rate property value of a process in which the entity is a participant.
Scalar form
Lineal shear stress
A shear stress that is the amount of force acting in the along a line spatial region normalized to the length of the line.
Temporal frequency
A temporal property that is the number events that occur during a temporal interval during a process.
Surface shear stress
A shear stress that is the amount of force acting in the plane of a surface spatial region normalized to the area of the region.
Discrete particulate
A discrete structure that can move by diffusion; i.e., can be a process participant in the diffusion domain, in addition to moving by advection or convection.
Signal amplitude
Rate transactor control process
Boundary flow dependency
Kelvin–Stokes theorem
per FLB: a boundary dependency is "equivalent to an asssertion of a Stokes' Theorem as the integral of the gradient over the boundary = rate of change of integral of the underlying field over the volume bounded."
i.e., change in volume of an entity equals the temporal integral of flow rate across the boundary of the entity; e.g., ∆volume = ∫(flow-rate) dt
Stokes Theorem
Boundary dependency in which a change in an amount of an entity is the temporal integral of flow rate across the entity boundary, or inversely, that a flow rate across the boundary equals the temporal differential of the amount of an entity.
It is not clear that there are other types of boundary dependency beyond this boundary flow dependency (Stokes theorem) because Boundary dependencies may overlap (be conflated with) State dependencies.
Stoke's theorem
Information domain
Physical domain that applies to the information content of an entity.
Charged molecule
A charged particle that is a molecule.
State transactor control process
Physical rate node
Kirchhoff's point rule
A physical network node for which the algebraic sum of values of rate properties of a single class is identically zero at all times.
Kirchhoff's circuit laws
Solid angle
Energy flow rate junction
A dynamical rate node that applies to energy flow rates.
Physical dependency network
Set of physics analytical entities that consists a set of physical continuant entities and the physical dependencies by which their physical states depend upon one another.
Physical source node
Rate transactor dependency
A transactor dependency by which a rate property of one entity depends on a dynamcal property of another entity with which there is no or negligible energy transfer
Portion of strain potential energy
Density dependency
...that defines an intensive property of a discrete physical entity as a ratio of an extensive property and the extent of spatial region occupied by the entity
Dynamical force junction
Kirchhoff's loop rule
Kirchhoff's second law
A dynamical rate node that applies to dynamical force properties
Kirchhoff's second rule
Fluid flow junction
Fluid flow source
Solid force source
Signalled transactor coefficient
...that is a proportionality of a signalled transactor dependency
Direct transactor coefficient
Incrementing control process
Decrementing control process
Charged polymolecular complex
Diffusion gradient
A potential energy field that is a spatial gradient of particle concentration.
Momentum flow junction
Electrical current junction
Dynamical flow rate junction
Kirchhoff's first law
Kirchhoff's junction rule
A dynamical rate node that applies to dynamical flow rate properties.
Kirchhoff's point rule
Mass flow junction
Electrochemical diffusion gradient
A potential energy field that is a combination of an electrostatic and a diffusion gradient.
Mechanical force junction
Fluid pressure junction
Electrical potential junction
Electrochemical potential junction
Energy density
Density
...that is the ratio of an extensive property of an entity to the volume of the spatial region occupied by the region.
For an inhomogenous entity, the density varies spatially within the entity and is determined at each point by the limit of the ratio of the extensive property to the spatial extent of a small region around the point as the region approaches zero volume.
Mixed state control process
Cavitated solid
Energy source node
Dynamical source node
Dynamical flow source
Dynamical force source
Uncavitated solid
Solid force property
A force property that acts to displace or deform a solid physical entity
Longitudinal tensile wall force
Circumferential tensile wall force
Space
Ion conductance
The conductance of ion flow driven by an electrodiffusion gradient as applied, for examples, to single ion channels or sets of ion channels in portions of biological or artificial membranes.
Filament shape
A shape model that is a solid cylinder that is longer than it is thick.
Plate shape
A shape model that is a planar solid that is broader than it is thick
Pipe shape
A shape model that is a hollow cylinder, longer than it is wide, composed of a wall part that bounds a lumen part, except at the ends of the shape.
Tank shape
A shape model that is a hollow sphere composed of a wall part enclosing a lumen part.
Torus shape
A shape model that is composed of a planar lumen part surrounded by ring-shaped wall part.
Constitutive flow proportionality
rate constant
Spatial region
Spatial regions are spatial entities as found in BFO, GFO, etc. and, as such, are generic entities that can apply to any line, surface, or volume. The problem is that such non-specificity minimizes their utility for model specification and annotation.
A spatial entity that is a contiguous portion of space
Volume region
Signal frequency
Curvature
A spatial base amount that is the degree to which a spatial line region or surface region deviates from being straight or flat, respectively.
Spatial coordinate domain
Dynamical acceleration property
A dynamical property that is the temporal rate of change of a flow rate property.
Dynamical amount node
...for which the physical entity is a dynamical entity
Energy amount node
...for which the physical entities are portions of energy of a dynamical entity.
One-dimensional spatial domain
Charge density
Material flow rate
Flow rate property that is the temporal rate of change of the a material amount or, equivalently, the temporal rate at which matter passes across a spatial boundary, or from one disecrete entity to another.
Physical state node
Two-dimensional spatial domain
Three-dimensional spatial domain
Kinetic energy domain
Thermodynamic domain that applies to a portion of kinetic energy.
Potential energy domain
Thermodynamic domain that applies to a portion of potential energy.
Mass of material entity
Force dimension
F
Constitutive dependency
Heat capacity
Transactor sender coefficient
...that is a proportionality between a signal receiver property and the signal property of a signalled transactor dependency
Transactor receiver coefficient
...that is a proportionality between a signal property and the controlled property of a signalled transactor dependency
Charge state
Energy lineal density
...that is the ratio of the amount of energy in a 1-dimensional spatial region to the volume of that region.
Energy areal density
...that is the ratio of the amount of energy in a 2-dimensional spatial region to the volume of that region.
Energy volumetric density
...that is the ratio of the amount of energy in a 3-dimensional spatial region to the volume of that region.
Charge volumetric density
...that is the ratio of the amount of charge in a 3-dimensional spatial region to the volume of that region.
Charge areal density
...that is the ratio of the amount of charge in a 2-dimensional spatial region to the volume of that region.
Charge lineal density
...that is the ratio of the amount of charge in a 1-dimensional spatial region to the volume of that region.
Discrete dynamical structure
A material dynamical entity that has a contiguous spatial boundary and may be composed of material dynamical entities as structural parts
Portion of material
Surface region
Line region
Spatial amount
An amount property that is a scalar measure of the spatial extent, location, or shape of a spatial entity.
Shape model amount
Shape model amount properties represent cardinal spatial extents of shape models used to represent physical states of 'real' anatomical entities. For example, the portion of blood in a ventricle has Fluid volume as a Dynamical state property which is identical to the Lumen volume of a Tank shape that is declared to represent a heart ventricle. Such an algebraic relation formally expresses the equality of a volume of a fluid portion with the volume of the vessel lumen that contains the fluid portion. Thus, shape model amounts are state properties of the entities for which they are analytical models.
As with representing shape models themselves, representing classes and subclasses of shape model spatial properties exposes a representational slippery-slope into the complexities of geometrical reasoning and computation if the OPB were to comprehend the multifarious dependencies between spatial properties, coordinate systems, and levels of abstraction. For purposes of annotation, model-model comparisons, and repository searches, this sparse representation leaves much to the modeler to resolve and code (or re-code) to reconcile difference geometrical representations. Our main aim is to provide sufficient annotation that such issues can be detected and isolated in comparing models.
For example, having declared a thick-walled, hollow sphere as a shape model of a ventricle, and identified the volume of the lumen with the volume of contained blood, the diameter of the lumen can be inferred from an available geometrical formula.
A spatial amount that is a scalar measure of spatial extent of a shape model
Shape model span
Shape model area
A shape model area that is a section area or a surface area of a volume region.
Shape model volume
Square plate
A plate shape whose perimeter is a square with equal sides.
Rectangular plate
A plate shape whose perimeter is a rectangle with unequal sides
Circular plate
A plate shape that whose perimeter is a circle.
Thin-walled pipe shape
Thick-walled pipe shape
Thin-walled tank shape
Thick-walled tank shape
Cuboid shape
A shape model that is a solid with six faces, each of which is a rectangle.
Square cuboid shape
A cuboid shape in which each face is a square congruent with the other faces.
Rectangular cuboid shape
A cuboid shape for which at most one face is a square.
Wall volume of shape
Lumenal volume of shape
Solid shape
A shape model that composed of a single spatial region.
Walled shape
A shape model that composed of a one spatial region, the wall part, that bounds a second spatial region, the lumen part.
Section area of shape
A shape model area that is the area of a plane that transects a volume region and is enclosed within the boundary of the volume region
Surface area of shape
A shape model area that is the area of the bounding region of a volume region
Inner span of shape
Outer span of shape
Length span of shape
Perimeter span of shape
Amount-driven flow proportionality
Process occurrence dependency
...that is a dependence of the occurrence of a physical process upon the state of physical entities that participate in the process
Precondition dependency
formalized as a PSL:precondition axiom
formalized as a SC:precondition axiom
...that is a physical state of physical process participants that is sufficient to initiate an occurrence of the process
Postcondition dependency
...that is the physical state of process participants at the last instant of the process
formalized as PSL:process postcondition axiom
formalized as SC:successor state axiom
Entity-type state
A physical entity state that is the type (or class) of an instance of a physical entity
Existential event dependency
...by which a change in the type or existence of a physical entity is a consequence of its physical state
Portion of fluid gravitational potential energy
Reaction rate constant
1
Structural event dependency
...by which a change in the type or existence of one a structural relation between process participants is a consequence of a change in the dynamical state of the entities
Ion conductance per membrane area
Ion conductance per membrane capacitance
Ion conductance per cell
Portion of charged particles
A portion of particles that bear a net electrical charge.
Coupled flow process
An energy flow process that is the transformation of thermodynamic energy within or between participating dynamical entities according to a dynamical dependency.
Diffusion coefficient
1
Portion of displacement potential energy
Dynamical control process
A dynamical process by which a rate or state process depends on the value of a physical property with transfer of negligible thermodynamic energy
Control processes represent modeling abstractions whereby the value of a physical property of one entity or process depends on the value of another physical property without specifying a thermodynamically valid mechanism for the dependence. Examples: neural firing rate is proportional to synaptic excitation; increasing body weight decreases insulin secretetory rate.
Normal stress
Dynamical boundary
Fluid dynamical boundary
Tensile wall force of tube
Event time
A temporal location of a process event
Molecule
A chemical substance composed of atoms linked by chemical bonds.
Thermodynamic dependency
A physical dependency that defines a thermodynamic property in terms of one or more dynamical properties.
Chemomechanical process
Examples: myocardial contraction fueled by ATP; actin-myosin cross-bridge contraction
...that transforms chemical energy into solid energy, or vice versa.
Mechanical joint
A biomechamical structure consisting of two or more mechanical solids that whose rigid-body motions are constrained to one or more spatial axes
Weight of material entity
Spatial entity
A physical continuant that is a portion of space or a geometrical abstraction of such portions
Impedence property
...that is the opposition to flow due to the combination of resistance, capacitance, and inductance of a flow path
Reactance property
...that is the opposition to flow due to the combination capacitance and inductance of a flow path
Impedance
...that is the opposition to flow due to the duration and/or rate of change of a flow property which combines resistance and inertance dependencies
Gravitational process
Examples: raising an arm; blood flowing downward in a vessel
...that is the change in gravitational potential energy of a material entity by virtue of forces that move the entity in a gravitational potential field
Advective cotransport dependency
...that is the flow of a portion of a conserved quantity by virtue of it being a part of a portion of fluid that is flowing.
Advection is the discrete, vectorial transport of portions of entities that are either dissolved (e.g., sugar, ions) or suspended (e.g., blood cells) in a flowing fluid (e.g., blood). It is a component of convection transport along with diffusive transport fluid however only advection has meaning in discrete formulations that do not represent spatial gradients of diffusible entities. Thus, the diffusion-gradient rate dependency (as in Ficks law) applies to diffusive transport across a boundary from one discrete portion of fluid to another with out bulk flow of fluid.
Dissipative process
...that is the conversion of non-heat energy into heat energy and entropy during an irreversible work process
Dissipative process
A physical process that increases a portion of entropy
Electrochemical process
...that transforms chemical potential energy into electrical potential energy, or vice versa.
Entropy-driven process
Transducer process
...that is the transformation of energy from one physical entity to an entity of a different domain
Tranformer process
...that is the transfer of energy between entities of the same energy domain wherein the ratio of displacement to force of one entity is inversely proportional to the ratio of displacement to force of the other entity
Dynamical state process
A dynamical process that is the accumulation (or depletion) of energy of a dynamical entity due to rate processes in which it participates.
Mathematically a state process is the temporal integral of a boundary flow in dimensions of amount per unit time.
Chemical mass-action rate dependency
1
1
0
1
...in which chemical flow rates of participating portions of chemicals depend on the amounts of the participants
chemical rate law
mass-action rate law
Portion of fluid elastance potential energy
Fluid flow process
1
Chemical reaction flow process
1
Heat transfer process
Diffusive flow process
Solid displacement process
Chemical capacitive process
Fluid capacitive process
Mechanical capacitive process
Electrical capacitive process
Physical process change
A physically observable attribute of a physical process that is a change in the physical continuant state of one or more participants in the process.
Diffusive capacitive process
Element
A chemical substance made up of a single kind atom.
Energy storage process
Electrochemical potential
1
A force property that drives charged chemical entities along an electrochemical gradient
Equilibrium potential
Equilibrium potentials are property players in the Elecro-diffusional capicitance dependency which defines the equilibrium potentials in terms of concentration gradients of an ion and constitutive property
An electrical potential which nullifies the charge flow of an ionic species along a diffusion gradient for the species
reversal potential
Nernst potential
Physical processural entity
A physical analytical entity that is a physical process or temporal entity.
Mechanical solid
A biomechanical structure with inherent shape that resists deformation by applied forces.
Inhibition control process
...that decreases the process flow rate.
Activation control process
...that increases the process flow rate.
Chemical state
Diffusive state
Fluid volume state
Heat capacity state
Displacement state
Tensile displacement
Mixed control process
...that increases or decreases the process flow rate depending the value of the controlling property
Fractional amount of chemical
Spatial fraction amount of chemical
Fractional amount of chemical that is the proportion of an amount chemical in a one spatial region normalized to the total amount of the same chemical in another spatial region.
State fraction of amount of chemical
Fractional amount of chemical that is the proportion of a chemical in a particular conformational state normalized to the total amount of the portion of chemical.
The "state" in the definition may refer to, say, the structural state of molecules in a portion of chemical be it molecules in a particular structural conformation. Examples: fraction of open channels, fraction of ion channels in a particular gating state (e.g., m, n, h of HH model); enzyme activity normalized to maximal activity (e.g., V/Vmax in MM enzyme model).
Process trajectory
A physical process change that is a time-series of changes of property values and process events that occur to participants in a process during an occurrence of the process.
Process precondition state
A process precondition is a concept in the situation calculus. A precondition is a necessary and sufficient condition of the participants for initiating an occurence of a process
A process conditional state of the participants in a physical process that is necessary and sufficient to initiate an occurrence of the process
Process postcondition state
A process conditional state of the participants that occurs at the end of a physical process, and may serve as the precondition state for a subsequent physical process.
A process postcondition is a concept in the situation calculus. A postcondition is the condition of the participants for at the end of an occurence of a process
Informational property
A physical property that is a measure of the information content of a spatial distribution of entities or physical property values, or of a temporal distribution of process events as occurs during a process tajectory.
Whereas information theory has broad applications and implications for the occurrence of biophysical processes, its formal representation in the OPB is deferred pending requirements for annotating use-cases.
Suitable references for information theory applications are:
1) http://en.wikipedia.org/wiki/Information_theory
2) Rieke, F., et al., Spikes. Exploring the neural code, in Computational Neuroscience, ed. Sejnowski T J and Poggio T A, 1997, Cambridge, MA: A Bradford Book.
Physical dependency
Physical dependencies represent a broad class of quantitative and qualitative relationships amongst physical entities and the attributes of physical entities, physical continuants, and physical processes. This includes, for examples, the value quantitative values of physical properties, the qualitative structural relations amongst physical entities, and the occurrences of processes and their events. Thus, dependencies represent the "rules" by which continuants are composed and how processes occur as described by physics principles, axioms, theorems, and laws.
Physics analytical entity that represents an axiom, definition or empirical law of classical physics that relates the existence, identity or attributes of a physical analytical entities to other entities.
Dynamical state dependency
A dynamical dependency that is a mathematical relationship or constraint on the values of physical state properties of a physical entity at a moment of time.
State dependencies represent static relations between state property values that, in "reality", are simultaneously true for an entity at any temporal instant. However, OPB is designed for annotating computational representations of that reality such that adjusting values does not occur instantaneously, as in reality, but is achieve sequentially by computational procedures.
For example, a computation may calculate the radius of a spherical entity according as its volume changes according to a boundary flow dependency, or in a different formulation, volume may be calculated as the sphere's radius changes according to a related boundary flow dependency.
Dynamical flow rate dependency
A dynamical dependency that determines the temporal rate of flow of a conserved quantity amongst physical entities that are participants in a physical process.
Spatial calculus dependency
Absolute amount of chemical
Joint displacement
Summation of momenta
A summation of state property values which holds for momentum properties.
Boundary force dependency
Newton's law
Newtons law
f = ma
f = ma
Boundary dependency by which a change of momentum is the temporal integral of a force acting across the boundary of the entity, or inversely, by which the a force acting across the boundary of an entity equals the temporal differential of its momentum.
Newtons law
This dependency is the equivalent (?) of Newton's law in that the temporal differential of the temporal integral of force is force (f) which is, by this dependency, equal to the temporal differential of momentum which is mass times acceleration (ma); hence f = ma.
Lever process
Summation dependency
A dynamical state dependency that is the value of a dynamical property of a physical entity that is an algebraic sum of the values the dynamical property values of those physical entities that are proper parts of the physical entity.
Summation of rate properties
A multiscaling dependency for instances of one class of rate property values.
Summation of state properties
A multiscaling dependency for instances of one class of state property values.
Rate-dependent hysteresis
Rate-independent hysteresis
real time lag
Myofibril contaction
Myocyte contraction
Muscle contraction
Membrane ion pump process
Organismal domain
Organ system domain
Organ domain
Organ part domain
Cellular domain
Resistive flow process
An energy flow process that in which the flow rate depends on the force properties of participating entities and proceeds according to a resistive dependency and during which energy is dissipated as heat.
Cell component domain
Molecular domain
Atomic domain
Spatial domain
Physical domain that applies to a spatial entity.
Standard deviation
Portion of solution
Portion of solvent
Portion of pure fluid
Amount-driven flow process
An energy flow process in which the rate of flow depends on the amounts properties of participating entities.
Portion of reactant
A portion of material comprised of chemical entities that can participate in chemical reactions.
OPB:Portion of reactant classes are used to represent chemical reactions involving innumerable (e.g., molar quantities) atoms and molecules. Whereas OPB:Chemical substance classes are intended for modeling denumerable discrete atomic or molecular-scale structures for purposes of analyzing the molecular dynamics by which they interact and deform.
Thus, a portion of reactant has dynamical properties and can participate in dynamical processes in the Chemical kinetic domain.
Joint rotational displacement
Process conditional state
A physical continuant state that is an aggregate of the physical continuant states of the participants in a physical process.
Ion flow conductance
1
hasPhysicalDomain exactly 1 'Electrochemcal domain'
Ion flow resistance
Ion flow resistance per membrane area
Ion flow resistance per cell
Ion flow resistance per membrane capacitance
Dynamical rate process
A dynamical process that is the flow of thermodynamic energy between dynamical entities that are its participants.
Primitive physical entity
A physical entity that is a portion or instance of a material or immaterial continuant that is so basic to our understanding that it cannot be defined in a non-circular manner.
Ion flow resistance per ion channel
Ion conductance per ion channel
Joint angular displacement
Kinetic energy dependency
An energy state dependency that defines a kind of kinetic energy.
Potential energy dependency
An energy state dependency that defines a kind of potential energy.
Flow rate junctional dependency
A flow rate distributor represents the point of convergence of multiple flows but which has no capacity to store flows so that the sum of flow rates at any moment in time is identically zero. Biophysical examples would include representing the bifurcation of a blood vessel as an inelastic distributor, or representing a set of reactions that share a common reactant as a chemical circuit node that has no volume and hence no concentration.
Force-driven flow proportionality
constitutive property
Trajectory time constant
A temporal duration that is interval during which an exponentially-decaying value of a dynamical state value reaches 1/e of a prior value.
time constant
tau
Wikipedia (time constant): The time constant is the main characteristic unit of a first-order LTI (linear time-invariant) system...Physically, the constant represents the time it takes the system's step response to reach 1/e of its final (asymptotic) value. In radioactive decay the time constant is called the decay constant (λ)
Trajectory half-time
A temporal duration that is interval during which the value of a dynamical state trajectory reaches 1/2 of a prior value.
t1/2
half-time
half time
Constitutive coefficient
A constitutive dependency property that is factor in a mathematical expression by which values of dynamical property players are not proportional to each other; i.e., having a non-linear relationship.
Property of Hodgkin-Huxley dependency
Maximal channel conductance
Ionic valence
...that is the maximum number of ionic bonds available to an ionic species
Charged atom
A charged particle that is a single, unbound atom.
Property of irreversible Michaelis-Menten dependency
Maximal enzyme flow-rate
Half-maximal substrate amount
Property of reversible Michaelis-Menten dependency
Half-maximal product amount
Force junctional dependency
A force distributor represents the point of convergence of multiple forces at a moveable but massless structural point so that the sum of forces at any moment in time is identically zero. Biophysical examples would include representing the convergence of fibre forces at common, massless point on a boine where one of the resultant forces is the force that moves the bone.
Activation gating variable
A H-H gating variable is actually a dynamical state variable that describes the fraction of (hypothetical) "gating particles" that control the open-closed state of the ion channel's activation gate.
Number of activation gating particles
The number of H-H gating particles is actually a dynamical state variable that describes the amount of (hypothetical) "gating particles" that control the open-closed state of the ion channel's activation gate.
Inactivation gating variable
A H-H gating variable is actually a dynamical state variable that describes the fraction of (hypothetical) "gating particles" that control the open-closed state of the ion channel's activation gate.
Number of inactivation gating particles
The number of H-H gating particles is actually a dynamical state variable that describes the amount of (hypothetical) "gating particles" that control the open-closed state of the ion channel's activation gate.
Property of non-proportional fluid flow dependency
Property of non-proportional elastance dependency
Property of non-proportional chemical rate law
Property of non-proportional ion flux dependency
Crystal
A chemical substance consisting of atoms, ions, and/or molecules that are arranged in an ordered pattern extending in all three spatial dimensions.
Electrical charge
Aprimitive physical entity that is a quantum electrical charge
Rate source dependency
A rate source is, typically, a boundary condition on the system of entities and processes. It can be a constant rate source or follow a parametrically determined value trajectory.
...that is a rate property trajectory that is independent of the state of other process participants
Fluid inductive process
Mechanical inductive process
Electrical inductive process
Force source dependency
Flow-rate source dependency
State source dependency
A dynamical state dependency by which a state property value is independent of state and rate properties of other entities and processes.
Electrical inductance
Physical attribute
Physics analytical entity that is an attribute of a physical continuant, process, or dependency that is observable by physical means at a moment in time or for a span of time.
Power dependency
A thermodynamic dependency that defines the power (i.e., rate of energy flow) of a process as the product of the flow-rate and force differential that drives the flow.
Amount source dependency
A state source dependency for an amount property value.
Momentum source dependency
A state source dependency for an momentum property value.
Summation of amounts
A summation of state property values which holds for amount properties
State transactor dependency
A transactor dependency by which a state property of one entity depends on a dynamcal property of another entity with which there is no or negligible energy transfer
Matter
Energy
Mechanical displacement
An amount property that is a temporal integral of a mechanical velocity property
Momentum
Torsional force
Bending moment
Polymolecular complex
Constitutive dynamical property
Constitutive proportionalities apply only to those constitutive dependencies that can be expressed by which the dependent property is proportional to the independent property. Any other algebraic form of the dependency may have specifially-defined parameters (e.g., offsets, rate parameters). Given the creativity and license of modelers for creating the best fit to constitutive dependencies, the parameters of such non-proportional dependencies must be annotated by some local mechanism that does not depend on OPB classifications.
Constitutive proportionalities are approximations to dependencies for which a first-order, linear approximation is sufficient for the purposes of analysis. Piecewise linear approximations may apply over a limited range of dynamical property values. In general, various algebraic functions may be required using one or more parameters to fit observed dependency relationships. Given the range of possible constitutive dependencies, OPB defers representing such possibilities on a case-by-case basis for specific use-cases.
Non-proportionality constants include coefficients and parameters required to characterize linear and nonlinear dependencies that are not simple proportionalities. Some may constitutive dependencies may include dynamic modeling schemes with internal dynamic states (e.g., the "gating variable" of Hodgkin-Huxley ion gating equations). We will treat such properties as "internal" to the constitutive dependency, shielded from other entities in the system and known solely as hypothetical constructs derived as constitutively observed dynamic phenomena. Thus, HH gating variables will be classified as properties of constitutive dependencies which are also subclasses of Dynamical property without, however, declaring a Dynamical entity of which it is a property.
Important to realize that MM params, HH params, etc. are all derived and asserted by virtue of curve-fits to the directly observed attributes of a system; number of gating particles and their respective states is entirely inferential by best fits and, so, are no more physically real than any other coefficient or parameter.
A physical property whose value depends on the structural and material composition of a process participant and determines the quantitative dependence of dynamical properties.
Energy state dependency
A thermodynamic dependency that defines a type of thermodynamic energy of a dynamic entity in terms of the entity's dynamical and thermodynamic properties.
Capacitive force dependency
Hooke's law
Hookes law
Capacitive storage dependencies represent the storage of stuff and its attendent energy where stuff accumulates in a device against an attendent force that counters the inflow. Subclasses apply to stores in all biophysical domains for which forces and amounts are defined.
All capacitive dependencies relate a force (or force differential) to an amount property which is a generalization on Hooke's law discovered by Robert Hooke in the 1660's. Hooke's law refers strictly to cases where the force-amount relation is, at least approximately, linear. Non-linear dependencies abound both in the fields of engineering (e.g., progressive rate springs) and biology (e.g., fluid accumulation in elastic vessels)
Constitutive storage dependency in which the force property of a participant depends on its amount property such that a change in stored potential energy is the temporal integral of the product of a flow rate and its conjugate force property.
Inductive flow dependency
A constitutive flow dependency whereby a force differential between participants depends on a rate of change of flow rate between participants such that the flow itself stores kinetic energy.
Physical boundary
Physical boundaries represent a disparate class of analytical boundaries between physical entities that are, for example, a "real" spatial boundary between spatially adjacent material entities such as two cells, a cell's nucleus within its cytoplasm, or the attachment of a muscle to a bone. There are also "kinetic" boundaries between spatially-mixed entities such as the portions of reactants in a cell cytoplasm as represented in chemical kinetic schema.
A physical continuant that partitions the spatial occupancy or thermodynamic content of a physical entity from other physical entities.
Noncovalent chemical bond
A chemical bond mediated by ionic (i.e., electrostatic) interactions, hydrophobic interactions, hydrogen bonds, and van der Waals forces.
Spatial boundary
Spatial boundaries are abstractions of the real world that assigns spatial regions to one or another physical entities. As such, specifying a spatial boundary requires a specification (usually implicitly) of spatial scale. For example, a partioning into intra- and extra-cellular spaces may require the specification of an intramembrane space, and further into intracellular and extracellular peri-membrane spaces, which may be further distinguished by the gradient of membrane proteins, glycoproteins, etc. that decorate cell membranes.
Physical boundary that is a spatial entity of one less spatial dimension than the bounded spatial entity it bounds or demarcates from another spatial entity.
A spatial entity that is a portion of space.
Chemical kinetic boundary
Physical boundary that distinguishes portions of diffusible and interacting particles or chemicals that are distributed within the same spatial region.
A kinetic boundary represents the virtual (non-spatial) segregation of dissolved chemical particpants in, say, chemical reactions as occurs, for examples, in a portion of cytoplasm, a region of cell membrane, or a portion of extracellular fluid. Thus for analytical purposes, such participants are imagined to be uniformally distributed and thoroughly intermixed as separate "pools" of reactants albeit with a shared spatial region of distribution
kinetic pool
pool
Hysteretical state dependency
...by which the value of dynamical property depends on one or more state property values at a prior moment in time
Covalent chemical bond
A chemical bond mediated by the sharing of electron pairs between atoms.
Spatial amount state
A property state composed of one or more spatial properties.
Constitutive rate property of substance
Amount-driven flow dependency
Amount-driven dependencies stand outside of the system dynamic [1] and the chemical biophysics [2] frameworks which are deeply based on thermodynamical principles in which a product of flow-rate times force-differential (as chemical- and diffusional-potentials) is a work term that has units of energy.
For both mass-action chemical rate laws and Fick diffusion equations the cross-products of flows and amount-diferentials have no thermodynamic meaning because the thermodic energy content of the flowing stuff is not represented; see:
1. Karnopp, D., D.L. Margolis, and R.C. Rosenberg, System dynamics: a unified approach. 2nd ed. A Wiley-Interscience Publication1990, New York: Wiley.
2. Beard, D.A. and H. Qian, Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge Texts in Biomedical Engineering2008: Cambridge University Press.
A constitutive flow dependency in which a flow rate between depends on the amounts of the dependency role players.
Mechanical inductive dependency
Fluid inductive dependency
Electrical inductive dependency
Fluid capacitive dependency
...in which an volume of a portion of substance depends its the differential of the pressures across its boundary.
Electrical capacitive dependency
...in which the electrical potential difference across the boundary of an entity depends on the amount of charge in the entity
Mechanical capacitive dependency
...in which an displacement of a solid entity depends its the differential of the solid forces acting across its boundary.
Chemical capacitive dependency
...in which a the chemical potential of a portion of chemical depends the amount of chemical within its boundary.
Fluid-mechanical transducer dependency
...by which energy is exchanged between a flulid-domain physical entity and a solid mechanical domain entity.
Examples:
1) transformation of mechanical strain potential energy into flluid potential energy as the myocardial contracts to pressurize ventricuar blood contained
Chemo-mechanical transducer dependency
...by which the chemical potential energy of portions of chemical is exchanged for solid mechanical kinetic and potential energy.
Examples:
1) transformation of chemical potential energy into mechanical potential energy as ATP is consumed to increase the tensile stress of myofibrils;
Mechanical transformer dependency
Biomechanical examples: the biceps tendon pulls on the forearm to raise a load held in the hand;
...by which energy is exchanged between solid mechanical domain entities.
Portion of fluid suspension
Algebraic geometric dependency
Value of physical property
Amount state
A property state composed of one or more amount properties.
Momentum state
A property state composed of one or more momentum properties.
Process change dependency
Ionic chemical bond
Chemo-diffusional transport dependency
...by which a change of chemical potential energy of a chemical reaction is coupled to a change in potential energy of a diffusion gradient due to transport of diffusible particles
Diffusion-diffusion coupled cotransport dependency
...by which a change of diffusion potential energy one diffusion gradient is coupled to a change in potential energy of another diffusion gradient due to cotransport of diffusible particles
Hydrophobic chemical bond
Diffusional capacitive dependency
Electrodiffusional capacitance dependency
equilibrium potential
reversal potential
Nernst potential
This dependency is as a nonproportional constitutive dependency which is described by the Nernst equation that contains a ln function and the constitutive constant K = RT/F:
reversal potential = K ln( amount of ion outside / amount of ion inside )
see: Wikpedia (Nernst potential):
The Nernst equation gives a formula that relates the numerical values of the concentration gradient to the electric gradient that balances it.
The Nernst equation has a physiological application when used to calculate the potential of an ion of charge z across a membrane. This potential is determined using the concentration of the ion both inside and outside the cell.
see: Wikpedia (reversal potential):
In a biological membrane, the reversal potential (also known as the Nernst potential) of an ion is the membrane potential at which there is no net (overall) flow of that particular ion from one side of the membrane to the other. In the case of post-synaptic neurons, the reversal potential is the membrane potential at which a given neurotransmitter causes no net current flow of ions through that neurotransmitter receptor's ion channel.
...in which an electrical potential difference across the boundary separating portions of diffusible charged particles depends on a differential of the concentrations of particles under conditions in which no other charge species traverses the boundary
Hydrogen bond
Van der waals bond
Set of physical network nodes
A physical network entity that represents a physical continuant entity as part of a physical network.
Set of physical network links
A physical network entity that represents a physical processural entity or a dependency entity as a component of a physical network.
A physical network entity that represents a physical processural or dependency entity that physical network.
Network domain
Physical domain that applies to physical network entities.
Resistive flow dependency
A force-driven flow dependency in which the flow rate of a conserved quantity from one entity to another is proportional to the difference in force property values of participants.
Property event dependency
Process event dependency
Transport dependency
A dynamical dependency that determines the flow rate substance or conserved quantity by to a fluid in a fluid flow process.
Convective cotransport dependency
Cotransport process
A coupled flow process by which the flow of a conserved quantity is coupled to the flow of a fluid.
Advective cotransport process
A cotransport process that is the flow of a portion of a conserved quantity by virtue of it being a part of a fluid participant in a is fluid flow process.
Convective cotransport process
A cotransport process which is the concerted, collective movement of groups or aggregates of molecules within fluids.
Set of physics analytical entities
A physics analytical entity that is an ordered or unordered collecion of other physics analytical entities.
Nernst potential
membrane equilibrium potential
ionic equilibrium potential
An electrochemical potential that nullifies flow of an ionic species along its diffusion gradient
Temporal coordinate origin
start time
zero time
A temporal location that is the origin of a temporal coordinate system, hence zero time.
time zero
Event interval
delay
Temporal duration between the occurrence of two temporal events.
delay time
delta t
∆t
Mathematical constant
A primitive physical continuant that is a real number defined for its use in mathematical computations.
Pi
Archimedes' constant
3.14159
π
A mathematical constant that is that is the ratio of a circle's circumference to its diameter.
e
Euler's number
exponential decay constant
exponential growth constant
A mathematical constant that is the limit of (1 + 1/n)n as n approaches infinity.
2.71828
Functional part of molecule
Modulator site of ion channel
Kinase site of molecule
Part of ion channel
Catalytic site of enzyme
Gating particle of ion channel
Ion channel pore
Ion-binding site in ion channel pore
Activation gating particle
Inactivation gating particle
Solid translational acceleration
A dynamical acceleration property that is the temporal rate of change of a Solid translational velocity.
Acceleration - Rate of change of speed with respect to time.
http://www.unitsofmeasurement.org/apidocs/index.html
Stimulator-site of ion channel
Inhibitor-site of ion channel
Phosphatase site of enzyme
Ligase site of enzyme
Solid angular acceleration
A dynamical acceleration property that is the temporal rate of change of a Solid angular velocity.
UoMo:AngularAcceleration - Rate of change of angular speed with respect to time.
http://www.unitsofmeasurement.org/apidocs/index.html
Heat energy dimension
H
Torque dimension
Base dimension
Derived dimension
Dynamical process
A physical process that is a flow, or the control of a flow, of energy and/or information amongst physical continuants that are participants in the physical process.
Physical event process
Physical structure process
Joint velocity
Joint angular velocity
Joint rotational velocity
Solid velocity
Tensile velocity
Angle
A spatial base amount that is required to superimpose two straight lines by rotation about an intersection of the lines