]>
synonym
IUPACclass
wikipedia
PATO_id
hasConstraint
hasSI-unit
This is the only system of units to be represented in OPB and is implemented according to the globaly-adopted system as described in:
https://en.wikipedia.org/wiki/International_System_of_Units. SI-unit classes.
Accordingly and by fiat, some are "base units" that are irreducible and some are "derived units" that are derived from base units by multiplication or division. In other foromal systems or conventional usages, other allocations between base/derived units may be encountered.
SI-unit classes map, non-exclusively to classes of OPB:PropertyDimension either as single classes, or as multiples/quotients of base units
hasMediatorParticipant
A hasParticipant relation that relates a dynamical process to a dynamical entity whose dynamical state is a precondition for the process to occur but whose dynamical state changes only by participation in some other process.
hasMathForm
...that relates a property to the mathematical form of an instance of the property
hasParticipant
The intuitive aim of "hasParticipant" is to relate an occurrence of a dynamical process to those dynamical entities that must exist in defined physical state for the process to occur during which the states of participants may, or may not be, changed.
Note that: "hasParticipant" relates physical processes to physical entities while "hasPropertyParticipant" relates physical properties to physical dependencies.
A topObjectProperty that relates an occurrence of a physical process to an instance of a physical continuant that is required for the process to occur or is changed by the process
occursDuring
...that relates an occurrence of a process to the temporal interval during which it occurs
hasMomentumPlayer
hasTemporalPartOfProcess
hasStructuralPartOfProcess
x_deferred object prop
hasForcePlayer
hasPropertyAttribute
A topObjectProperty that relates a property to a property attribute
hasFlowPlayer
hasAmountPlayer
hasSpatialCoordinate
...that relates a property to the spatial coordinate system in which an instance of the property is defined
hasDimension
...that relates a property to the dimension of the property
hasNegPropertyPlayer
hasConstitutivePlayer
...that is a algebraic relation that relates the values of dynamical properties in a constitutive dependency
hasDynamicalPlayer
hasThermodynamicPlayer
hasDependencyPlayerProperty
hasPropertyValue
hasProcessDependency
hasDynamicalParticipant
A hasParticipant property that relates the flow of material or charge to a portion of material or charge that is a source or sink for the flow.
successorTo
hasFlowSink
partOf
hasPart
hasForceSink
...that tends to accelerate or move an entity away from the origin of its spatial location
successorOf
hasForceSource
...that tends to accelerate or move an entity toward the origin of its spatial location
hasPosPropertyPlayer
hasPropertyPlayer
The intuitive aim of "hasPropertyPlayer" is to relate an occurrence of a dynamical dependency to instances of dynamical properties that .
Note that: "hasParticipant" relates physical processes to physical entities while "hasPropertyPlayer" relates instances of physical properties to occurrences of physical dependencies.
A topObjectProperty that relates an occurrence of a physical dependency to an instance of a physical property upon which dependency
hasPartOfProcess
hasPropertyAttribute deferred
occurenceOf
...that relates an occurrence to the process class of which it is an instance
subProcessOf
hasSubProcess
hasFlowSource
propertyOf
A topObjectProperty that relates a physical property to the physical entity in which the property inheres
hasThermoParticipant
The intuition "hasThermodynamicEntity" is designed to fulfil is that any dynamical (i.e., energy-bearing) entity possesses its own portion of energy whch can be a participant in a thermodynamic process during which can be exchanged with portions of energy belonging to other participating dynamic entities.
A hasParticipant property that defines a polarity by which thermodynamic energy flows from a dynamical entity that is the source of the flow into a dynamical entity that is a sink.
hasProperty
A topObjectProperty that relates an instance of a physical entity to an instance of a property that inheres in the entity
hasPhysicalDomain
A topObjectProperty that relates a physical property to the domain of the entity or dependency for 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
A topObjectProperty that relates an instance of a dynamical entity to an instance of a thermodynamic entity that inheres in the dynamical entity.
hasInfoSink
A hasInfoParticipant relation that establishes a dynamical entity as a reciever of an information.
hasInfoSource
A hasInfoParticipant relation that establishes a dynamical entity as a sender of an information.
hasSIunit
topObjectProperty that assigns an instance of an SI unit class to physical property class
hasFlowSource
A hasDynamicalParticipant relation by which a positive process flow diminishes the energy content of the participating dynamical entity.
hasTransactorParticipant
A hasParticipant relation by which the dynamical state of dynamical entity can change the rate of a dynamical process.
hasFlowSink
A hasDynamicalParticipant relation by which a positive process flow augments the energy content of the participating dynamical entity.
hasConstraint
A hasPropertyAttribute that specifies or limits the value of a physical property
hasThermoSource
hasThermoSink
hasThermodynamicEntity
A topObjectProperty that relates an instance of a thermodynamical entity to an instance of a dynamical entity
hasReciprocalProperty
hasInfoParticipant - pending
A hasParticipant property that relates a flow of information to a dynamical entity that is either a source or sink for the flow
hasMultiplierUnit
hasPropertyAttribute that relates a derived SI unit to an SI unit that is a multiplicative component of the derived SI unit.
hasDivisorUnit
hasPropertyAttribute that relates a derived SI unit to an SI unit that is a divisor component of the derived SI unit.
hasProcessDependency
...that attributes a process dependency to a process
isPhysicalDomainFor
A topObjectProperty that relates a physical domain to the entity or dependency for which it is a domain
synonym
discussion
displayName
Information entropy amount
An entropy amount that is ∑ p ln(p), where p = liklihood of a particular message amongst all the messages that can be possibly occur
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)
4) the force in a spring as applied by entities at either end and as transmitted through the length of the spring.
Rate properties can be properly attributed to entities in two mathematically equivalent, but logically different, ways.
1) Representing the source/sink of a process where the rate properties are attributed to participants in a process. For example, a fluid flow process has a fluid-source entity and a fluid-sink entity so that the fluid rate is expressed as flow from source-to-sink. Similarly, mechanical process is due to forces exerted by "entity A" upon "entity B" . This kind of formulation asserts that the flow/force properties are so-called "cross properties" because they describe how energy is transmitted across a process in which entities participate.
2) Representong rates as "through" properties as attributes of a "mediator" that is an entity through which the process occurs. For a fluid flow process, the fluid flow rate is thus attributed to the flow conduit (or more properly, the lumen of the conduit) that mediates the source-to-sink flow. Or, in the case of the transmission of mechanical force, across the interface or boundary between two mechanical solid entities.
These different approaches yield mathematically equivalent results yet their semantic-logical representations differ ways that is a burden for the reasoning required to detect and resolve their equivalence. In the "cross" representation, source/sink enities are represented as source/sink participants in a process. In the "through" representation, source/sink entities are represented as parts of an entity that "mediates" the process.
The distinction between "through" and "cross" properties (variables in math models) is commonly used in engineerng analyses such the PhysSys ontology; 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.
Imaginary numerical form
Complex numerical form
Chemical conductance
1
Solid conductance
1
Spatial differential dependency
Portion of potential energy
A portion of energy proportional to the amount and displacement of a dynamical entity in a potential energy field or potential energy difference.
Fluid conductance
1
Heat conductance
1
PATO:0001756
Portion of kinetic energy
A portion of energy attributed to the motion of a dynamical entity.
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
PATO:0001757
Diffusion kinetic domain
Dynamical domain for which process participants are portions of particles and processes are the transport of particles from one portion to another portion
Partial gas pressure
Fluid pressure of a portion of gas in a mixture of gasses contained in a spatial region as if that portion of gas were the only gas contained the region.
Electromagnetic constant
Portion of energy
A themodynamic entity that is a portion of energy inhering in a dynamical entity
Fluid kinetic energy
A portion of kinetic energy attributed to the motion of a portion of fluid.
Solid kinetic energy
A portion of kinetic energy attributed to the motion of a solid.
Fluid potential energy
Domain potential energy of a portion of fluid due to changes in its volume, pressure or position in a gravitational field
Solid elastic potential energy
Chemical potential energy
Heat potential energy
Diffusion potential energy
Electrical potential energy
Magnetic potential energy
Magnetic inductive energy
A portion of kinetic energy attributed to an electrical current.
Translational momentum
A solid momentum property that is the temporal integral of a force, or the product of linear velocity and mass of a solid material entity
Mechanical force
PATO:0001035
...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
An energy amount that is the sum of kinetic and potential energies that inhers in a physical entity
Thickness of wall of shape
Conductance
A force-driven flow proportionality that is the ratio of flow to force in a resistive flow dependency.
Event rate
Temporal rate of aperiodic events during a temporal interval.
frequency
event frequency
Electrical resistivity
1
Solid sphere
Bending displacement
Constitutive proportionality
ideal property
A constitutive property that is a proportionality between values of dynamical property players.
i.e., having a linear relationship that intersects the origin; a characteristic of "ideal" dynamical elements
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.
Amount of chemical
1
A material amount that is the temporal integral of a chemical flow ro the amount of chemical in a portion of chemical
Chemical amount
Polar coordinate system 2D
2D-Polar coordinate system
Length dependency
A geometrical dependency of the length of a one-dimensional spatial region on the locus of points that bound the region.
Geometric form
...that is the mathematical structure of a property value.
Cardinality dimension
number of entities
count
Property dimension that is the set of positive integers and zero
N
Fluid momentum
1
A momentum property that is the temporal integral of a fluid pressure or the fluid flow rate 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 a portion, flow or distribution of thermodynamic energy or entropy.
Solid elastance
1
Shear capacitance
Kinetic energy amount
Energy amount that is an attribute of a material entity by virtue of its motion.
Potential energy amount
Real numerical form
Electrical elastance
1
Particle diffusive elastance
Faraday constant
1
...is the amount of electric charge per mole of electrons;
Faraday constant
Chemical resistive dependency
1
Resistive dependency of a chemical flow rate on the difference 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
Property coordinate form that is a spatial coordinate system.
Transformer modulus
1
Constitutive coupling proportionality that is a non-dimensional ratio of dynamical properties of players in a transformer dependency
Thermodynamic entropy amount
1
An entropy amount, S, that is Boltzmann's constant, Kb, times the liklihood, p, of a particular system microstate given a system macrostate; i.e., S = Kb * ∑ p ln(p)
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 inertance
1
...that is the mass of a portion of fluid that is a participant in an "ideal" fluid inductance process
fluid inertance
fluid inductance
Fluid viscosity
1
Time dimension
t
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.
Time
Shear force
Shear force
Tensile force
Tensile force
PATO:0002284
Inertance proportionality
A constitutive storage proportionality that is the ratio of force to momentum in a inductance dependency.
Amount
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
http://goldbook.iupac.org/list_goldbook_quantities_defs_A.html
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 physics attribute that is a scalar, vector or tensor quantity of a physics continuant, physic processural entity or physics dependency that is observable and measureable by physical means or derived by computations on such measures.
Electrical resistance
1
Temporal instant
1
A temporal entity that is a point in time
Fluid flow resistance
1
Rotational momentum
A solid momentum property that is the temporal integral of a torque, or the product of rotational velocity and rotational moment of inertia about a common axis of a solid material entity
rotational momentum
Thermodynamic emperature dimension
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.
T
temperature
Property dimension
Physics property attribute that is a fundamental coordinate basis of a property value.
As for SI and IUPAC conventions, OPB distinguishes:
1) physical dimensions as orthogonal aspects of measureable physical entities (e.g., mass, temperature),
vs.
2) the physical units by which such aspects are conventionally quantified (e.g., kilogram, degree Celsius)
_______________________________________
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
Chemical resistance
1
Solid capacitance
1
mechanical compliance
solid complliance
Solid momentum
1
Solid momentum
A momentum property that is the temporal integral of a force, or the product of velocity and the mass of a solid material entity
Cardinality of set
A statistical property that is the number of individuals in a set
Electrical resistive dependency
1
Resistive dependency of the flow rate of electrical charge flow (electrical current) on an electrical potential difference.
Fluid resistive dependency
1
Resistive dependency of a fluid flow rate on a fluid pressure differential.
Solid resistive dependency
1
Force-driven rate dependency of a solid velocity and solid force differential.
Diffusion gradient rate dependency
1
Fick's law of diffusion
Ficks law
An amount-driven rate dependency 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
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 and the processes are their spatial rotations and/or translations and their accelerations.
Heat transfer resistance
1
Heat flow rate
1
Energy flow rate that is the temporal rate of the loss of heat energy of a dynamical entity that is the product of the entity's temperature times the difference of its entropy with that of its surroundings.
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
Property of value distribution
...that is a
Electrochemical domain
Dynamical domain in which the physical entity is a portions of ions and the processes are the flows of ions from one portion to another
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
1
formerly dielectric constant
Elastance proportionality
A constitutive storage proportionality that is the ratio of force to displacement in a capacitive dependency and is the reciprocal of an capacitance. property.
Resistance
A force-driven flow proporionality 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.
theta
ang
plane angle
Chemical flow rate
1
Flow rate property that is the temporal derivative of the amount of chemical
Dynamical domain
Analytical domain in which dynamical entities exchange energy by the dynamical processes in which they participate.
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
Lineal 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.
Event trajectory
A trajectory that is a temporally-ordered series of events.
Material dynamical entity
1
1
A dynamical entity that is composed of elements.
Per BFO2.0: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part.
Capacitive force process
A constitutive process determined by a capacitive force dependency.
Temporal duration
Second SI-unit
duration
Temporal property that is the amount of time between two temporal instants.
time span
Translational displacement
Translational displacement
Thermodynamical domain
Physics analytical domain in which the participants have portions of thermodynamical energy.
Potential energy field
An immaterial dynamical entity that is the distribution of potential energy due to the separation of material, charge, or magnetic monopoles
Constitutive transactor coefficient
2
...that is the proportionality between two dynamical properties in a transactor dependency
Temperature
1
Because temperature is an intensive property that properly only applies to a single point in an entity, assigning a "temperature" as a property of a discretized physical entity that extends is space presents problems. If temperature is constant over the spatial extent of an entity (i.e., it is "isothermic") then it is fair to say that the entity has a single value of temperature. Such an assumption is quite often made for homeothermic biological organisms and their parts. However, it is not meaningful to calculate a spatial integral of temperature derive an "average” temperature because such integrals have meaning only for extensive properties like mass density or current density. However, some analyses do aim to account explicitly for temperature gradients that drive heat transfers between entities or parts of entities. In such cases it is useful to define, for continuum modeling, a spatial distribution for temperature and heat fluxes.
However, for discrete modeling, the temperature of an entity can be assigned a value while its parts are assigned different temperatures — the discrete analogue of a continuum temperature distribution. For example, the temperature of mitochondria is likely to be higher than the surrounding portion of cytosol. That being said, there is utility in expressing that a discrete, dynamical entity can have a discrete temperature property with one value while allowing one or more of its parts to have separate temperature properties with different values. For computational purposes one can make the assumption that all parts of an entity share the same temperature property instance as the (whole) entity while parts that have a different temperature will have their own temperature property with a value that may difffer from the temperature value of the whole entity (and the other parts).
PATO:0000146
A thermodynamical property that is a measure of and is driving force for the flow of heat energy.
"A temperature is an objective comparative measurement of hotness or coldness."
https://en.wikipedia.org/wiki/Temperature
Because temperature is an intensive property that properly only applies to a single point in an entity, assigning a "temperature" as a property of a discretized physical entity that extends is space presents problems. If temperature is constant over the spatial extent of an entity (i.e., it is "isothermic") then it is fair to say that the entity has a single value of temperature. Such an assumption is quite often made for homeothermic biological organisms and their parts. However, it is not meaningful to calculate a spatial integral of temperature derive an "average” temperature because such integrals have meaning only for extensive properties like mass density or current density. However, some analyses do aim to account explicitly for temperature gradients that drive heat transfers between entities or parts of entities. In such cases it is useful to define, for continuum modeling, a spatial distribution for temperature and heat fluxes.
However, for discrete modeling, the temperature of an entity can be assigned a value while its parts are assigned different temperatures — the discrete analogue of a continuum temperature distribution. For example, the temperature of mitochondria is likely to be higher than the surrounding portion of cytosol. That being said, there is utility in expressing that a discrete, dynamical entity can have a discrete temperature property with one value while allowing one or more of its parts to have separate temperature properties with different values. For computational purposes one can make the assumption that all parts of an entity share the same temperature property instance as the (whole) entity while parts that have a different temperature will have their own temperature property with a value that may difffer from the temperature value of the whole entity (and the other parts).
Spatial area
A spatial property that is the two-dimensional extent of a surface region.
PATO:0001323
area
surface area
Fluid flow rate
1
volume flow rate
volume flow
A flow rate property that is the temporal derivative of a fluid volume
VolumetricFlowRate - Volume of fluid passing a point in a system per unit of time.
http://www.unitsofmeasurement.org/apidocs/index.html
One dimensional spatial coordinate basis
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.
charge flow
amperes
current
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
PATO:0000040
A mechanical displacement that is the temporal integral of a solid velocity.
Volumetric capacitance
1
compliance
fluid compliance
volumetric compliance
vascular compliance
Shear displacement
Shear displacement
Heat capacitance
1
Concentration of chemical
1
hasPhysicalDomain exactly 1 'Chemical kinetic domain'
The molar amount of a portion of molecules normalized to the spatial amount of the spatial region occupied by the molecules
Property form
Property form classes are provided for the annotation and reconciliation of potentially different expression, definition and/or form of a physical property value
A physics property attribute that is the spatial scope, mathematical form or spatial coordinate basis of a property value.
Portion of liquid
A portion of fluid that is incompressible
Lineal shear velocity
Cartesian 3D-coordinate system
Initial instant of process
A temporal instant that is the first temporal instant in a temporal interval
Terminal instant of process
A temporal instant that is the last temporal instant in a temporal interval
Geometrical dependency
A mathematical dependency of values of geometrical spatial properties.
Magnetic constant
1
Magnetic constant
Chemical potential
1
A flow-driving potential that drives the chemical transformation of one kind of chemical species into another.
Gibbs free energy
"...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
G
partial molar free energy
Fluid kinetic domain
Dynamical domain in which the physical entity is a portion fluid and the processes are flows od fluid from one portion to another
Transducer dependency
2
transducer
A constitutive dependency for two participants of different physical domains in which the products of force-times-rate of one participant equals the force-times-rate of the other participant
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.
An example of the quantitative property dependency is: E1 = nE2, and nF1 = F2, where E and F are force and flow properties, respectively, of patticipants 1 and 2, and is a positive scalar transformer ratio..
Statistical property
1
A physical property that is a scalar statistical attribute of a set of physical property values.
As with Informational properties, statistical properties are sketched in as placeholders for further development as use-cases require.
Temporal property
1
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 mathematical form
--- outsource this class to existing ontology??
A property form that is the mathematical form of a property value
Charge amount
1
Electrical charge
An amount property that is the temporal integral of an electrical current
PATO:0002193
Solid inertance
1
solid inductance
...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
Real-imaginary form
Gravitational constant
1
Constitutive state property of continuum
...that is a physical property of matter or space whose value is invariant with respect to time
Molar amount of chemical
1
Absolute amount of chemical that is the mass a portion of a chemical within a spatial region normalized to the molecular weight of the chemical.
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
Constitutive flow proportionality for a constitutive coupling dependency.
Chemical kinetic domain
Dynamical domain for which process participants are portions of chemical reactants and the processes are chemical reactions.
Tensor form
...is a physical property whose value is a multidimensional array of scalars whose values are invariant under spatial coordinate transformation.
Statistical domain
Abstract domain that applies to sets of physics analytical entities and their relationships as expressed with statistical metrics.
Portion of electrical charge
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.
An Immaterial dynamical entity that is a countable or uncountable set of quantal charges.
Electrical capacitance
1
PATO:0002205
Temporal coordinate basis
Property coordinate form 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
displacement
span
L
Mean value
Mass density
1
Mass density
Cylindrical coordinate system
Cylindrical coordinate system
Amount of particles
1
Particle amount
An amount property that is the temporal integral of a particle flow or
amount of particles in a portion of particles.
Physics model domain
A physics model entity that is a branch of physical analysis such as fluid kinetics, chemical kiinetics, or thermodynamics within which physical continuants, dependencies, and processes share physical properties.
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.
Property spatial scope
A property form that defines the spatial dimensions for which the value of an extensive physical property is defined.
Heat kinetic domain
Dynamical domain in which heat energy is transported from one portion of heat to another
Angular displacement
Inductive momentum process
A constitutive process determined by an inductive momentum dependency.
Momentum property
A dynamical state property that is the temporal integral of a force, or the product of the mass and velocity of a material entity
Angular velocity
Heat energy amount
1
Heat amount
A amount property that is the temporal integral of a heat flow
Area dependency
A geometrical dependency of the area of a two-dimensional spatial region on the locus of points that bound the region.
Spherical coordinate system
Spherical coordinate system
Electrodiffusional potential
1
A force property that drives the flux electrically-charged particles from one portion of particles to another according to the electrical charge and concentration of the particles.
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
PATO:0001025
A momentum driving force that is the force per unit area that a fluid exerts on itself or on a surface that bounds the fluid, and can accelerate or displace a portion of fluid
Temporal entity
A physics processural entity that is an instant or span of time.
Capacitance proportionality
A constitutive storage proportionality that is the ratio of displacement to force in a capacitive dependency and is the reciprocal of an elastance. property.
compliance
Thermodynamical entity
A physics continuant that is portion of thermodynamic energy or entropy.
OPB strongly distinguishes the terms "dynamical" and "thermodynamical":
"Dynamical" is used as an adjective applied to continuant entities, processes, attributes, etc. that possess thermodynamic energy whereas "thermodynamical" is applied to portions, fluxes, etc. of energy (a primitive) that inher in continuants and are exchanged during dynamical processes.
Electrostatic field
A potential energy field produced by electrically charged objects that attracts of repels other electrically charged objects.
Spatial volume
PATO:0000918
volume
A spatial property that is the quantity of space enclosed in a bounded volume region
Temporal span
1
1
A temporal entity that is a contiguous interval of time bounded by temporal instants.
Physics model entity
The OPB is an ontology of the abstractions created by the science of classical physics (including thermodynamics) particularly as formulated for analytical purposes by the science of engineering system dynamics.
OPB is not intended to represent physical "reality" as is the aim of upper ontologies such as Basic Formal Ontology and General Formal Ontology. Rather, we aim to facilitate and expedite the annotation and cross-referencing of physics-based analytical models in the broad realm of biomedicine. In curating the OPB, we have strived to represent biophysical knowledge of biological function using the formal tools and concepts of computational ontology as expressed in description logic (DL), web ontology language (OWL).
OPB has classes that represent abstractions of key"realist" classes in BFO such as BFO:Continuant (OPB:Physics continuant). BFO:Processural entity (OPB:Processural entity), and BFO:Attribute (OPB:Physics attribute). The main differentiator is that OPB represents physical entities not represented in BFO. These include representations of thermodynamic energy, potential energy fields, information, and, in particular, physical processes are defined as the flow of energy and/or information amounst process participants. These are essential concepts for explaining, understanding and testing of biophysical hypotheses.
To emphasize intent of the OPB as an ontology of analytical concepts, we have purposely named its top class and its subclasses using the term "Physics" to reference the science of physics rather than the term "physical" which could imply realist view of the "physical world".
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.
A physics entity that is a theoretical or computational representation of real-world entity that is useful for describing and analyzing real continuants and processes, their respective attributes, and the dependencies by which they are related.
Particle diffusion coefficient
1
partiicle diffusivity
mass diffusivity
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 continuum
A constitutive proportionality that is defined at a spatial point within a portion of material or a field
Spatial scale domain
Spatial scales are listed for annotation purposes only and are a subset of more extensive ontological representations such as subclasses of FMA:postnatal anatomical structures.
Spatial domain in which the physical entities are approximately of a specific anatomical spatial size
Three dimensional spatial coordinate basis
Spatial coordinate basis that is comprised of three orthogonal spatial dimensions
Two dimensional spatial coordinate basis
Spatial coordinate basis that is comprised of two orthogonal spatial dimensions
Volume dependency
A geometrical dependency of the volume of a three-dimensional spatial region on the locus of points that bound the region.
Potential field dependency
Gravitational potential dependency
Electrostatic potential dependency
Energy amount
1
1
Energy property that is the amount of energy in a portion of energy
PATO:0001021
Energy flow rate
1
1
An energy property that is the temporal rate at which energy is transported across an entity boundary.
PATO:0001024
power
Entropy flow rate
1
1
An entropy property that is the trmporal rate if change of a portion of entropy
Entropy amount
https://en.wikipedia.org/wiki/Entropy_in_thermodynamics_and_information_theory
A thermodynamic property for the amount of entropy in a portion of entropy
Dynamical property
A physical property that is an attribute of a dynamical entity, a dynamical process or a constitutive dynamical dependency whose value determines the amount or rate of change 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.
http://en.wikipedia.org/wiki/Dynamical_system
Dynamical state property
http://en.wikipedia.org/wiki/State_variable
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.
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 or amount property
Chemical molar flow rate
molar flow rate
molar flow
Chemical flow rate measured in concentration per unit time; moles/s
Chemical concentration flow rate
Chemical flow rate property measured in chemical concentration per unit time.
chemical flux
chemical concentration flux
Diffusion potential
1
A flux driving potential that drives the flow of particles from one portion of particles to another according to the difference in concentration of the particles
Spatial integral dependency
Particle concentration
Particle count
Rotational inertance
1
Portion of chemical
Lineal mechanical inductive dependency
1
Rotational mechanical inductive dependency
1
Section area of spatial region
Geometrical form
https://en.wikipedia.org/wiki/Shape
A shape is the form of an object or its external boundary, outline, or external surface, as opposed to other properties such as color, texture, or material composition....
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Our current representation of geometrical forms is based implicitly on engineering intuitions and, thus, may be changed to reflect the rigor of available spatial ontologies
––––––––
Shape models provide a set of geometrical abstractions commonly used by physiologists to represent anatomical participants in biological processes.
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.
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.
A mathematical entity that is the spatial form of a dynamical boundary.
Sum of rates
A sum of rates dependency that holds for rate properties.
Electrical domain
Immaterial dynamical domain in which a participating entity is a physical entity is an electrical field.
Total energy dependency
An energy state dependency of a portion of total energy on the portions of kinetic and potential energy that inher in a set of dynamical entities.
Energy dissipation dependency
1
1
1
Heat flow dependency
An energy rate dependency of the heat dissipation rate generated by resistive forces acting on a dynamical flow.
Dynamical entity
1
A physics continuant that occupies a spatial region, is a bearer of energy, has dynamical properties, and can participate in dynamical processes.
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.
Flexional joint
A mechanical joint whose parts are constrained to rotate around a longitudinal axis.
Loop rate constraint
1-junction
Kirchhoff's loop rule
Kirchhoff's mesh rule
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.
A loop rate constraint by which the sum of all rate properties acting in a closed loop is identically zero; a "one junction" in bond graph theory
Kirchhoff's second law
Kirchhoff's second rule
Sum of forces
A sum of rate properties that holds for force properties.
Existential event
A physical state event that is the appearance, disappearance, or transformation of a physical entity as a participant in a physical process
Section area
Magnetism
Primitive physical entity that is a magnetic field.
Poisson ratio
coefficient of expansion on the transverse axial
https://en.wikipedia.org/wiki/Poisson%27s_ratio
negative ratio of transverse to axial strain
Time
A primitive physical entity that is time.
PATO:0002284
Structural event
A physical state evernt that is a discrete change in a structural relation between participants in a process
...that is a structural fluent.
Dynamical process
energy bond
A physical process whose rate is determined by a constitutive dependency.
Lagrangian energy dependency
An energy dependency that is the difference between the kinetic energy and the potential energy content of a dynamical entity.
Constitutive storage proportionality
Solid potential energy amount
1
Fluid potential energy amount
1
Chemical potential energy amount
1
∆G
Gibbs free energy
Fluid kinetic energy amount
1
Kinetic energy amount that is an attribute of a fluid entity by virtue of its flow rate.
Solid kinetic energy amount
1
Energy amount that is an attribute of a solid entity by virtue of its velocity.
Immaterial dynamical entity
A dynamical entity that is not composed of elements
Temporal calculus constraint
A calculus dependency that is the derivative or integral of a property value with respect to time
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.
Conservation law
Axial 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
PATO:0001461
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)
Amount of fluid
A material amount of a portion of gas or liquid
Property dependency graph
A physics network model in which nodes represent physical properties and arcs are dynamical dependencies by which property values depend upon one another.
Energy flow dependency
1
1
1
Atomic anion
A charged atom that has a net positive electrical charge
Property value trajectory
A process state trajectory that is the temporally-ordered locus of values of a physical property value of a process participant.
Surface area
Surface area of spatial region
Property coordinate form
A property form that is the spatial and/or temporal coordinate system within which a property value is defined.
Statistical property of value set
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.
Property value that is used to characterize the distribution of property values.
Threshold value 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 relation trajectory
Process state trajectory that is the temporal ordering of the structural relations of a participant in a physical process
Existential type trajectory
A physical state trajectory that is the temporally ordering of the entity-type of a process participant.
Mechanical stress
A mechanical force property that is the amount of force per unit of spatial extent.
Structural state
A physical state that is the set of structural relations of a physical continuant to other continuants.
Dynamical state
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.
A physical state that is the set of values of one or more dynamical properties.
Perimeter span of spatial region
Property value
A physics property attribute that is the magnitude of an instance of a physical property.
"Property value" classes provide formal classifications of the kinds of measurements made in the course of physical experiments and analyses according to the use intended for the value. For example a value may represent a single measurement recorded from an instrument, the value as scaled to a system of measures such as Systeme Internationale, the value as a statistical measure of a set of values, or the value of a correlation between two sets of measures.
Annotations of Property value classes are intended to formally distiguish property values that should be compared or analyzed with care.
Membrane potential
An electrical potential that exists across an electrodiffusion barrier such as a cell membrane.
Amount-driven flow process
A dynamical process whose dynamical rate is determined the amount properties of its participants.
Participant state event
A physical event that is a discrete change of physical state of a physical entity
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.
Clearly, no physical event is truly discrete as that implies a change of physical dynamical state that occurs instantaneously which implies an infinite rate of energy flux; clearly, an impossibility.
Fluid volume
An amount property that is the temporal integral of an fluid flow rate
Property of ion channel flux dependency
Plane angle of shape model
Spatial span
PATO:0001708
A spatial property that is the spatial distance between two spatial points.
Plane angle of spatial region
Solid angle of spatial region
Chemical structure
compound
substrate
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.
molecular species
chemical substrate
reactant
chemical product
chemical reactant
A solid dynamical entity that can participate in chemical reaction processes.
Solid potential energy
Solid angle of shape model
Bounded volume region
A three-dimensional region that has a finite spatial extent defined by on or more contiguous spatial surfaces.
Plane angle
Solid gravitational potential energy
Unbounded volume region
A three-dimensional region that has a infinite spatial extent incompletely limited by zero or more two-dimensional regions.
Bounded surface region
A two-dimensional region that has finite spatial extent that is limited by one or more bounded line regions
Unbounded surface region
A two-dimensional region that has a infinite spatial extent limited incompletely by zero or more one-dimensional regions.
Bounded line region
A one-dimensional region that has a finite spatial extent limited by spatial points at each end.
Entity fusion event
Existential event during which two or more physical entity instances becomes a single entity instances.
Entity fission event
Existential event during an instance of a physical entity becomes more than one entity instances
Atomic cation
A charged atom that has a net negative electrical charge
Entity appearance event
Existential event that is the appearance of a physical entity of a classifiable type
Entity disappearance event
Existential event that is the disappearance of a physical entity as a classifiable type.
Byte
Pressure differential
A fluid pressure that is the difference in pressure that exists between two portions of fluid.
Absolute pressure
A fluid pressure that is measured relative to the absolute zero pressure of a vacuum
Resistive flow process
A constitutive process whose rates are determined by a resistive rate dependency for which thermal energy is dissipated as the product of a flow rate times a potential difference.
Chemical mass-action flow process
1
1
Amount-driven flow process for the chemical kinetic domain
Diffusion-gradient flow process
1
1
Amount-driven flow process for the diffusion kinetic domain
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
A relative value that is the maximum value within a set or continuum of values
Thermodynamical state
A physical state that is the set of values of one or more thermodynamical properties of a thermodynamical entity.
Charged particulate
ionic species
ion
A particulate that bears a net electrical charge
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
Physical property attribute
Physics model entity that is the value, dimension, unit, or mathematical form of a physical property as measured or as a model variable.
Change adjacency event
Change connectivity event
Change location event
Entity transformation event
Existential event during which an entity becomes an entity of a different type.
Property value event
A physical state event that occurs when the value of a physical property value traverses a minimum, maximum or threshold value.
Unbounded line region
A one-dimensional region that has a infinite spatial extent limited by one or no spatial points.
Material amount
1
inertia
An amount property that is the mass of matter that inhers in a material dynamical entity
mass
synonyms: mass, inertia, inertial mass
PATO:0000125
https://en.wikipedia.org/wiki/Inertia
No physical difference has been found between gravitational and inertial mass in a given inertial frame.
Inertial mass is found by applying a known net force to an unknown mass, measuring the resulting acceleration, and applying Newton's Second Law, m = F/a.
Gravitational mass is measured by comparing the force of gravity of an unknown mass to the force of gravity of a known mass.
Constitutive transformer ratio
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
Unbounded plate
Threshold value
Material dynamical domain
Dynamical domain in which entity are material dynamical entities
Uncharged particulate
A particulate that bears no net electrical charge.
Rotational joint
A mechanical joint in which one or both parts are constrined to rotate about a longitudinal axis.
Unbounded filament
Threshold exceeded event
Physics continuant
Physics real entity that is a physically-observable continuant in the real world.
Physics continuant is an abstraction of a "real" continuant represented by upper level biomedical ontologies. Thus OPB aims to represent the physics of abstracted, simplified models of complex biological entities and processes
See, for example, "spherical cow" as an abstract model of a real cow (Wikipedia:Spherical cow).
Portion of uncharged particles
A portion of particles that bear no net electrical charge
Quantal positive charge
A quantum charge that is the electrical charge of a positron
Physical condition
A physics attribute of a physics continuant that includes: its existential type, its structural relations to other entities, the values of at least one of its physical properties at a moment in time.
The class 'Physical conditon' 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 quantal charge that is the elecrtical charge of an electron
Start process event
Boundary amount constraint
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.
Chemical resistive flow process
Force-driven flow process for which a chemical flow is driven by the chemical potentials of reactants
Fluid resistive flow process
Spatiotemporal coordinate basis
Property coordinate form that is a spatial coordinate system and a temporal coordinate system.
Bounded filament
Thermal conductivity
1
Magnetic domain
Immaterial dynamical domain in which a participating entity is a physical entity is a magnetic field.
Because OPB is designed for representing discrete dynamical systems, the representation of magnetic theory and system is attenuated and deferred.
Thermal diffusivity
1
Minimum value
Variance value
Mean value
Electrical energy flow dependency
1
Standard deviation value
Tensor form
Gravitational field potential energy dependency
1
A dependency of the potential energy of a material entity due to vertical displacement in the earth's gravitational field.
https://en.wikipedia.org/wiki/Gravitational_energy
Bit
Variability value
Distributive property value that is a measure of the dispersion of magnitudes in a set or trajectory of values.
Lineal particle diffusion coefficient
Areal particle diffusion coefficient
Atomic weight
Molecular weight
End process event
Scalar form
Perimeter span of shape model
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.
Physical event rate
A temporal property that is the number physical events that occur during a temporal interval.
Electrical resistive flow process
Heat transfer flow process
A amount-driven flow process whose flow rate is determined the temperature property of its participants.
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.
Particulate
A solid dyamical entity that can participate in a diffusive process, advection or convection.
Energy bond graph
bond graph
energy bond graph
A physics model in which nodes represent portions of energy and arcs represent flows of energy.
Zero-dimensional spatial region
A spatial region that is a point in space.
Spatial location
A spatial property that is a set of coordinate values (in 1-, 2-, or 3-dimensions) of point in space relative to the origin of a coordinate system.
Information domain
Abstract domain that encompasses the quantification, storage, and communication of information amongst participants in a physics process.
Charged molecule
A charged particulate that is a molecule.
Mathematical domain
A physics analytical entity that is a mathematical function or quantitative value useful for the analysis and simulation of biophysical models.
Portion of fluid
A portion of material that has no inherent shape and assumes the shape of its container
Solid angle
Transport process
A constitutive process whose rates are determined by a transport dependency.
Physics real entity
A physics entity that is a real-world continuant, process or an attribute of such.
Advective transport process
Lagrangian energy amount
An energy amount for a dynamical ehtity that is the algebraic difference its kinetic energy minus its potential energy.
Portion of strain potential energy
Electrical potential
Flow-driving potenrial that drives electrical charge through an electrically conducting medium.
Convective transport process
Calculus constraint
Algebraic dependency
Temporal integrative constraint
A temporal calculus dependency that is the temporal rate of change of a property value.
Signalled transactor coefficient
...that is a proportionality of a signalled transactor dependency
Direct transactor coefficient
Electrical inductive energy dependency
1
Magnetic field potential energy dependency
A potential energy dependency a magnetic or ferrous entity in a magnetic field.
Charged polymolecule
A charged particulate that is a polymolecule.
Diffusion gradient
A potential energy field that is a spatial gradient of particle concentration.
Temporal derivative constraint
A temporal calculus dependency that is the temporal rate of change of a property value.
Boundary momentum constraint
Electrochemical diffusion gradient
A potential energy field that is a combination of an electrostatic and a diffusion gradient.
Diffusive transformer
A constitutive process whose rates are determined by a diffusive transformer dependency.
Mechanical transformer process
A transformer process whose rates are determined by a mechanical transformer dependency.
Portion of heat energy
A portion of energy that is in the form of heat of a material entity.
Spatial entity
1
A physics continuant that is a portion of space in a spatial reference frame.
Definition ("comment") is verbatim from the definition of BFO:Spaatial region. However, physical analytical entities must include bounded regions (ala BFO "realism") as well as unbounded physical regions of electrical and gravitational fields, as well as for analytical fictions such as used for spatial integrals from a spatial origin to spatial infinity.
Energy density
1
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.
Electrical resistive dissipation
1
Osmolality
1
A chemical concentration the amount of solute per liter of solution.
PATO:0002027
Multiplicative dependency
Additive dependency
Difference dependency
Divisor dependency
Osmolarity
1
A chemical concentration the amount of solute per kilogram of solution.
PATO:0001655
Solid force
1
A momentum driving force that acts to accelerate, displace, or deform a solid physical entity
Longitudinal tensile wall force
Circumferential tensile wall force
Space
A primitive physical entity that is space.
Calculus dependency
https://en.wikipedia.org/wiki/Calculus
Filament form
A shape form that is a solid cylinder that is longer than it is thick.
Plate form
A shape form that is a planar solid that is broader than it is thick
Pipe form
A walled form 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 form
A walled form that is a hollow sphere composed of a wall part enclosing a lumen part.
Differential dependency
https://en.wikipedia.org/wiki/Calculus#Differential_calculus
Constitutive flow proportionality
rate constant
Constitutive proportionality between properties in a dynamical flow dependency.
Standard property value
A property value that serves as a standard value for a system of units of measure for the property.
Spatial region
A spatial entity that is a spatially bound, contiguous portion of space
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.
Three-dimensional region
A spatial region that is a volumetric region in space with three spatial dimensions.
Event frequency
Temporal rate of periodic events during a temporal interval.
Spatial curvature
A spatial property that is the degree to which a spatial line region or surface region deviates from being straight or flat, respectively.
Spatial coordinate domain
Spatial domain in which spatial scales are restricted to one, two or three spatial dimensions
Dynamical acceleration property
A dynamical property that is the temporal rate of change of a flow rate property.
Integrative dependency
https://en.wikipedia.org/wiki/Integral
Definite integrative dependency
One-dimensional spatial domain
Spatial coordinate domain in which all spatial properties are referred to a single spatial coordinate system
Charge density
1
Material flow rate
1
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.
Indefinite integrative dependency
Two-dimensional spatial domain
Spatial coordinate domain in which all spatial properties are referred to a two dimensional spatial coordinate system
Three-dimensional spatial domain
Spatial coordinate domain in which all spatial properties are referred to a three dimensional spatial coordinate system
Kinetic energy domain
Thermodynamical domain in which physics continuants each have and exchange a portion of kinetic energy.
Potential energy domain
Thermodynamical domain in which physics continuants each have and exchange a portion of potential energy.
Mass of solid entity
Force dimension
F
Dynamical dependency
Physics dependency that is a quantitative relationship amongst values of dynamical properties.
Heat capacity
1
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
Tensor dependency
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.
Scaled property value
Property value that is the ratio of two or more observed or standard property values.
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.
Solid dynamical entity
A material dynamical entity that occupies a portion of space and has inherent shape and solid mechanical properties.
Portion of material
A material dynamical entity that occupies a spatial region, has no inherent shape and consists of innumerable energy-bearing material parts.
Two-dimensional region
A spatial region that is a surface having two spatial dimensions.
One-dimensional region
A spatial region that is a line in space.
Spatial property
1
A physical property that is a scalar or vectorial measure of the spatial extent, location, or shape of a spatial entity.
Solid resistive motion process
Fluid viscous dissipation
1
Discrete value change event
Thermal efficiency
Thermal efficiency can be defined in many ways that always require distinguishing "useful" energy flow from "waste" energy flow. Definitions, even for engineering systems or mechanisms, may differ in different contexts and present complex fdefineitional issues. For a biochemical system, for example, "useful" depends on context and "purpose" of a process. If one is concerned with transducing biochemical potential energy into useful mechanical energy of muscle contraction, the attendant heat production and loss may be viewed a inefficient. However, the usefulness of brown fat in rodents is that they very efficiently convert biochemical energy into heat (in a so-called "futile cycle) for the goal of temperature regulation.
A thermodynamical property that is the fraction of energy flow through a dynamical process that is biologically useful.
A thermodynamical property whose value depends on the material composition and spatial attributes of a dynamical entity that determines rates of heat flow within the entity
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 form
A solid form 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.
Physical process
A physics processual entity that is the flow or exchange of thermodynamic energy and/or information amongst dynamical entities that are its partcipants.
Property value boundary
A bona fide dynamical boundary that is a spatially contiguous discontinuity of physical property values.
Solid form
A geometrical form that composed of a single spatial region.
Walled form
A geometrical form that composed of a one spatial region, the wall part, that bounds a second spatial region, the lumen part.
Walled forms are intended to be geometrical abstractions of biological entities such as blood vessels, cardiac chambers, membrane-bound cells, etc. The distinctions between thick- vs. thin-walls depends on whether lumped parameters for the wall (e.g., a diffusion coefficient) depend on wall thickness (e.g., D vs. d*thickness)
Gravitational domain
Immaterial dynamical domain in which a participating entity is a physical entity is a gravitational field.
Section area of shape model
An area of a plane that transects a volume shape model and that is enclosed within the boundary of a shape model.
Surface area of shape model
A shape model area that is the area of the bounding region of a volume region
Span of lumen
Span of outer bound of shape
Transverse span
A span of spatial entity that is straight-line distance between two points on the bounds of a spatial entity
Perimeter span
A span of spatial entity that is the spatial distance along a path, straight or curved, that is within the boundary of a spatial entity from one point to itself or to another point.
Reversal potential
Here we distinguish two subclasses of membrane reversal potential that account for either
(1) the "Nernst potenial" for a single ionic species whether or not it permeates the membrane as calculated by the Nernst equation that has terms the ratio of inner-to-outer ion concentrations (e.g., [Nai] / [Nao]) but no term of ionic permebility. That is, Nernst potentials are function only of the ion gradient (as a ratio) and not of ion permeability according to the Nernst equation. Thus, a Nernst reversal potential (for a single ion) can only be measured empirically under strict equilibrium conditions where membranes are permeable only to ions and there are no transmembrane ion currents, as from electrogenicl pumps.
(2) the "GHK potential" (Goldman-Hodgkin-Katz potential) applies multiple ionic species and depends on their relative permeabilities as can be calculated using the GHK equation if all ion gradient ratios and relative permeabilities are known. The GHK reversal potential can be determined experimentally for a membrane as its resting membrane potential for which there is no net ion flux.
See, amongst many others, for mathematical treatments:
Hille, B. (2001). Ion Channels of Excitable Membranes. Sunderland, MA, USA, Sinauer Associates, Inc.
http://www.physiologyweb.com/lecture_notes/resting_membrane_potential/resting_membrane_potential_nernst_equilibrium_potential.html
The electrical potential across an electrodiffusion barrier that nullifies net ion diffusion
GHK reversal potential
membrane reversal potential
An electrical potential that nullifies net ionic flux of a permeant ionic species according to the membrane permeability of each species as determined by the Goldman-Hodgkin-Katz equation.
Spatial calculus constraint
A calculus dependency that is the derivative or integral of a property value with respect to a spatial displacement.
Spatial integrative constraint
Boundary state constraint
A state constraint that determine state property values of a physics model boundary.
Kirchoff constraint
Kirchoff's laws
A dynamical constraint on the values of two or more rate properties
Boundary rate constraint
A rate constraint that determine rate property values of a physics model boundary.
Mathematical dependency
A mathermatical entity that is a mathematical function.
OPB representation of mathematical entities is left primitive in deference to other mathematical resources. To attempt a more thorough representation opens a slippery slope into representing the entirety of math theory and practice. It seems useful to represent commonly used mathematical functions (e.g., trig functions, differential & integral calculus, complex numbers) there is a danger in doing so in manner that is as stringent and complete as are the representations of physics.
Set of physics properties
Summation constraint
A dynamical constraint on the sum of a set of dynamical property values.
Thermodynamical state property
A thermodynamical property that is the amount of energy or entropy of a dynamical entity.
Thermodynamical rate property
A thermodynamical property that is the temporal rate of energy or entropy flow.
Thermodynamical constitutive property
A thermodynamical property whose value determines how heat and entropy flow depends on the material composition and spatial properties of a dynamical entity
Information transmission process
Information transformation process
Statistical dependency
A mathematical dependency of values of staistical properties.
Amount of solid entity
1
An amount property that is the amount of material that inhers in a solid entity
Amount-driven flow proportionality
Constitutive flow proportionality for an amount-driven flow proportionality
Process conditional dependency
An process dependency that defines a physical continuant state of process participants that is a necessary and sufficient condition to initiate or terminate an occurrence of the process.
Precondition dependency
formalized as a PSL:precondition axiom
formalized as a SC:precondition axiom
A process conditional dependency that defines a physical continuant state of process participants the is a necessary and sufficient condition to initiate an occurrence of the process.
Postcondition dependency
formalized as PSL:process postcondition axiom
formalized as SC:successor state axiom
A process occurrence dependency that defines a physical continuant state of process participants that is sufficient to terminate the process.
Spatial derivative constraint
Existential event dependency
...by which a change in the type or existence of a physical entity is a consequence of its physical state
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
State fraction of chemical
Ion conductance per area
Ion conductance per capacitance
Liquid kinetic domain
Fluid kinetic domain in which the physical entity is a portion liquid
Gas kinetic domain
Fluid kinetic domain in which the physical entity is a portion gas.
Ion conductance per path
Portion of charged particles
A portion of particles that bear a net electrical charge.
Solid friction dissipation
1
Diffusion coefficient
1
Portion of displacement potential energy
Thermal conductivity
A thermodynamical property that is the rate of heat energy flow between physical entities to the difference of their temperatures
Thermal capacity
A thermodynamical property that is the ratio of the heat energy added or removed to a physical entity to the change in its temperature
Geometrical domain
Abstract domain that encompasses the properties of space and the shape, size, relative position of spatial shapes.
Dynamical boundary
Dynamical 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 physics continuant that mediates energy or information flow amongst dynamical entities that are participating in a physical process.
Fluid dynamical boundary
Fiat dynamical boundary that is a spatial separation between portions of fluid distinguished by the values of their physical properties as they participate in a fluid kinetic process
Examples of fluid kinetic boundaries are the boundary between contiguous portions of blood that have turbulent vs. laminar flow, or have pulsatile vs. non-pulsatile flow.
Tensile wall force of tube
Amount property
Molecule
The distinction between micromolecule and macromolecule subclasses is necessarily vague because there is no universally agreed upon or satisfactory molecular weight or structural criteria by which these subclasses are to be distinguished. In service to the representing function, OPB distinguishes micro/macro more along the lines of function: micromolecules play the roles of substrate/product/modifier/transportee in processes while macromolecules serve as the catalysts and mediators of the processes. Clearly, such a distinction admits to many exceptions which we leave for subsequent OPB versions or the cleverness of OPB user to work around
A chemical structure composed of elements linked by covalent chemical bonds.
Thermodynamical dependency
1
A physics dependency that relates values of thermodynamical properties to the values of dynamical properties or to other thermodynamical properties
Thermodynamic potential
Thermodynamic potentials are quantified by scalar, extensive variables (e.g., U, H, F, G...) and are used predominanty (historically?) for the analysis of chemical and fluid systems. Consequently, the kinetic and potential energies of other entities
A portion of energy defined as algebraic sums or differences of portions of energy defined according to constraints on the values of physical properties.
Mechanical joint
A mechanical joint is a structural region that joins two or more solid dynamical entities but has less structural rigiity than either solid entity.
A bona fide dynamical boundary between two or more solid dynamical entities that constrains their relative motions along at least one spatial axis.
Portion of gas
A portion of fluid that is compressible
Weight of solid entity
Physics graph model
Physics model entity that is a node-arc graph that is useful for the representation and analysis of physics real entities
Amount of liquid
1
A material amount of a portion of liquid
Hybrid physics graph model
A physics model composed of portions of physics graph models that share nodes and arcs.
Heat transfer dependency
1
Thermal contact conductance
Thermal conduction#Fourier's law
Fourier's law
Impedence property
An impedance that is the opposition to flow due to the combination of resistance, capacitance, and inductance along a flow path
Reactance property
An impedance that is the opposition to flow due to the combination capacitance and inductance of a flow path
Impedance
A force-driven flow proporionality that is the opposition to flow due to the duration and/or rate of change of a flow property.
Absolute amount of particle
Coaxial joint
A mechanical joint whose parts are constrained to extend along a longitudinal axis.
Spatial fraction of particle
Advective transport dependency
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) and is a combination of convective and diffusive transport. It is usually computed using partial differential equations so that diffusive transport applies only to 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.
A transport dependency that is the flow of a conserved quantity by virtue of it being a part of a portion of fluid or particles that is flowing.
Set of physics processes
Statistical entity
A physics model that is an entity or dependency used for the statistical analysis of sets of physics analytical enitites
Boundary flow constraint
Boundary force constraint
x-deferred thing
Transducer modulus
Constitutive coupling proportionality that is a dimensional ratio of dynamical properties of players in a transducer dependency
Constitutive dependency
A dynamical dependency that depends on the material constitution and structural composition and determines the rates of energy, charge, and material flow amongst paticipants in a constitutive process.
"Constitutive" is used very specifically to refer to dependencies that depend on the values of material properties (e.g., resistivity of a conductor; viscosity of fluid, stiffness of a solid material), and/or the structural shape and size properties of an entity that participates in the process.
Thus constitutive dependencies differ from constraint dependnecies that describe only topological relationships of entities and processes such as the convergence of flow paths at a node, or the integral dependence of a state properties on the sum of rate properties.
Portion of ideal gas
A portion of fluid that is a theoretical gas composed of many randomly moving point material particles that interact only by elastic collisions.
Electrical acceleration
1
A dynamical acceleration property that is the temporal rate of change of a elctrical current flow rate.
Property SI-unit
This is the only system of units to be represented in OPB and is implemented according to the globaly-adopted system as described in:
https://en.wikipedia.org/wiki/International_System_of_Units. SI-unit classes.
Accordingly and by fiat, some are "base units" that are irreducible and some are "derived units" that are derived from base units by multiplication or division. In other foromal systems or conventional usages, other allocations between base/derived units may be encountered.
SI-unit classes map, non-exclusively to classes of OPB:PropertyDimension either as single classes, or as multiples/quotients of base units
A physics property attribute that is the unit of measure of a physical property as standardized in the International System of Units.
Radian SI-unit
1
1
A derived SI-unit for plane angles
Property SI-base dimension
OPB:Property SI-based quantities are map to definitions available in
https://en.wikipedia.org/wiki/International_System_of_Quantities
The International System of Quantities (ISQ) is a system based on seven base quantities: length, mass, time, electric current, thermodynamic temperature, amount of substance, and luminous intensity. Other quantities such as area, pressure, and electrical resistance are derived from these base quantities by clear, non-contradictory equations. The ISQ defines the quantities that are measured with the SI units[1] and also includes many other quantities in modern science and technology.[2] The ISQ is defined in the international standard ISO/IEC 80000, and was finalised in 2009 with the publication of ISO 80000-1.[3]
Coulomb SI-unit
1
1
A derived SI-unit for a quantity of electrical charge.
Newton SI-unit
2
1
1
A derived SI-unit for force or weight
Chemical mass-action rate dependency
1
1
chemical rate law
An amount-driven rate dependency in which a chemical flow rate of participating chemicals depends on the amounts of its players
mass-action rate law
Fluid capacitive potential energy
Joule SI-unit
2
2
1
A derived SI-unit for energy, work or heat
Metre SI-unit
A base SI-unit for length
Candela SI-unit
A base SI-unit for luminous intensity
Kilogram SI-unit
A base SI-unit for mass
Kelvin SI-unit
A base SI-unit for temperature
Chemical capacitive process
Fluid capacitive process
Mechanical capacitive process
Electrical capacitive process
Physical change
A physical processural entity that is a discrete or continuous change in the physical state of a participant in a physical process during the occurrence of the process.
Diffusive capacitive process
Element
A chemical structure that is a single atom composed of protons, neutrons and electrons.
Second SI-unit
second
s
A base SI-unit for time
Flow-driving potential
A force property that can change only the potential energy of a portion of entity.
Momentum-driving force
Momentum driving forces are so-named to capture the idea that such forces are relevant only in-so-far as they may change the kinetic energy of material entities (solid or fluid) as well as changing their potential energy by changes of elevation (in a gravitational field) or by changes of elastic potential energy.
A force property that can change both the kinetic and potential energy of a material entity.
Liquid junction potential
An electrodiffusional potential across a diffusional barrier due to differences in diffusional mobility of anions and cations in the fluids separated by the barrier.
Wikipedia: Liquid junction potential http://en.wikipedia.org/w/index.php?title=Liquid_junction_potential&redirect=no
Physics processual entity
A physics real entity that is a physical process or change, or a temporal entity.
Mechanical solid
A solid dynamical entity that has contiguous structure. {not quite right yet}
Electric current dimension
Bona fide dynamical boundary
Dynamical boundary that is a spatial boundary across which there is a discontinuity of structural composition or physical property values.
Base SI-unit
Ampere SI-unit
A base SI-unit for electrical current
Mole SI-unit
A base SI-unit for amount of substance
Informational process
Informational process comprise an especially rich domain of phenomena across a broad range; e.g.,:
1) a simple transactor process whereby the value of a dynamical property of one entity depends on a property of a separate entity with out the flow or conversion of thermodynamic energy.
2) transformation of synaptic input into fire/no-fire decisions by the neuronal cell body
3) the reliabiliy transmission of information along an axon that accounts for ambient noise, transmission delays, etc.
For purposes of dynamical modeling and until there are compelling use-cases and representational needs for represensting informational processes, we will only define and use property value transactors and event-controlled processes.
A physics process that is the transmission, transduction or transformation of information amongst process participants with negligible exchange of thermodynamic energy.
Tensile displacement
Derived SI-unit
An SI-unit that is composed of a multiple or ratio of two or more base SI-units
i
A mathematical constant that is the square root of the real number minus one.
imaginary unit
Spatial fraction 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.
Debye length
A spatial span that is characteristic length of the distribution of mobile electrical charges in a fluid electrolyte near an electrically-charge boundary.
Debye length
Debye radius
Molar fraction of chemical
A fractional amount of chemical that is the ratio of the molar concentration of one portion of chemical to that of another species occupying the same spatial region
Abstract domain
Physics analytical domain that defines entities that do not occupy space and do not possess either material or energy.
Fractional 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).
State trajectory
A physical state change that is a time-series of changes of physical asttributes of a participant in a physical process.
Process pre-condition
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 occurrence condition that is necessary and sufficient to initiate an occurrence of a physical process
Process post-condition
A process occurrence condition that terminates a 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
Mass amount of chemical
Absolute amount of a chemical that is the mass of a portion of a chemical within a spatial region.
Informational entity
A physics modeling entity 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 trajectory.
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.
Physics dependency
Physics model entity that is a rule that relates the existence and attributes of physics continuants to the occurrence and time-course of changes of physical conditions during physical processes.
Physical dependencies are represented as an axioms, definitions and empirical laws of physics for the observation, understanding, and analysis of real biophysical systems. They are represented by a broad class of quantitative and qualitative relationships amongst physical entities and the attributes of physical entities, physical continuants, and physical processes. These are the rules by which dynamical and information systems operate and are routinely encoded for analysis and simulation in a variety of computational and mathematical systems.
Examples include: Ohm's law for electricity and for fluid flow, the definition of kinetic energy in terms of mass and velocity,
Dynamical constraint
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.
A dynamical constraint on the values of the physical state property values of a physical entity.
Binary quantity
Spatial calculus dependency
Absolute amount of chemical
Volumetric concentration of solute
Activity of protons
PATO:0001842
pH
Joint displacement
A mechanical displacement that is the temporal integral of a rotational velocity.
Sum of momenta
A sum of state property which holds for momentum properties
Activity of chemical
An amount of a chemical that is its effective concentration due to its interactions with other chemicals in a portion of a solution or a gas.
Constraint dependency
1
A dynamical dependency that constrains the values of one or more dynamical properties independently of constitutive properties.
Sum of rate properties
A dynamical rate dependency that is a sum of rate property values.
Sum of state properties
A sum of properties for the state properties of more than one physical entity.
Steradian SI-unit
2
2
A derived SI-unit for solid angles
Watt SI-unit
1
1
A derived SI-unit for power, radiant flux
Planar form
PATO:0002006
A geometrical form that extends in two spatial dimensions.
Line form
A geometrical form that extends in a single spatial dimension.
Material density
An amount density for a material entity.
PATO:0001019
Material volumetric density
A material density expressed per unit volume
PATO:0001353
Volt SI-unit
1
2
1
3
A derived SI-unit for electrical potential difference, voltage, or electromotive force
Farad SI-unit
2
1
2
4
A derived SI-unit for electrical capacitance
Ohm SI-unit
1
2
3
2
A derived SI-unit for elctrical resistance, impedance, reactance
Seimen SI-unit
1
3
2
2
A derived SI-unit for electrical conductance
Organismal scale
Organ system scale
Organ scale
Organ part scale
Cell scale
Weber SI-unit
2
1
1
2
A derived SI-unit for magnetic flux
Cell component scale
Molecular scale
Atomic scale
Spatial domain
Physics analytical domain in which the entities are spatial entities
Spatial domain classes are represented primarily for annotation purposes to distinguish, for example, models of glucose as an atomic structure vs. as player is cell metabolism or as a component of whole-body glucose uptake.
Standard deviation
Portion of liquid solution
Portion of liquid solvent
Portion of pure liquid
Tesla SI-unit
1
2
1
A derived SI-unit for magnetic flux density
Henry SI-unit
2
1
2
2
A derived SI-unit for electrical inductance
Material areal density
A material density expressed per unit area
PATO:0001351
Joint rotational displacement
Process occurrence condition
A physical condition of a physical pocess participant at the start or end ofthe process.
Ion flow conductance
1
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.
Ion flow resistance
1
Ion flow resistance per area
Ion flow resistance path
Ion flow resistance per capacitance
degree Celsius SI-unit
1
A derived SI-unit for temperature relative to 273.15 K
Primitive physics entity
Physics continuant 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
Statistical set
Joint angular displacement
Energy state dependency
A thermodynamic dependency the thermodynamic energy of a physical entity on its dynamical properties
Potential energy dependency
1
1
1
An energy state dependency of the energy content of a physical entity on its diplacement in a force gradient or field or, conversely, the energy stored in potential energy field to the displacement of an entity within the field.
Flow junction rate constraint
A junction rate constraint for flow rate properties.
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 flow proportionality for a force-driven flow proportionality.
Material lineal density
PATO:0001352
A material density expressed per unit length
Solid strain
PATO:0001034
Shear strain
Tensile strain
Lumen SI-unit
1
A derived SI-unit for luminous flux
Lux SI-unit
2
1
A derived SI-unit for illuminance
Constitutive parameter
A constitutive property that of a non-proportional (i.e., non-linear) dependency of dynamical physical properties.
Whereas the classical physical laws (e,g. Ohm's, Hooke's...) define propotionality parameters for each (e.g., resisistance (R), elastance (E)...) biological rate dependencies are frequently very non-proportional are require non-linear dependencies that require more than a single, linear parameter.
Property of Hodgkin-Huxley dependency
Maximal channel conductance
Katal SI-unit
1
1
A derived SI-unit for catalytic activity or metabolic flux
Charged atom
A charged particle that is a single element.
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 junction rate constraint
A junction rate constraint for force properties.
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 bone 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
1
Property of non-proportional elastance dependency
1
Property of non-proportional chemical rate law
1
Property of non-proportional ion flux dependency
1
Amount of substance dimension
Charge
Primitive physical entity that is a quantal electrical charge
Lineal mechanic domain
Fluid inductive process
An inductive momentum process in the fluid kinetic domain
Mechanical inductive process
An inductive momentum process in the solid mechanical domain
Electrical inductive process
An inductive momentum process in the electrical domain
Rotational mechanic domain
Lineal mechanical force
Rotational mechanical force
Rotational strain
Total energy flow rate
An energy flow rate that is the sum of the kinetic energy flow rate, potential energy flow rate, and heat flow rate for a dynamical process.
Electrical inductance
1
Physics attribute
Physics real entity that is a physically observable attribute of a physics continuant, dependency or processural entity.
Energy rate dependency
A thermodynamic dependency energy flow rate of a process as the product of the flow-rate and force differential that drives the flow.
Lineal solid velocity
Rotational solid velocity
Sum of amounts
A sum of state property which holds for amount properties
Property derived dimension
Matter
Primitive physical entity that is matter.
Energy
Primitive physical entity that is capacity to do physical work.
Richard Feynman on "energy" (Feynman Lectures on Physics, v1, p4-1, 1963):
"...there is a certain quantity, which we call energy, that does not change in the manifold changes which nature undergoes. That is a most abstract idea, because it is a mathematical principle; it says that there is a numerical quantity that does not change when something happen."
Solid displacement
1
An amount property that is a temporal integral of a mechanical velocity property
Plane angle dimension
Torsional force
Bending moment
Polymolecule
A chemical structure composed of molecules bound to each other by non-covalent bonds.
Enthalpic energy
H
A thermodynamic potential that is the energy required to create a system, and the amount of energy required to make room for it by displacing its environment and establishing its volume and pressure - Wikipedia.
Joule SI-unit
Event frequency
Dynamical constitutive property
Constitutive dynamical properties ultimately depend on an empirically determined material property (e.g., density, resistivity) of a participant in the process. For example, mass density depends on both the spatial distribution of atoms and the atomic weight of each. Resistance of a conductor depends on the resistivity of the material in the wire which is only defined and determinable empirically.
There are two conflicting views of constitutive properties as properties of processes or of continuant entities:
1. The definition of constitutive property as a "ratio or partial derivative" of physical property values necessarily implicates a measurement process whereby values of two or more physical properties are varying and are measured and computed. However...
2. Constitutive properties are conventionally viewed as inherent attributes of a continuant or a process:
. mass density is the ratio of a material amount to the extent of the spatial region that it occupies.
. resistivity is the ratio of a potential difference to current flow rate for a an electrical flow process
.
3) what is common to each case is that "constitutive properties" are defined in the context of a specific entity or process in a manner that depends on the material and structural composition of the entities participating in the measurement process.
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 dynamical property whose value depends on the material composition and spatial properties of a physical process or process participant.
Solid angle dimension
Spatial frequency
Immaterial dynamical domain
Physical domain in which process participants are immaterial dynamical entities.
Rotational mechanical capacity dependency
1
Fiat dynamical boundary
Dynamical boundary declared for analytical purposes to distinguish physical entities between which there is no discontinuity of structural composition or physical property values
Boundary-condition
A physical state that is a set of dynamical state and rate properties that hold at a dynamical boundary
Dynamical surrounds are analytical artefacts, as typically found in thermodynamic analysis, to represent the so-called "boundary conditions" by which a dynamical entity interacts with other dynamical entities. Entities of the surround remain otherwise unspecified and are represented only by the imposition of boundary state property values (e.g., a pressure or temperature) or boundary flow rates (e.g., time-dependent, or -independent flows of material or energy) that drive changes of dynamical state of the surrounded dynamical entity.
Rotational moment of inertia
rotational inertia
Entropic domain
Thermodynamical domain in which physics continuants each have and exchange a portion of entropy.
Intensive spatial scope
Threshold subceeded event
Extreme value event
A property value event that occurs a maximum
Frequency dimension
Pressure dimension
Capacitive dependency
1
1
1
Hooke's 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 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.
Hookes law
Inductive dependency
1
1
A constitutive dependency between an entity's momentum and its rate property.
Electrical inductance
1
Electrical inductance is include only to encompass the very few cases where inductance due to current flow is a significant factor in biological systems.
A momentum property that is proportional to the temporal differential of an electrical current
Activity of solute
1
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.
Spatial boundary that is a spatial region that has of one less spatial dimension than the spatial region that it bounds.
A spatial entity that is a partition between spatial regions
Chemical kinetic boundary
kinetic pool
Fiat dynamical 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 boundaries disinguish, say, a portion of glucose and a portion of G6P that exist in a cell's cytoplasm that are superimposed in a macroscopic space while individual molecules are spatially discrete on a molecular scale.
pool
Velocity dimension
Covalent chemical bond
A chemical bond mediated by the sharing of electron pairs between atoms.
Lineal concentration of chemical
1
Areal concentration of chemical
1
Areal concentration of particles
1
Lineal concentration of particles
1
Volumetric concentration of particles
1
Kinetic energy flow rate
Energy flow rate that is the temporal rate of the transfer of kinetic energy from one material dynamical entity to another.
Potential energy flow rate
Energy flow rate that is the temporal rate of the transfer of potential energy from one dynamical entity to another.
Physical state
A component of a physical condition that defines a physical state of a physical entity.
Area dimension
Activity of chemical
Constitutive rate property of continuum
Amount-driven rate dependency
1
1
1
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 dependency in which a flow rate between its players depends on the differences in the amount properties of its players.
Mechanical inductive dependency
A dynamical inductive dependency of a solid entity's momentum on its velocity.
Fluid inductive dependency
1
A dynamical inductive dependency of an fluid entity's momentum on its fluid flow rate.
Electrical inductive dependency
1
A dynamical inductive dependency of an electrical entity's inductance property on its electrical current property.
Fluid capacitive dependency
1
Capacitive force dependency in which the volume of a fluid depends the differential of fluid pressures across its boundary.
Electrical capacitive dependency
1
Capacitive force dependency by which the electrical potential difference across the boundary of an entity depends on the amount of electrical charge in the entity.
Mechanical capacitive dependency
Capacitive force dependency in which an displacement of a solid entity depends its the differential of the solid forces acting on it.
Chemical capacitive dependency
1
Capacitive force dependency by which the chemical potential of a portion of chemical depends the amount of chemical that it contains.
Fluid-mechanical transducer dependency
1
1
Transducer dependency by which a fluid pressure and flow generates a solid force and displacement.
Examples:
1) transformation of mechanical strain potential energy into flluid potential energy as the myocardial contracts to pressurize blood contained in a ventricle or atrium
2) the skeletal muscle venous pump by which muscle contractile forces pressurize venous blood an propel it back to the heart.,
3) bowel wall sooth muscle contractions propel bowel contents through the gastrointestinal system
Chemo-mechanical transducer dependency
1
1
Transducer dependency by which a chemical potential difference and reaction rate generates a solid force and displacement.
Examples:
Transformation of chemical potential energy as ATP is transduced into the mechanical tensile force of myofibrils and, hence, the contractie force of muscles of all types
Transformer dependency
1
Biomechanical examples: the biceps tendon pulls on the forearm to raise a load held in the hand;
A constitutive dependency of the flow rates of two role-players in a single dynamical domain are coupled to the respective forces of the role players.
Portion of liquid suspension
Volume dimension
Activity of cation
Activitiy of anion
pH
pCa
Process occurence dependency
A physics process that relates an occurrence of a process to the physical condition of its participants.
Ionic chemical bond
Chemo-diffusional transducer dependency
1
1
Transducer dependency that couples a chemical reaction potential times flow rate to the vectorial transport diffusible particles across a diffusion barrier.
This is one of the fundamental mechanisms by which metabolically generated chemical energy is transduced into transmembrane electrochemical gradients.
Examples:
The cell membrane sodium-potassium pump (NKP) hydrolyses Mg-ATP to Mg-ADP plus phosphate to propel Na ions out of cells and K ions into cells (see https://en.wikipedia.org/wiki/Na%2B/K%2B-ATPase ).
The cell membrane calcium pump hydrolyses Mg-ATP to Mg-ADP plus phosphate to propel Ca ions from cell cytoplasm out to of cells (see https://en.wikipedia.org/wiki/Calcium_ATPase )
Diffusive transformer dependency
1
Transformer 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
1
Capacitive force dependency by which the diffusional potential of a portion of particles depends the amount of particles that it contains.
Electrochemical capacitance dependency
1
equilibrium potential
This dependency is a nonproportional constitutive dependency described by the Nernst equation that contains a natural log (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 relates the chemical concentration gradient to the electric gradient at which there is no net electrodiffusional driving force between two portion of charged particles.
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.
Capacitive force dependency in which an electrical potential difference across the boundary betweem portions of diffusible charged particles depends on an electrodiffusional potential difference.
reversal potential
Nernst potential
pCl
Hydrogen bond
Van der waals bond
Fluid energy flow dependency
1
Set of physics dependencies
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.
Existential state
A physical state that is the ontological type of a physics continuant.
Ionic charge
A physical constant that is the amount of electrical charge of a single atom or single molecule
Network domain
Abstract domain that is concerned with the connectivity relations of vertices and their connections as they represent physics entities, processes and their properties and dependencies.
Resistive dependency
1
1
1
Resistive rate dependencies represent the rate of 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 dependency by which a flow rate of a process depends on the difference in force properties of the process participants.
Ohms law
Property event dependency
Physical state event dependency
An process dependency that relates a physical state event to changes of continuant state of participants during an occurrence of a process.
Transport dependency
A constitutive dependency of a flow rate property of one dynamical entity depends on the force property of another dynamical entity
Convective transport dependency
A transport dependency that is the flow of a portion of a conserved quantity that is a combination of advective and diffusive transport.
Chemical energy flow dependency
1
Gibbs energy
Joule SI-unit
free enthalpy
G
https://en.wikipedia.org/wiki/Gibbs_free_energy
A thermodynamic potential that is the amount work that may be performed by a dynamical entity at a constant temperature and pressure.
Gibbs free energy
Gibbs function
Helmholtz free energy
For dynamical entity the amount of Helmholtz free energy, A, is the difference between the entity's internal energy, U, and the product of its temperature, T, and its entropy, S; i.e, A = U-TS.
F
Joule SI-unit
A thermodynamic potential that is amount of energy of dynamical entity that is available for doing useful work at a constant temperature and volume.
A
https://en.wikipedia.org/wiki/Helmholtz_free_energy
Physics model set
A physics modeling entity that is an ordered or unordered collection of instances of physics attributes. continuants, dependencies or processes that are the parts of a physical model.
Nernst reversal potential
ionic equilibrium potential
Equilibrium potential
An electrical potential that nullifies the electrical driving force for the chemical diffusion gradient of a single ionic species as determined by the Nernst equations.
Temporal coordinate origin
A temporal instant that is the origin of a temporal coordinate system.
time zero
start time
zero time
Dynamical event dependency
Internal energy
Joule SI-unit
https://en.wikipedia.org/wiki/Internal_energy
A thermodynamic potential that is the total energy of a dynamical entity excluding its kinetic energy of motion as a whole and the potential energy of the system as a whole due to external force fields.
U
Physics entity
A thing that is a real entity or is a physics-based model of such an entity.
A physics modeling entity is a mathematical, logical or computational construct that is useful for the representation and analysis of "real" biophysical entities and processes. Examples include a geometrical sphere, vector of real numbers, algebraic equations, the domain of fluid dynamics, a set of ODE's or PDE's
Entropy SI-unit
1
1
pi
π
3.14159
pi
Archimedes' constant
A mathematical constant that is that is the ratio of a circle's circumference to its diameter.
e
exponential growth constant
A mathematical constant that is the limit of (1 + 1/n)n as n approaches infinity.
2.71828
Euler's number
exponential decay constant
Kinetic energy dependency
1
1
1
An energy state dependency of the energy of a material entity on its rate of motion or flow
Solid kinetic energy dependency
1
Fluid kinetic energy dependency
1
Areal density of mass
1
Electrical potential energy dependency
1
A dependency of the potential energy of an electrically charged entity due to its displacement in an electrical field.
Elastic potential energy dependency
1
A dependency of the potential energy stored in an elastic entity due to changes of its shape
Lineal density of mass
1
Mathematical constant
A maathematical entity that is a real or imaginary scalar quantity.
Portion of entropy
1
per Lambert, 2002:
'entropy is the spreading and sharing of energy"; i.e., dispersal of energy amongst microstates.
A measure of the total quantity of energy that had to be dispersed within a quantity of substance at a given temperature beginning at absolute zero.
"entropy change = quantity of energy dispersed at a temperature T"
Lambert, Frank L., "Entropy is Simple, Qualitatively", JChemEd.chem.wisc.edu. Vol 79, No. 10, October 2002
Thermodynamic entity that is the portion of energy dispersed into a portion of substance at a given absolute temperature.
Thermodynamical constraint
A thermodynamical dependency that defines a physical property of a dynamical entity whose value is temporally and/or spatially invariant.
Isobaric constraint
1
A thermodynamic constraint that the fluid pressure within a dynamical entity is invariant both spatially and temporally.
Isothermal constraint
1
A thermodynamic constraint that the temperature within a dynamical entity is invariant both spatially and temporally.
Isovolumetric constraint
1
A thermodynamic constraint that there is no change in the volume of a dynamical entity
Isentropic constraint
1
A thermodynamic constraint that there is no exchange of entropy across the dynamical boundary nor change in the entropy of a dynamical entity.
Adiabatic constraint
1
A thermodynamic constraint that there is no flow of energy or matter across the dynamical boundary of a dynamical entity
Solid translational acceleration
Acceleration - Rate of change of speed with respect to time.
http://www.unitsofmeasurement.org/apidocs/index.html
A dynamical acceleration property that is the temporal rate of change of a mechanical velocity.
Lagrangian constraint
1
A thermodynamic constraint that the sum of potential energy plus kinetic energy of a dynamical entity is temporally invariant.
Viscoelastic dynamical entity
https://en.wikipedia.org/wiki/Viscoelasticity
A material dynamical entity composed of material that has both viscous and elastic material properties that depend temporal rates of deformation.
Heat flow dependency
1
1
Geometrical entity
A physics modeling entity that is a geometrical form used to represent physics continuants, process or modelting entities.
Solid angular acceleration
UoMo:AngularAcceleration - Rate of change of angular speed with respect to time.
http://www.unitsofmeasurement.org/apidocs/index.html
A solid acceleration property that is the temporal rate of change of a Solid angular velocity.
Energy dimension
H
Torque dimension
Lagrangian energy
A portion of energy that is the difference in the amounts of kinetic and of potential energy that inhers in a dynamical entity
Volumetric density of mass
1
Set of physics continuants
Physical constant
A physical property that is a constitutive scalar that defines the ratio of a dynamical property to a property of a different type.
Avogadro constant
A physical constant that is the number of constituent particles, usually atoms or molecules, in one mole of a substance.
NA
https://en.wikipedia.org/wiki/Avogadro_constant
Avogadro constant is 6.022140857(74)×1023 per mole in the International System of Units (SI).
Faraday constant
https://en.wikipedia.org/wiki/Faraday_constant
F
A physical constant that is the amount electric charge of a mole of electrons.
Faraday constant has the currently accepted value of 96485.3365(21) C mol−1 that is the product of the unit charge of an electron (1.6021766×10−19 C) and the Avogadro constant (NA ≈ 6.022141×1023 mol−1).
Ionic charge
1
An amount property that is the diifference between the number of protons and the number of electrons composing a material dynamic entity
Boltzmann constant
The Boltzmann constant is the gas constant R divided by the Avogadro constant: k = R / Na which has the dimension energy divided by temperature.
The accepted value in SI units is 1.3806488(13)×10−23 J/K.
https://en.wikipedia.org/wiki/Boltzmann_constant
A physical constant that is the ratio of the energy of a particle to its temperature.
k
Gas constant
universal gas constant
A physical constant that is the increment in the total energy of a mole of matter due to an increment of temperature.
R
https://en.wikipedia.org/wiki/Gas_constant
The gas constant is the Boltzmann constant (k) times the number of moles of a gas (N) such that R = Nk.
molar gas constant
ideal gas constant
Atomic mass constant
https://en.wikipedia.org/wiki/Atomic_mass_constant
A physical constant that is one twelfth of the mass of an unbound atom of carbon-12 at rest and in its ground state
Standard atmosperic pressure
A physical constant that is the standard atmospheric pressure defined as 101325 Pa (1.01325 bar) as used as a reference or standard pressure.
https://en.wikipedia.org/wiki/Atmosphere_(unit)
Thermodynamical potential dependency
A thermodynamical dependency that defines the amount of a thermodynamical potential as algebraic sums and differences of two or more energy amounts of disparate kinds.
Cotransport domain
Cotransport domain will be implemented to represent coupled transport within and between dynamical domains. Examples include:
1. molecular cotransport across cell membranes such as for the sodium-potassium pump, sodium-glucose transporter, sodium-calcium exchante pump, etc.
2. material advection as when blood constituents (blood cells, chemicals) are cotransported through the circualtory system, or when filtered blood constituents are cotransported through the urinary tract.
More complete OPB support for cotransport will await the needs of suitable use-cases.
A dynamical domain in which movement of one physical entity is coupled to and results in the movement of another physical entity.
Enthalpic energy dependency
Pump counter transport
Pump cotransport
Gibbs free energy dependency
Junctional rate constraint
A rate constraint that the sum of the rates of all flows converging at a common node is identically zero; a "zero junction" in bond graph theory
Kirchhoff's junction rule
0-junction
Kirchhoff's first rule
Kirchhoff's point rule
A junction 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 material, charge or any other conserved species
Flow loop rate constraint
A loop rate constraint for flow rate properties
Force loop rate constraint
A loop rate constraint for force properties.
Helmholtz free energy dependency
Lagrangian energy dependency
Internal energy dependency
Mechanical transformer dependency
1
Constitutive rate dependency by which energy is exchanged between solid mechanical entities.
Amount density
An amount property that is the amount of dynamical entity distributed over a spatial region normalized to the size of the region
Charge density
1
An amount density for electrical charge.
Lineal mechanical capacity dependency
1
Lineal mechanical transformer
lever
Rotational mechanical transformer
gear
Total energy dependency
Entropy-driven heat flow
1
1
Temperature-driven heat flow
1
1
Joint velocity
A mechanical velocity that is the rate of angular displacement of a mechanical joint about one of its axes
Joint angular velocity
Joint rotational velocity
Solid velocity
A mechanical velocity that is the rate of displacement of solid entity,
Physiomap graph
A physics network model in which nodes are dynamical entities node-node arcs are physical processes.
Spatial angle
A spatial property that is the rotation required to superimpose two straight lines by rotation about an intersection of the lines
Index of member in set
A statistical property that is the a unique identifier assigned to an instance that is a member of a set.
Gas law dependency
1
A constitutive dependency of dynamical properties of a portion of an hypothetical ideal gas.
A gas law...is the equation of state of a hypothetical ideal gas. It is a good approximation to the behavior of many gases under many conditions, although it has several limitations.
An ideal gas is a theoretical gas composed of many randomly moving point particles that do not interact except when they collide elastically.
Charles gas law
1
from Wikipedia: Charle's law
V/T = k
where:
V is the volume of the gas
T is the temperature of the gas (measured in Kelvin).
k is a constant.
A gas law that relates the values of volume and temperature of a portion of gas when its amount and pressure are unchanged.
Boyle gas law
1
1
from Wikipedia: Boyle's law
The absolute pressure exerted by a given mass of an ideal gas is inversely proportional to the volume it occupies if the temperature and amount of gas remain unchanged within a closed system.
PV = k
where:
P is the pressure of the gas,
V is the volume of the gas, and
k is a constant.
A gas law that relates the values of volume and pressure of a portion of gas when its amount and temperature are unchanged.
Guy-Lussac gas law
1
1
Amontons's Law of Pressure-Temperature
from Wikipedia: Gay-Lussac's law
The pressure of a gas of fixed mass and fixed volume is directly proportional to the gas's absolute temperature:
P / T = k
where:
P is the pressure of the gas
T is the temperature of the gas (measured in kelvin).
k is a constant.
A gas law that relates the values of temperature and pressure of a portion of gas when its amount and volume are unchanged.
Avogadro gas law
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A gas law that relates the values of volume and amount of gas when its pressure and temperature are unchanged.
From Wikipedia:Avogadro's Law
V = nK
where:
V is the volume of the gas
n is the amount of substance of the gas (measured in moles).
k is a constant equal to RT/P, where
R is the universal gas constant,
T is the Kelvin temperature, and
P is the pressure.
As temperature and pressure are constant, RT/P is also constant and represented as k. This is derived from the ideal gas law.
Ideal gas law
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1
1
A gas law that relates the values of pressure, volume, amount and temperature of a portion of an ideal gas.
universal gas law
From Wikipedia: Ideal gas law
PV = nRT. where
P is the pressure of the gas
V is the volume of the gas
n is the amount of substance of gas (also known as number of moles)
T is the temperature of the gas
R is the ideal, or universal, gas constant, equal to the product of the
Boltzmann constant and the Avogadro constant.
problem: I can't get the subclassing statement
"hasPropertyPlayer exactly 1 'Amount of gas'
to work for the class 'Temerature', i.e.,
'hasPropertyPlayer exactly 1 'Temperature'
despite copy/pasting 'Temperature' from its class definition box.
??????
The ideal gas law is the equation of state of a hypothetical ideal gas. It is a good approximation to the behavior of many gases under many conditions, although it has several limitations. It was first stated by Émile Clapeyron in 1834 as a combination of the empirical Boyle's law, Charles' law and Avogadro's Law
Gas law constant
A constitutive state property of continuum that relates state properties of a portion of ideal gas
Energy conservation dependency
A thermodynamical property dependency of the portion of total energy of a closed, thermodynamically isolated set of dynamical entities is invariant.
Process occurrence event
An physical event that initiates or terminates a process occurrence.
Physical event
1
A physical change that is a temporally discrete change of physical state of a process participant.
Trajectory
A physical change that is the time-course of changes, either discrete or continous, in physical state of a process participant.
Process trajectory
A trajectory that is a temporally ordered series of values of a physical property of a physics process
Lineal scope
A property spatial scope of a physical property whose value is expressed on per length basis.
lineal density
Areal scope
areal density
A property spatial scope of a physical property whose value is expressed on per area basis.
Volumnal scope
volumetric density
A property spatial scope of a physical property whose value is expressed on per volume basis.
Discrete spatial scope
A spatial scope of a property whose value applies to an entire physical entity.
Correlative value
Correlation coefficient
Standard error of mean
Solid acceleration
1
Fluid acceleration
1
A dynamical acceleration property that is the temporal rate of change of a fluid flow rate.
Ideal gas constant
R
universal gas law constant
A gas law constant for the ideal gas law
gas constant
Boyle gas constant
A gas law constant for the Boyle's gas law
Avogadro gas constant
A gas law constant for the Avogadro's gas law
Charles gas constant
A gas law constant for Charles' gas law
Guy-Lussac gas constant
A gas law constant for Guy-Lussac's gas law
Amount of gas
1
A material amount of a portion of gas
Event-control process
A informational process by which an occurrence of a physical event changes the value of a dynamical property.
Transformer process
A constitutive process whose rates are determined by a transformer dependency.
Transducer process
2
A constitutive process whose rates are determined by a transducer dependency.
Transport flow process
Chemo-diffusional transducer process
Chemo-mechanical transducer process
Fluid-mechanical transducer process
Advective transport process
Convective transport process
Pump transport process