synonym
IUPACclass
wikipedia
PATO_id
hasConstraint
hasSI-unit
A annotation property that assigns a class of "SI-unit" to OPB:Physical property classes. Multiple instances of hasSI-unit and hasReciprocal-SI-unit may be assigned to a given property class to express, as factors and reciprocols, compound units such as for a velocity (distance/time) or density (mass / volume).
SI-units are 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
maps_to_BFOclass
An annotation property that assigns the reciprocal of an SI-unit as the measurement unit for a physical property
hasReciprocal-SI-unit
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.
hasMediatorParticipant
...that relates a property to the mathematical form of an instance of the property
hasMathForm
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
hasParticipant
...that relates an occurrence of a process to the temporal interval during which it occurs
occursDuring
hasMomentumPlayer
hasTemporalPartOfProcess
hasStructuralPartOfProcess
x_deferred object prop
hasForcePlayer
A topObjectProperty that relates a property to a property attribute
hasPropertyAttribute
hasFlowPlayer
hasAmountPlayer
...that relates a property to the spatial coordinate system in which an instance of the property is defined
hasSpatialCoordinate
...that relates a property to the dimension of the property
hasDimension
hasNegPropertyPlayer
...that is a algebraic relation that relates the values of dynamical properties in a constitutive dependency
hasConstitutivePlayer
hasDynamicalPlayer
hasThermodynamicPlayer
hasDependencyPlayerProperty
hasPropertyValue
hasProcessDependency
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.
hasDynamicalParticipant
successorTo
hasFlowSinkPlayer
partOf
hasPart
...that tends to accelerate or move an entity away from the origin of its spatial location
hasForceSink
successorOf
...that tends to accelerate or move an entity toward the origin of its spatial location
hasForceSource
hasPosPropertyPlayer
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
hasPropertyPlayer
hasPartOfProcess
hasPropertyAttribute deferred
...that relates an occurrence to the process class of which it is an instance
occurenceOf
subProcessOf
hasSubProcess
hasFlowSourcePlayer
A topObjectProperty that relates a physical property to the physical entity in which the property inheres
propertyOf
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.
hasThermoParticipant
A topObjectProperty that relates an instance of a physical entity to an instance of a property that inheres in the entity
hasProperty
A topObjectProperty that relates a physical property to the domain of the entity or dependency for which it is a property
hasPhysicalDomain
...that relates a property to the spatial scope for which an instance of the property is defined
hasSpatialScope
hasBoundary
boundaryOf
A topObjectProperty that relates an instance of a dynamical entity to an instance of a thermodynamic entity that inheres in the dynamical entity.
isThermodynamicEntityOf
A hasInfoParticipant relation that establishes a dynamical entity as a reciever of an information.
hasInfoSink
A hasInfoParticipant relation that establishes a dynamical entity as a sender of an information.
hasInfoSource
topObjectProperty that assigns an instance of an SI unit class to physical property class
hasSIunit
A hasDynamicalParticipant relation by which a positive process flow diminishes the energy content of the participating dynamical entity.
hasFlowSource
A hasParticipant relation by which the dynamical state of dynamical entity can change the rate of a dynamical process.
hasTransactorParticipant
A hasDynamicalParticipant relation by which a positive process flow augments the energy content of the participating dynamical entity.
hasFlowSink
A hasPropertyAttribute that specifies or limits the value of a physical property
hasConstraint
hasThermoSource
hasThermoSink
A topObjectProperty that relates an instance of a thermodynamical entity to an instance of a dynamical entity
hasThermodynamicEntity
hasReciprocalProperty
A hasParticipant property that relates a flow of information to a dynamical entity that is either a source or sink for the flow
hasInfoParticipant - pending
hasPropertyAttribute that relates a derived SI unit to an SI unit that is a multiplicative component of the derived SI unit.
hasMultiplierUnit
hasPropertyAttribute that relates a derived SI unit to an SI unit that is a divisor component of the derived SI unit.
hasDivisorUnit
A topObjectProperty that relates a physical domain to the entity or dependency for which it is a domain
isPhysicalDomainFor
synonym
discussion
displayName
An entropy amount that is ∑ p ln(p), where p = liklihood of a particular message amongst all the messages that can be possibly occur
Information entropy amount
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.
Dynamical rate property
Imaginary numerical form
Complex numerical form
1
Chemical conductance
1
Solid conductance
Spatial differential dependency
A portion of energy proportional to the amount and displacement of a dynamical entity in a potential energy field or potential energy difference.
Portion of potential energy
1
Fluid conductance
1
PATO:0001756
Heat conductance
A portion of energy attributed to the motion of a dynamical entity.
Portion of kinetic energy
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.
Magnetic field
1
PATO:0001757
Electrical conductance
Dynamical domain for which process participants are portions of particles and processes are the transport of particles from one portion to another portion
Diffusion kinetic domain
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.
Partial gas pressure
Electromagnetic constant
A themodynamic entity that is potential for the entity to do work
Portion of energy
A portion of kinetic energy attributed to the motion of a portion of fluid.
Fluid kinetic energy
A portion of kinetic energy attributed to the motion of a solid.
Solid kinetic energy
Domain potential energy of a portion of fluid due to changes in its volume, pressure or position in a gravitational field
Fluid potential energy
Solid elastic potential energy
Chemical potential energy
Heat is the portion of energy that can flow from one material continuant to another due to a difference in their temperatures, or by any means other than through work or the transfer of matter
Heat potential energy
Diffusion potential energy
Electrical potential energy
Magnetic potential energy
A portion of kinetic energy attributed to an electrical current.
Magnetic inductive energy
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
Translational momentum
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)
Mechanical force
A potential energy field that is the combination of an electrostatic field and a magnetic field.
Electromagnetic field
1
Chemical capacitance
Joule SI-unit
An energy amount that is the sum of kinetic and potential energies that inhers in a physical entity
Total energy
Thickness of wall of shape
A force-driven flow proportionality that is the ratio of flow to force in a resistive flow dependency.
Conductance
event frequency
frequency
Temporal rate of aperiodic events during a temporal interval.
Event rate
1
Electrical resistivity
Solid sphere
Bending distortion
ideal property
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.
A constitutive property that is a proportionality between values of dynamical property players.
Constitutive proportionality
1
Chemical amount
A material amount that is the temporal integral of a chemical flow or the amount of chemical in a portion of chemical
Amount of chemical
2D-Polar coordinate system
Polar coordinate system 2D
A geometrical dependency of the length of a one-dimensional spatial region on the locus of points that bound the region.
Length dependency
...that is the mathematical structure of a property value.
Tensor form
N
count
number of entities
Property dimension that is the set of positive integers and zero
Cardinality dimension
1
Pressure momentum
A momentum property that is proportional to the temporal differential of an fluid flow rate
Fluid momentum
1
Fluid volumetric elastance
1
Chemical elastance
1
Flow rate property that is the temporal derivative of a mechanical displacement
Mechanical velocity
1
A physics quality that is an attribute of a portion, flow or distribution of thermodynamic energy or entropy.
Thermodynamical property
1
Solid elastance
Shear capacitance
Real numerical form
1
Electrical elastance
Particle diffusive elastance
1
F
https://en.wikipedia.org/wiki/Faraday_constant
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).
A physical constant that is the amount electric charge of a mole of electrons.
Faraday constant
1
...that is the dependence of chemical flow rate on the differential of the chemical potentials of the reacting participants
Resistive dependency of a chemical flow rate on the difference of the chemical potentials of reactants (e.g., substrates, products) in a chemical reaction.
Chemical resistive dependency
Heat elastance
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.
Gravitational field
Property coordinate form that is a spatial coordinate system.
Spatial coordinate basis
1
Constitutive coupling proportionality that is a non-dimensional ratio of dynamical properties of players in a transformer dependency
Transformer modulus
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)
Thermodynamic entropy amount
...that is the ratio of the amount of material in a 3-dimensional spatial region to the volume of that region.
Mass volumetric density
1
fluid inductance
fluid inertance
...that is the mass of a portion of fluid that is a participant in an "ideal" fluid inductance process
Fluid inertance
1
Fluid viscosity
Time
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 dimension
Shear force
Shear force
PATO:0002284
Tensile force
Tensile force
A constitutive storage proportionality that is the ratio of force to momentum in a inductance dependency.
Inertance proportionality
A dynamical state property that is the temporal integral of a flow rate property
Amount
... is the nominal acceleration due to gravity at the Earth's surface at sea level; http://en.wikipedia.org/wiki/Standard gravity
Standard gravity constant
2D-Cartesian coordinate system
Cartesian coordinate system 2D
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 real entity that is a physically observable attribute of physics continuant or process that can be represented as a scalar, vector or tensor, or as an aggregate of such measures, or as can be computationally derived from such measures.
Physics property
1
Electrical resistance
An amount property that is the temporal integral of an fluid flow rate relative to an initial volume
Fluid volume
1
instant
point in time
Zero-DimensionalTemporal Region
A temporal region that is a point or zero-dimensional temporal region
Zero-dimensional temporal region
1
Fluid flow resistance
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
T
temperature
thermodynamic temperature
defined as "temperature", a BASE dimension per:
Schadow, G., C. J. McDonald, J. G. Suico, U. Fohring and T. Tolxdorff (1999). "Units of measure in clinical information systems." J Am Med Inform Assoc 6(2): 151-162.
and as 'thermodynamic temperature', a BASE dimension in:
IUPAC. (2011). "A concise summary of Quantities, Units and Symbols in Physical Chemistry", see: http://www.iupac.org/publications/ci/2011/3304/July11_green-sup-4p.pdf.
Temperature dimension
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
Physics property variant that is a fundamental coordinate basis of a property value.
Property dimension
1
Chemical resistance
1
mechanical compliance
solid complliance
Solid capacitance
1
Solid momentum
A momentum property that is the temporal integral of a momentum-driving force property
Mechanical momentum
1
Resistive dependency of the flow rate of electrical charge flow (electrical current) on an electrical potential difference.
Electrical resistive dependency
1
Resistive dependency of a fluid flow rate on a fluid pressure differential.
Fluid resistive dependency
1
Force-driven rate dependency of a solid velocity and solid force differential.
Solid resistive dependency
1
Fick's law of diffusion
Ficks law
An amount-driven 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
Diffusion gradient dependency
1
Solid viscous resistance
Bending capacitance
m
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.
Mass dimension
...that is the ratio of the amount of material in a 2-dimensional spatial region to the volume of that region.
Mass lineal density
Tensile capacitance
Dynamical domain in which the physical entity is a discrete structure and the processes are their spatial rotations and/or translations and their accelerations.
Solid mechanical domain
1
Heat transfer resistance
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.
Heat flow rate
Q
electrical charge
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.
Charge dimension
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
Electrochemical domain
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
1
formerly dielectric constant
Electric constant
A constitutive storage proportionality that is the ratio of force to displacement in a capacitive dependency and is the reciprocal of an capacitance. property.
Elastance proportionality
A force-driven flow proporionality is the derivative of force versus flow in a resistive dependency; reciprocal of kinetic conductance property
Resistance
1
Diffusion resistance
Torsional capacitance
ang
plane angle
theta
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.
Angle dimension
1
Flow rate property that is the temporal derivative of the amount of chemical
Chemical flow rate
Physics domain in which dynamical entities exchange energy or information by the dynamical processes in which they participate.
Dynamical domain
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
Chemical bond
Lineal translational velocity
...that is the ratio of the amount of material in a 1-dimensional spatial region to the volume of that region.
Mass areal density
A physics trajectory that is a temporally-ordered series of physics events.
Event trajectory
1
Per BFO2.0: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part.
A dynamical entity that is composed of elements.
Material dynamical entity
A constitutive process determined by a capacitive force dependency.
Capacitive force process
duration
time span
Second SI-unit
Temporal property that is the amount of time between two temporal instants.
Temporal duration
Translational displacement
A mechanical displacement that is the temporal integral of a mechanical velocity.
Translational displacement
Physics domain in which the participants have portions of thermodynamical energy.
Thermodynamical domain
An immaterial dynamical entity that is spatial distribution of potential energy due to the separation of material, charge, or magnetic monopoles
Potential energy field
2
...that is the proportionality between two dynamical properties in a transactor dependency
Constitutive transactor coefficient
1
"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).
PATO:0000146
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).
A thermodynamical property that is the driving force for the flow of heat energy and is a measure of the heat content of a material entity
Temperature
area
surface area
PATO:0001323
A spatial property that is the two-dimensional extent of a surface region.
Spatial area
1
VolumetricFlowRate - Volume of fluid passing a point in a system per unit of time.
http://www.unitsofmeasurement.org/apidocs/index.html
volume flow
volume flow rate
A flow rate property that is the temporal derivative of a fluid volume
Fluid flow rate
Spatial coordinate basis that is comprised of a single spatial dimension
One dimensional spatial coordinate basis
1
amperes
charge flow
current
electrical current
Flow rate property that is the temporal derivative of an amount of portion of electrical charge.
Charge flow rate
lum
luminous intensity
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.
Luminosity dimension
PATO:0000040
A mechanical displacement that is a change in the shape of a solid entity
Solid distortion
1
compliance
fluid compliance
vascular compliance
volumetric compliance
Volumetric capacitance
Shear displacement
Shear distortion
1
Heat capacitance
1
The molar amount of a portion of molecules normalized to the spatial amount of the spatial region occupied by the molecules
hasPhysicalDomain exactly 1 'Chemical kinetic domain'
Concentration of chemical
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 variant that is the spatial scope, mathematical form or spatial coordinate basis of a property value.
Property value basis
A portion of fluid that is incompressible
Portion of liquid
Bending distortion velocity
Cartesian 3D-coordinate system
A temporal instant that is the first temporal instant in a temporal interval
Initial instant of process
A temporal instant that is the last temporal instant in a temporal interval
Terminal instant of process
A mathematical dependency of values of geometrical spatial properties.
Geometrical dependency
1
Magnetic constant
Magnetic constant
1
G
Gibbs free energy
partial molar 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
A flow-driving potential that drives the chemical transformation of one kind of chemical species into another.
Chemical potential
Dynamical domain in which the physical entity is a portion fluid and the processes are flows od fluid from one portion to another
Fluid kinetic domain
2
transducer
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..
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
Transducer dependency
1
1
A physics quality that is a measure of the occurrence of events within a temporal coordinate system.
Temporal property
A temporal property that is the amount of time between the origin of a temporal coordinate and a temporal instant
Temporal location
--- outsource this class to existing ontology??
A property basis that is the mathematical form of a property value
Property mathematical form
R
gas constant
universal gas law constant
The gas constant is the Boltzmann constant (k) times the number of moles of a gas (N) such that R = Nk.
A gas law constant for the ideal gas law. It is the increment in the total energy of a mole of matter due to an increment of temperature.
Ideal gas constant
1
PATO:0002193
Electrical charge
An amount property that is the temporal integral of an electrical current relative to an initial amount
Charge amount
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
Solid inertance
Numerical form
1
Gravitational constant
...that is a physical property of matter or space whose value is invariant with respect to time
Constitutive state property of continuum
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.
Molar amount of chemical
A tensor form whose value is expressed as a combination of a scalar and a spatial coordinate.
Vector form
Constitutive flow proportionality for a constitutive coupling dependency.
Constitutive coupling proportionality
Dynamical domain for which process participants are portions of chemical reactants and the processes are chemical reactions.
Chemical kinetic domain
...is a physical property whose value is a multidimensional array of scalars whose values are invariant under spatial coordinate transformation.
Multilinear form
Abstract domain that applies to sets of physics analytical entities and their relationships as expressed with statistical metrics.
Statistical domain
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.
Portion of electrical charge
1
PATO:0002205
Electrical capacitance
Property coordinate form that is a temporal coordinate system.
Temporal coordinate basis
L
displacement
span
spatial displacement
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.
Length dimension
1
Mass density
Mass density
Cylindrical coordinate system
Cylindrical coordinate system
1
Particle amount
An amount property that is the temporal integral of a particle flow rate or the number of particles in a portion of particles.
Amount of particles
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.
A physics analytical entity that represents a division of analytical investigation or discipline with the the domain of the physical sciences.
Physics domain
A property form that defines the spatial dimensions for which the value of an extensive physical property is defined.
Property spatial scope
Dynamical domain in which heat energy is transported from one portion of heat to another
Heat kinetic domain
Torsional distortion
A constitutive process determined by an inductive momentum dependency.
Inductive momentum process
A dynamical state property that is the temporal integral of a force relative to an initial value of the state property
Momentum property
A geometrical dependency of the area of a two-dimensional spatial region on the locus of points that bound the region.
Area dependency
Spherical coordinate system
Spherical coordinate system
Flow-driving potenrial that drives electrical charge through an electrically conducting medium.
Electrical potential
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
Fluid pressure
Temporal Region
A physics occurrent that is an instant or span of time.
Temporal region
compliance
A constitutive storage proportionality that is the ratio of displacement to force in a capacitive dependency and is the reciprocal of an elastance. property.
Capacitance proportionality
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.
A physics continuant that is portion of thermodynamical energy or entropy.
Thermodynamical entity
A potential energy field produced by electrically charged objects that attracts of repels other electrically charged objects.
Electrostatic field
volume
PATO:0000918
A spatial property that is the quantity of space enclosed in a bounded volume region
Spatial volume
1
1
A temporal entity that is a contiguous interval of time bounded by temporal instants.
One-dimensional temporal region
The OPB is an ontology of the real entities and their abstractions modeled using the science of classical physics for the description and analyisis of physical entities such as an apple or rope, or for systems of interacting entities. It includes branches of engineering system dynamics and classical thermodynamics.
OPB has been formulated to support the development, annotation, description and sharing of analytical models. Although developed in the domain of biology, biophysics and physiology, its underlying assumptions, form and content is applicable for the analysis of non-biological engineering systems.
OPB aims 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 applicable to biological physical entities, processes, and functions using the formal tools and concepts of computational ontology as expressed in description logic (DL),and web ontology language (OWL).
OPB has classes that represent abstractions of key classes in BFO such as BFO:Continuant (OPB:Physics continuant). BFO:Processural entity (OPB:Processural entity), and BFO:Attribute (OPB:Physics attribute). A key differentiator is that OPB represents physical entities not represented in BFO such thermodynamic energy, potential energy fields, information. In particular, OPB:Physical process ia defined as the flow of energy and/or information amongst 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 that OPB intends to represent the "real" physical world.
The OPB does not extend to include quantum or relativistic physics, nor is it intended to recapitulate the axiomatic basis of physics as a theoretical framework. Rather, OPB is focuses on foundational theory of classical physics particularly as applied in system dynamics. For example, it encompasses discrete systems analysis (using ordinary differential equations; ODEs), continuum systems analysis (using partial differential equations; PDEs), discrete "agent-based" modeling, and causal propagation models.
the first version of the OPB is targeted solely to discrete systems analysis.
A Thing that is a quality, definition, abstraction, or law of classical physics as discovered and applied to the explanation, analysis, and simulation of biophysical entities and processes.
Physics entity
1
mass diffusivity
partiicle diffusivity
Particle diffusion coefficient
1
Flow rate property that is the temporal derivative of the amount of particles in a portion of particles.
Particle flow rate
A constitutive proportionality that is defined at a spatial point within a portion of material or a field
Constitutive proportionality of continuum
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
Spatial scale domain
Spatial coordinate basis that is comprised of three orthogonal spatial dimensions
Three dimensional spatial coordinate basis
Spatial coordinate basis that is comprised of two orthogonal spatial dimensions
Two dimensional spatial coordinate basis
A geometrical dependency of the volume of a three-dimensional spatial region on the locus of points that bound the region.
Volume dependency
Potential field dependency
Gravitational potential dependency
Electrostatic potential dependency
1
1
PATO:0001021
Thermodynamical state property that is the amount of energy in a portion of energy
Energy amount
1
1
power
PATO:0001024
A thermodynamical rate property that is the temporal rate at which energy is transported across an entity boundary.
Energy flow rate
1
1
A thermodynamical rate property that is the trmporal rate if change of a portion of entropy
Entropy flow rate
https://en.wikipedia.org/wiki/Entropy_in_thermodynamics_and_information_theory
A Thermodynamical state property for the portion of entropy in a portion of entropy
Entropy amount
http://en.wikipedia.org/wiki/Dynamical_system
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.
A physics 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.
Dynamical 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.
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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
Dynamical state property
Dynamical rate property that is the temporal differential of an amount property
Flow rate property
A dynamical rate property that is a temporal differential of a momentum or amount property
Force property
molar flow
molar flow rate
Chemical flow rate measured in number of molecules per unit time; moles/s
Chemical molar flow rate
chemical concentration flux
chemical flux
Chemical flow rate property measured in chemical concentration per unit time.
Chemical concentration flow rate
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
Diffusion potential
Spatial integral dependency
Particle concentration
Particle count
1
Rotational inertance
Portion of chemical
1
Lineal mechanical inductive dependency
1
Rotational mechanical inductive dependency
Section area of spatial region
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
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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.
Geometrical form
A sum of rates dependency that holds for rate properties.
Sum of rates
Immaterial dynamical domain in which a participating entity is a physical entity is an electrical field.
Electrical domain
Osmotic pressure is the fluid pressure needed prevent the inward flow of its solvent across a semipermeable membrane.
Osmotic pressure
1
1
1
Heat flow dependency
An energy rate dependency of the heat dissipation rate generated by resistive forces acting on a dynamical flow.
Energy dissipation dependency
1
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.
A physics continuant that occupies a spatial region, is a bearer or conduit of energy and/or information, has dynamical properties, and can participate in a physics process.
Dynamical entity
A mechanical joint whose parts are constrained to rotate around a longitudinal axis.
Flexional joint
1-junction
Kirchhoff's loop rule
Kirchhoff's mesh rule
Kirchhoff's second law
Kirchhoff's second 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
Loop rate constraint
A sum of rate properties that holds for force properties.
Sum of forces
A physical state event that is the appearance, disappearance, or transformation of a physical entity as a participant in a physical process
Entity existence event
Section area
Primitive physical entity that is a magnetic field.
Magnetism
coefficient of expansion on the transverse axial
negative ratio of transverse to axial strain
https://en.wikipedia.org/wiki/Poisson%27s_ratio
Poisson ratio
PATO:0002284
A primitive physical entity that is time.
Time
...that is a structural fluent.
A physical state evernt that is a discrete change in a structural relation between participants in a process
Structural event
energy bond
A dynamical process that is the flow of thermodynamic energy as determined by a constitutive dependency.
Constitutive process
A constitutive dependnecy relating measures of solute concentration
Osmotic dependency
Constitutive storage proportionality
A physics analytical entity that is a set of interrelated mathematical abstractions that represent one or more structurally or functionally related physics real entities.
Physics model
A physics entity that is a continuant or process in the real world, occupies space and time, and possesses a portion of matter, energy, or information.
Physics real entity
A property spatial scope of a physical property whose value applies to a single point in space.
Punctal scope
Spatial amount
Extensive spatial scope
A dynamical entity that is not composed of elements
Immaterial dynamical entity
Conservation law
Per Wikipedia: In physics, a conservation law states that a particular measurable property of an isolated physical system does not change as the system evolves.
A calculus dependency that is the derivative or integral of a property value with respect to time
Temporal calculus constraint
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)
A Tensile stress that is the amount of force normal to a spatial line region normalized to the length of the line region.
Axial normal tensile stress
A material amount of a portion of gas or liquid
Amount of fluid
A physics network model in which nodes represent physical properties and arcs are dynamical dependencies by which property values depend upon one another.
Property dependency graph model
1
1
1
The dependence of an energy flow rate on the potential energy difference between two entities
Energy flow dependency
A charged atom that has a net positive electrical charge
Atomic anion
A state trajectory that is the temporally-ordered locus of values of a physical property of a process participant.
Property value trajectory
Surface area
Surface area of spatial region
A property form that is the spatial and/or temporal coordinate system within which a property value is defined.
Property coordinate basis
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.
Statistical property
Threshold value event
...that is a minimal value during an interval of a property value trajectory
Minimal value event
...that is a maximal value during an interval of a property value trajectory
Maximal value event
A state trajectory that is a temporally ordering of the structural relations of a participant in a physical process
Structural state trajectory
A state trajectory that is the temporally ordered entity-type and cardinality of a physics process participant.
Existential state trajectory
A mechanical force property that is the amount of force per unit of spatial extent.
Mechanical stress
A physical state that is the set of structural relations of a physical continuant to other continuants.
Structural 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 the dynamical properties of a physical entity
Dynamical state
Perimeter span of spatial region
"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.
A physics property variant that is the magnitude of an instance of a physical property.
Property value scale
An electrical potential that exists across an electrodiffusion barrier such as a cell membrane.
Membrane potential
A constitutive process whose dynamical rate is determined a difference in the amount properties of its participants.
Amount-driven flow process
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.
A physics event that is a discrete change of physical state of a physical entity
Physics state event
per Jacobus van 't Hoff; see:
https://en.wikipedia.org/wiki/Osmotic_pressure
An osmotic dependency relation osmotic pressure to solute concentration
van't Hoff law
Property of ion channel flux dependency
Plane angle of shape model
PATO:0001708
A spatial property that is the spatial distance between two spatial points.
Spatial span
Plane angle of spatial region
Solid angle of spatial region
chemical product
chemical reactant
chemical substrate
compound
molecular species
reactant
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.
A solid dynamical entity that can participate in chemical reaction processes.
Chemical structure
Solid potential energy
Solid angle of shape model
A three-dimensional region that has a finite spatial extent defined by on or more contiguous spatial surfaces.
Bounded volume region
Plane angle
Solid gravitational potential energy
A three-dimensional region that has a infinite spatial extent incompletely limited by zero or more two-dimensional regions.
Unbounded volume region
A two-dimensional region that has finite spatial extent that is limited by one or more bounded line regions
Bounded surface region
A two-dimensional region that has a infinite spatial extent limited incompletely by zero or more one-dimensional regions.
Unbounded surface region
A one-dimensional region that has a finite spatial extent limited by spatial points at each end.
Bounded line region
Existential event during which two or more physical entity instances becomes a single entity instances.
Entity fusion event
Existential event during an instance of a physical entity becomes more than one entity instances
Entity fission event
A charged atom that has a net negative electrical charge
Atomic cation
Existential event that is the appearance of a physical entity of a classifiable type
Entity appearance event
Existential event that is the disappearance of a physical entity as a classifiable type.
Entity disappearance event
A fluid pressure that is the difference in pressure that exists between two portions of fluid.
Pressure differential
A fluid pressure that is measured relative to the absolute zero pressure of a vacuum
Absolute pressure
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.
Potential-driven flow process
1
1
Amount-driven flow process for the chemical kinetic domain
Chemical mass-action flow process
1
1
Amount-driven flow process for the diffusion kinetic domain
Diffusion-gradient flow process
A Property mathematical form that is an 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.)
Algebraic form
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.
An algebraic form that one property value can be subtracted from, but not divided by, another property value of the same class
Difference form
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.
An algebraic form that is a property value that is divided another property value of the same class.
Ratiometric 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.
Ordinal form
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.
Tensile stress
A relative value that is the maximum value within a set or continuum of values
Maximum value
A physical state that is the set of values of one or more thermodynamical properties of a thermodynamical entity.
Thermodynamical state
ion
ionic species
A particulate that bears a net electrical charge
Charged particulate
A tensile stress that is the amount of force normal to a surface region normalized to the area of the surface region.
Surface normal tensile stress
Change containment event
Change parthood event
Physics analytical entity that is the value, dimension, measurement unit, or the mathematical form of a physics property as observed in the real world or represented by a physics model.
Physics property variant
Change adjacency event
Change connectivity event
Change location event
Existential event during which an entity becomes an entity of a different type.
Entity transformation event
A physical state event that occurs when the value of a physical property value traverses a minimum, maximum or threshold value.
Property value event
A one-dimensional region that has a infinite spatial extent limited by one or no spatial points.
Unbounded line region
1
inertia
mass
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.
PATO:0000125
synonyms: mass, inertia, inertial mass
An amount property that is the temporal integral of a material flow rate relative to and initial amount.
Material amount
Constitutive transformer ratio
A portion of material that is comprised of an uncountably large set of particles that have diffusion kinetic properties and participate in diffusion processes.
Portion of particles
1
Diffusion conductance
Unbounded plate
Threshold value
Dynamical domain in which entity are material dynamical entities
Material dynamical domain
A particulate that bears no net electrical charge.
Uncharged particulate
A mechanical joint in which one or both parts are constrined to rotate about a longitudinal axis.
Rotational joint
Unbounded filament
Threshold exceeded event
Physics continuants represent real entities that are portions of primitive physics entites and may be spatially-bounded (e.g, a heart, a portion of blood, a cell's cytoplasmic sodium ions) or may be spatially-unbounded (e.g., an electrical field or gravitational potential field).
A physics entity that is a continuant in the real world.
Physics continuant
A portion of particles that bear no net electrical charge
Portion of uncharged particles
A quantum charge that is the electrical charge of a positron
Quantal positive charge
'Physics conditon' is intended to represent the physics concept of the "state" of a system in its broadest sense that comprehends all physical state variables (locations, energies, dynamic properties, etc.) as well as its structural relations to its parts and other physical entities with which it is a physical process participant.
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.
A physical state of a physics continuant that is composed of its dyanmical state, its structural state, and its thermodynamical state.
Process state
A quantal charge that is the elecrtical charge of an electron
Quantal negative charge
Start process event
Boundary amount constraint
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.
Shear stress
Force-driven flow process for which a chemical flow is driven by the chemical potentials of reactants
Chemical resistive flow process
Fluid resistive flow process
Property coordinate form that is a spatial coordinate system and a temporal coordinate system.
Spatiotemporal coordinate basis
Bounded filament
Kinetic energy amount
Because OPB is designed for representing discrete dynamical systems, the representation of magnetic theory and system is attenuated and deferred.
Immaterial dynamical domain in which a participating entity is a physical entity is a magnetic field.
Magnetic domain
1
Thermal diffusivity
Minimum value
Variance value
Mean value
1
Electrical energy flow dependency
Standard deviation value
Potential energy amount
1
https://en.wikipedia.org/wiki/Gravitational_energy
A dependency of the potential energy of a material entity due to vertical displacement in the earth's gravitational field.
Gravitational field potential energy dependency
Physics agent-based model
Distributive property value that is a measure of the dispersion of magnitudes in a set or trajectory of values.
Variability value
Lineal particle diffusion coefficient
Areal particle diffusion coefficient
We defer creating subclasses of Informational processes.
A physics occurrent that is the transmission, transduction or transformation of information amongst process participants with negligible exchange of thermodynamic energy.
Informational process
Physical constant that is the mass of a molecule calculated as the sum of the atomic weights of each constituent element multiplied by the number of atoms of that element in the molecular formula
Molecular weight
A process occurrence event that is
End process event
A tensor form that is a real number
Scalar form
Perimeter span of shape model
A shear stress that is the amount of force acting in the along a line spatial region normalized to the length of the line.
Lineal shear stress
A physics entity that encodes or expresses a theory, hypothesis, or explanation that relates instances of physics continuants and processural for purposes of demonstration, calculation, education, or simuation.
A physics model aims to describe the physical interactions, dependencies amongst property values, and temporal changes amongst a set of physics continuants and the physics processes in which they participate.
A physics model may exist solely as an idea or it can be expressed verbally, graphically, or computationally so be representable by a class of the OBO Information Artefact Ontology (IAO).
Instances of Physics Model class are intended for annotating parts or the entirety of computational representations of physics continuants, dependencies, and processurals, in part, or as a whole.
Physics analytical entity
Electrical resistive flow process
A amount-driven flow process whose flow rate is determined the temperature property of its participants.
Heat transfer flow process
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.
Surface shear stress
A matrial dyamical entity that can participate in a diffusive process, advection or convection.
Particulate
bond graph
energy bond graph
A physics model in which nodes represent portions of energy and arcs represent flows of energy.
Energy bond graph model
A spatial region that is a point in space.
Zero-dimensional spatial region
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.
Spatial location
Abstract domain that encompasses the quantification, storage, and communication of information amongst participants in a physics process.
Information domain
A charged particulate that is a molecule.
Charged molecule
A physics analytical entity that is a mathematical function or quantitative value useful for the analysis and simulation of biophysical models.
Mathematical domain
A portion of material that has no inherent shape and assumes the shape of its container
Portion of fluid
Solid angle
A Physics differential model that includes at least one ordinary differential equation (ODE) that may be a temporal differential versus temporal extent or a spatial differential with respect to spatial extent.
Physics ODE model
A Physics differential model that includes at least one partial differential equation (PDE) of at least one multivariable function.
Physics PDE model
A physics model expressed in terms of algebraic symbols and operators.
Physics algebraic model
Portion of strain potential energy
1
voltage
Measured as the difference in electric potential between two points or the difference in electric potential energy per unit charge between two points.
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.
Electrodiffusional potential
Algebraic state model
A constraint dependency that mathematically expresses a property value as an integral or derivate of some other property value.
Calculus constraint
Algebraic dependency
A temporal calculus dependency that is the temporal rate of change of a property value.
Temporal integrative constraint
...that is a proportionality of a signalled transactor dependency
Signalled transactor coefficient
Direct transactor coefficient
1
Electrical inductive energy dependency
A potential energy dependency a magnetic or ferrous entity in a magnetic field.
Magnetic field potential energy dependency
A charged particulate that is a polymolecule.
Charged polymolecule
A potential energy field that is a spatial gradient of particle concentration.
Diffusion gradient
A temporal calculus dependency that is the temporal rate of change of a property value.
Temporal derivative constraint
Boundary momentum constraint
A potential energy field that is a combination of an electrostatic and a diffusion gradient.
Electrochemical diffusion gradient
A constitutive process whose rates are determined by a diffusive transformer dependency.
Diffusive transformer
A transformer process whose rates are determined by a mechanical transformer dependency.
Mechanical transformer process
Heat energy amount
1
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.
A physics continuant that is a portion of space in a spatial reference frame.
Spatial entity
1
Energy density
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.
...that is the ratio of an extensive property of an entity to the volume of the spatial region occupied by the region.
Density
1
Electrical resistive dissipation
1
solute concentration
PATO:0002027
A chemical concentration the total amount of solute per liter of solution.
Osmolality
Multiplicative dependency
Additive dependency
Difference dependency
Divisor dependency
1
PATO:0001655
A chemical concentration the total amount of solute per kilogram of solution.
Osmolarity
1
A momentum driving force that acts to accelerate, displace, or deform a solid physical entity
Solid force
Activity of anion for univalent sodium ions
pNa
An amount of chemical that is the thermodynamic activity of a chemical as affected by interactions with other chemical species
Chemical activity
A primitive physical entity that is space.
Space
https://en.wikipedia.org/wiki/Calculus
Calculus dependency
A shape form that is a solid cylinder that is longer than it is thick.
Filament form
A shape form that is a planar solid that is broader than it is thick
Plate 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.
Pipe form
A walled form that is a hollow sphere composed of a wall part enclosing a lumen part.
Tank form
https://en.wikipedia.org/wiki/Calculus#Differential_calculus
Differential dependency
rate constant
Constitutive proportionality between properties in a dynamical flow dependency.
Constitutive flow proportionality
A property value that serves as a standard value for a system of units of measure for the property.
Standard property value
Spatial regions are spatial entities as found in BFO, GFO, etc. and, as such, are generic entities that can apply to any line, surface, or volume. The problem is that such non-specificity minimizes their utility for model specification and annotation.
A spatial entity that is a spatially bound, contiguous portion of space
Spatial region
A spatial region that is a volumetric region in space with three spatial dimensions.
Three-dimensional region
Temporal rate of periodic events during a temporal interval.
Event frequency
A spatial property that is the degree to which a spatial line region or surface region deviates from being straight or flat, respectively.
Spatial curvature
Spatial domain in which spatial scales are restricted to one, two or three spatial dimensions
Spatial coordinate domain
A dynamical property that is the temporal rate of change of a flow rate property.
Dynamical acceleration property
https://en.wikipedia.org/wiki/Integral
Integrative dependency
Definite integrative dependency
Spatial coordinate domain in which all spatial properties are referred to a single spatial coordinate system
One-dimensional spatial domain
1
Charge density
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.
Material flow rate
Indefinite integrative dependency
Spatial coordinate domain in which all spatial properties are referred to a two dimensional spatial coordinate system
Two-dimensional spatial domain
Spatial coordinate domain in which all spatial properties are referred to a three dimensional spatial coordinate system
Three-dimensional spatial domain
Thermodynamical domain in which physics continuants each have and exchange a portion of kinetic energy.
Kinetic energy domain
Thermodynamical domain in which physics continuants each have and exchange a portion of potential energy.
Potential energy domain
Mass of solid entity
F
Force dimension
A physics dependency that is a quantitative relationship amongst values of physical properties.
Dynamical dependency
Algebraic conservation model
...that is a proportionality between a signal receiver property and the signal property of a signalled transactor dependency
Transactor sender coefficient
...that is a proportionality between a signal property and the controlled property of a signalled transactor dependency
Transactor receiver coefficient
Tensor dependency
...that is the ratio of the amount of energy in a 1-dimensional spatial region to the volume of that region.
Energy lineal density
...that is the ratio of the amount of energy in a 2-dimensional spatial region to the volume of that region.
Energy areal density
...that is the ratio of the amount of energy in a 3-dimensional spatial region to the volume of that region.
Energy volumetric density
Property value that is the ratio of two or more observed or standard property values.
Scaled property value
...that is the ratio of the amount of charge in a 3-dimensional spatial region to the volume of that region.
Charge volumetric density
...that is the ratio of the amount of charge in a 2-dimensional spatial region to the area of that region.
Charge areal density
...that is the ratio of the amount of charge in a 1-dimensional spatial region to the length of that region.
Charge lineal density
A material dynamical entity that occupies a portion of space and has inherent shape and solid mechanical properties.
Solid dynamical entity
A material dynamical entity that occupies a spatial region, has no inherent shape and consists of innumerable energy-bearing material parts.
Portion of material
A spatial region that is a surface having two spatial dimensions.
Two-dimensional region
A spatial region that is a line in space.
One-dimensional region
1
A physics quality that is a scalar or vectorial measure of the spatial extent, location, or shape of a spatial entity.
Spatial property
Solid resistive motion process
1
Rate of energy dissipation due to forces and flow rates of a viscous material
Fluid viscous dissipation
Portion of negative charge
A physics model expressed in terms of logical symbols and operators.
Physics logical model
A plate shape whose perimeter is a square with equal sides.
Square plate
A plate shape whose perimeter is a rectangle with unequal sides
Rectangular plate
A plate shape that whose perimeter is a circle.
Circular plate
Thin-walled pipe shape
Thick-walled pipe shape
Thin-walled tank shape
Thick-walled tank shape
A solid form that is a solid with six faces, each of which is a rectangle.
Cuboid form
A cuboid shape in which each face is a square congruent with the other faces.
Square cuboid shape
A cuboid shape for which at most one face is a square.
Rectangular cuboid shape
Total energy amount
A bona fide dynamical boundary that is a spatially contiguous discontinuity of physical property values.
Property value boundary
A geometrical form that composed of a single spatial region.
Solid form
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)
A geometrical form that composed of a one spatial region, the wall part, that bounds a second spatial region, the lumen part.
Walled form
Immaterial dynamical domain in which a participating entity is a physical entity is a gravitational field.
Gravitational domain
An area of a plane that transects a volume shape model and that is enclosed within the boundary of a shape model.
Section area of shape model
A shape model area that is the area of the bounding region of a volume region
Surface area of shape model
Span of lumen
Span of outer bound of shape
A span of spatial entity that is straight-line distance between two points on the bounds of a spatial entity
Transverse 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.
Perimeter span
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
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.
GHK reversal potential
A calculus dependency that is the derivative or integral of a property value with respect to a spatial displacement.
Spatial calculus constraint
Spatial integrative constraint
A boundary constraint on the value of a state property at a physics model boundary.
Boundary state constraint
Kirchoff's laws
A dynamical constraint on the values of two or more rate properties
Kirchoff constraint
A boundary constraint on the value of a rate property at a physics boundary.
Boundary rate constraint
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.
A mathermatical entity that is a mathematical function.
Mathematical dependency
A physics model that expresses equations and logic based on the qualitative, topological relations and/or quantitative relations of linear, planar, or solid geometry,.
Physics geometrical model
A dynamical constraint on the sum of a set of dynamical property values.
Summation constraint
A thermodynamical property that is the amount of energy or entropy of a dynamical entity.
Thermodynamical state property
A thermodynamical property that is the temporal rate of energy or entropy flow.
Thermodynamical rate property
A thermodynamical property that determines how heat and entropy flow depend on the material composition and spatial properties of a dynamical entity
Thermal constitutive property
A Physics Model that includes a mathematical equation at least one term that is a mathematical derivative of the value of a physical property such as time, space, or others.
Physics differential model
A dynamical physics process that is the flow of energy or information through a circuit or into/out of a junction.
Topological process
1
An amount property that is the amount of material that inhers in a solid entity
Amount of solid entity
Constitutive flow proportionality for an amount-driven flow proportionality
Amount-driven flow proportionality
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.
Process condition 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.
Precondition 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.
Postcondition dependency
Spatial derivative constraint
...by which a change in the type or existence of a physical entity is a consequence of its physical state
Existential event dependency
Fluid gravitational potential energy
1
Reaction rate constant
...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
Structural event dependency
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.
State fraction of chemical
Ion conductance per area
Ion conductance per capacitance
Fluid kinetic domain in which the physical entity is a portion liquid
Liquid kinetic domain
Fluid kinetic domain in which the physical entity is a portion gas.
Gas kinetic domain
Ion conductance per path
A portion of particles that bear a net electrical charge.
Portion of charged particles
1
Solid friction dissipation
1
Diffusion coefficient
Portion of displacement potential energy
https://en.wikipedia.org/wiki/Thermal_conductivity
A thermal constitutive property that is the ratio of the rate of heat energy between physical entities to the difference of their temperatures
Thermal conductivity
https://en.wikipedia.org/wiki/Heat_capacity
A thermal constitutive property that is the ratio of the heat energy added or removed to a physical entity to the change in its temperature
Heat capacity
Abstract domain that encompasses the properties of space and the shape, size, relative position of spatial shapes.
Geometrical domain
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.
Dynamical boundary
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.
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
Fluid dynamical boundary
An amount of chemical that is the thermodynamic activity of a chemical solute as affected by other solutes in a solution.
Activity of solute
Amount property
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.
Molecule
1
A physics dependency that relates values of thermodynamical properties to the values of dynamical properties or to other thermodynamical properties
Thermodynamical dependency
Joule SI-unit
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.
Thermodynamic potential
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.
Mechanical joint
A portion of fluid that is compressible
Portion of gas
Weight of solid entity
Physics model represents the relationships of physics continuants and processes, and properties and dependencies as node-arc graphs that is useful for the representation and analysis of systems of physics entities
Physics network model
1
A material amount of a portion of liquid
Amount of liquid
1
Fourier's law
Thermal conduction#Fourier's law
Thermal contact conductance
Heat transfer dependency
An impedance that is the opposition to flow due to the combination of resistance, capacitance, and inductance along a flow path
Impedence property
An impedance that is the opposition to flow due to the combination capacitance and inductance of a flow path
Reactance property
A force-driven flow proporionality that is the opposition to flow due to the duration and/or rate of change of a flow property.
Impedance
The molar heat capacity is the heat capacity per molar amount of a pure substance,
Molar heat capacity
A mechanical joint whose parts are constrained to extend along a longitudinal axis.
Coaxial joint
Spatial fraction of particle
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.
Advective transport dependency
A topological dynamical process that is a flow of energy, information, or matter through a contiguous loop.
Circuit flow process
A topological dynamical process that is a flow of energy, information, or matter into and out of a flow junction.
Junctional flow process
Boundary flow constraint
Boundary force constraint
Constitutive coupling proportionality that is a dimensional ratio of dynamical properties of players in a transducer dependency
Transducer modulus
"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.
A dynamical dependency that determines flow rates of energy, charge, and/or material amongst paticipants in a constitutive process.
Constitutive dependency
A portion of fluid that is a theoretical gas composed of many randomly moving point material particles that interact only by elastic collisions.
Portion of ideal gas
1
A dynamical acceleration property that is the temporal rate of change of an electrical current flow rate.
Electrical acceleration
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 variant that is the unit of measure of a physical property as standardized in the International System of Units.
Property SI-unit
1
1
A derived SI-unit for plane angles
Radian SI-unit
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]
Property SI-base dimension
1
1
A derived SI-unit for a quantity of electrical charge.
Coulomb SI-unit
1
1
2
A derived SI-unit for force or weight
Newton SI-unit
1
1
chemical rate law
mass-action rate law
An amount-driven dependency in which a chemical flow rate of participating chemicals depends on the amounts of its players
Chemical mass-action dependency
Fluid capacitive potential energy
1
2
2
A derived SI-unit for energy, work or heat
Joule SI-unit
A base SI-unit for length
Metre SI-unit
A base SI-unit for luminous intensity
Candela SI-unit
A base SI-unit for mass
Kilogram SI-unit
A base SI-unit for temperature
Kelvin SI-unit
Chemical capacitive process
Fluid capacitive process
Mechanical capacitive process
Electrical capacitive process
A physics occurrent that is a change in the physical state of a physics continuant.
Physical change
Diffusive capacitive process
A chemical structure that is a single atom composed of protons, neutrons and electrons.
Element
s
second
A base SI-unit for time
Second SI-unit
A force property that can change only the potential energy of a portion of entity.
Flow-driving potential
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 the momentum of a material entity and can change either/both the kinetic and potential energy.
Momentum-driving force
Wikipedia: Liquid junction potential http://en.wikipedia.org/w/index.php?title=Liquid_junction_potential&redirect=no
An electrodiffusional potential across a diffusional barrier due to differences in diffusional mobility of anions and cations in the fluids separated by the barrier.
Liquid junction potential
A solid dynamical entity that has contiguous structure. {not quite right yet}
Mechanical solid
Electric current dimension
Dynamical boundary that is a spatial boundary across which there is a discontinuity of structural composition or physical property values.
Bona fide dynamical boundary
Base SI-unit
A base SI-unit for electrical current
Ampere SI-unit
A base SI-unit for amount of substance
Mole SI-unit
Tensile distortion
An SI-unit that is composed of a multiple or ratio of two or more base SI-units
Derived SI-unit
imaginary unit
A mathematical constant that is the square root of the real number minus one.
i
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.
Spatial fraction of chemical
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
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
Molar fraction of chemical
Physics domain that encompasses theoretical entities that do not occupy space are not composed of material and/or energy.
Abstract domain
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).
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.
Fractional amount of chemical
A physics trajectory that is a time-series of changes of physical asttributes of a participant in a physical process.
State trajectory
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 state that is necessary and sufficient to initiate an occurrence of a physical process
Process pre-state
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
A process state that terminates a physical process.
Process post-state
Absolute amount of a chemical that is the mass of a portion of a chemical within a spatial region.
Mass amount of chemical
Physical dependencies are axioms, definitions and empirical laws of physics that, once discovered, may be articulated verbally, mathematically, or computationally as aids to understanding and analyzing real biophysical systems.
Physical dependencies may be represented by a broad class of quantitative and qualitative relationships amongst physical entities and the qualitities of physics continuants, and processes. Dependencies are the rules by which dynamical and information systems operate, and comprise computations 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,
A physics occurrent that relates the existence and attributes of physics continuants to the occurrences and time-courses of physics processural entities.
Physics dependency
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 constraint dependency that fixes the value of a physical property at a boundary of a physical entity.
Boundary constraint
Causal propagation model
Spatial calculus dependency
Absolute amount of chemical
A material volumnal density that is the amount soluble matter that is contained in a volume of solvent.
Volumnal concentration of solute
A physics entity that is a temporal region, a physics dependency, or a physics change or process
Physics occurrent
A mechanical displacement that is the temporal integral of a rotational velocity of two solid entites that are constrained to rotate relative to each other around a rotational axis or planar axis.
Joint displacement
A sum of state property which holds for momentum properties
Sum of momenta
1
A dynamical dependency that mathematically constrains the values of properties according to conservation laws
Constraint dependency
A dynamical rate dependency that is a sum of rate property values.
Sum of rate properties
A sum of properties for the state properties of more than one physical entity.
Sum of state properties
2
2
A derived SI-unit for solid angles
Steradian SI-unit
1
1
A derived SI-unit for power, radiant flux
Watt SI-unit
PATO:0002006
A geometrical form that extends in two spatial dimensions.
Planar form
A geometrical form that extends in a single spatial dimension.
Line form
PATO:0001019
An amount density for a material entity.
Material density
PATO:0001353
A material density expressed per unit volume
Material volumnal density
1
2
1
3
A derived SI-unit for electrical potential difference, voltage, or electromotive force
Volt SI-unit
2
4
1
2
A derived SI-unit for electrical capacitance
Farad SI-unit
1
2
2
3
A derived SI-unit for elctrical resistance, impedance, reactance
Ohm SI-unit
2
3
1
2
A derived SI-unit for electrical conductance
Seimen SI-unit
Organismal scale
Organ system scale
Organ scale
Organ part scale
Cell scale
1
2
1
2
A derived SI-unit for magnetic flux
Weber SI-unit
Cell component scale
Molecular scale
Atomic scale
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.
Physics domain in which the entities are spatial entities
Spatial domain
Portion of liquid solution
Portion of liquid solvent
Portion of pure liquid
1
1
2
A derived SI-unit for magnetic flux density
Tesla SI-unit
1
2
2
2
A derived SI-unit for electrical inductance
Henry SI-unit
PATO:0001351
A material density expressed per unit area
Material areal density
Joint rotational displacement
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 conductance
1
Ion flow resistance
Ion flow resistance per area
Ion flow resistance path
Ion flow resistance per capacitance
1
A derived SI-unit for temperature relative to 273.15 K
Degree-C SI-unit
Primitive physics entity classes serve as "mass nouns" for the stuff of physical analysis.
A physics continuant that is a portion or instance of a material or immaterial part of reality that is so basic to our understanding that it cannot be defined in a non-circular manner.
Primitive entity
Ion flow resistance per ion channel
Joint angular displacement
A thermodynamic dependency the thermodynamic energy of a physical entity on its dynamical properties
Energy state dependency
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.
Potential energy dependency
A flow rate distributor represents the point of convergence of multiple flows but which has no capacity to store flows so that the sum of flow rates at any moment in time is identically zero. Biophysical examples would include representing the bifurcation of a blood vessel as an inelastic distributor, or representing a set of reactions that share a common reactant as a chemical circuit node that has no volume and hence no concentration.
A junction rate constraint for flow rate properties.
Flow junction rate constraint
Constitutive flow proportionality for a force-driven flow proportionality.
Force-driven flow proportionality
PATO:0001352
A material density expressed per unit length
Material lineal density
PATO:0001034
A mechanical displacement that is a local solid displacement normalized to the extent of the solid entity
Solid strain
Shear strain
Tensile strain
1
A derived SI-unit for luminous flux
Lumen SI-unit
1
2
A derived SI-unit for illuminance
Lux SI-unit
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.
A constitutive property that of a non-proportional (i.e., non-linear) dependency of dynamical physical properties.
Constitutive parameter
Property of Hodgkin-Huxley dependency
Maximal channel conductance
1
1
A derived SI-unit for catalytic activity or metabolic flux
Katal SI-unit
A charged particle that is an element.
Charged 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
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.
A junction rate constraint for force properties.
Force junction rate constraint
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.
Activation gating variable
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.
Number of activation gating particles
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.
Inactivation gating variable
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.
Number of inactivation gating particles
1
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
Amount of substance dimension
Primitive physical entity that is a quantal electrical charge
Charge
Lineal mechanic domain
An inductive momentum process in the fluid kinetic domain
Fluid inductive process
An inductive momentum process in the solid mechanical domain
Mechanical inductive process
An inductive momentum process in the electrical domain
Electrical inductive process
Rotational mechanic domain
Lineal mechanical force
Rotational mechanical force
Rotational strain
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.
Total energy flow rate
1
Electrical inertance
A thermodynamic dependency energy flow rate of a process as the product of the flow-rate and force differential that drives the flow.
Energy rate dependency
Torsional distortional velocity
Rotational solid velocity
A sum of state property which holds for amount properties
Sum of amounts
Property derived dimension
Primitive physical entity that is composed of atoms.
Matter
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."
Primitive physical entity that is capacity to do physical work.
Energy
1
An amount property that is a temporal integral of a mechanical velocity property of a solid kinetic entity relative to an inertial frame.
Mechanical displacement
Plane angle dimension
Torsional force
Bending moment
A chemical structure composed of molecules bound to each other by non-covalent bonds.
Polymolecule
H
enthalpy
Joule SI-unit
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.
Enthalpic energy
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.
Dynamical constitutive property
Solid angle dimension
Physical domain in which process participants are immaterial dynamical entities.
Immaterial dynamical domain
1
Rotational mechanical capacity dependency
Dynamical boundary declared for analytical purposes to distinguish physical entities between which there is no discontinuity of structural composition or physical property values
Fiat 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.
A physical state that is a set of dynamical state and rate properties that hold at a dynamical boundary
Boundary-condition
specific heat
A heat capacity that is the heat capacity per unit mass of a material
Specific heat capacity
Thermodynamical domain in which physics continuants each have and exchange portions of entropy.
Entropy domain
A property spatial scope of a physical property whose value applies to a span of space.
Intensive spatial scope
Ar
https://en.wikipedia.org/wiki/Relative_atomic_mass
Atomic amount that is a dimensionless (number only) that is the ratio of the average mass of atoms of an element in a given sample to one atomic mass constant.
Relative atomic mass
Atomic constant
Threshold subceeded event
A property value event that occurs a maximum
Extreme value event
Frequency dimension
Pressure dimension
1
1
1
Hooke's law
Hookes law
Capacitive storage dependencies represent the storage of stuff and its attendent energy where stuff accumulates in a device against an attendent force that counters the inflow. Subclasses apply to stores in all biophysical domains for which forces and amounts are defined.
All capacitive dependencies relate a force (or force differential) to an amount property which is a generalization on Hooke's law discovered by Robert Hooke in the 1660's. Hooke's law refers strictly to cases where the force-amount relation is, at least approximately, linear. Non-linear dependencies abound both in the fields of engineering (e.g., progressive rate springs) and biology (e.g., fluid accumulation in elastic vessels)
Constitutive 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.
Capacitive dependency
1
1
A constitutive dependency between an entity's momentum and its rate property.
Inductive dependency
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
Electrical inductance
A chemical bond mediated by ionic (i.e., electrostatic) interactions, hydrophobic interactions, hydrogen bonds, and van der Waals forces.
Noncovalent chemical bond
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.
Spatial boundary
kinetic pool
pool
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.
Fiat dynamical boundary that distinguishes portions of diffusible and interacting particles or chemicals that are distributed within the same spatial region.
Chemical kinetic boundary
Velocity dimension
A chemical bond mediated by the sharing of electron pairs between atoms.
Covalent chemical bond
1
Lineal concentration of chemical
1
Areal concentration of chemical
1
Areal concentration of particles
1
Lineal concentration of particles
1
Volumnal concentration of particles
Energy flow rate that is the temporal rate of the transfer of kinetic energy from one material dynamical entity to another.
Kinetic energy flow rate
Energy flow rate that is the temporal rate of the transfer of potential energy from one dynamical entity to another.
Potential energy flow rate
A physics quality composed of the set of dynamical, structural, and thermodynamical properties of a physical continuant at a moment in time.
Physical state
Area dimension
https://en.wikipedia.org/wiki/Thermodynamic_activity
p(ion) is the decimal logarithm of the reciprocal of the ion activity in a solution.
A chemical activity that is the decimal logarithm of the reciprocal of the activity of an ion in solution
p-Ion
Constitutive rate property of continuum
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.
Amount-driven dependency
A dynamical inductive dependency of a solid entity's momentum on its velocity.
Mechanical inductive dependency
1
A dynamical inductive dependency of an fluid entity's momentum on its fluid flow rate.
Fluid inductive dependency
1
A dynamical inductive dependency of an electrical entity's inductance property on its electrical current property.
Electrical inductive dependency
1
Capacitive force dependency in which the volume of a fluid depends the differential of fluid pressures across its boundary.
Fluid 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.
Electrical capacitive dependency
Capacitive force dependency in which an displacement of a solid entity depends its the differential of the solid forces acting on it.
Mechanical capacitive dependency
1
Capacitive force dependency by which the chemical potential of a portion of chemical depends the amount of chemical that it contains.
Chemical capacitive dependency
1
1
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
Transducer dependency by which a fluid pressure and flow generates a solid force and displacement.
Fluid-mechanical transducer dependency
1
1
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
Transducer dependency by which a chemical potential difference and reaction rate generates a solid force and displacement.
Chemo-mechanical transducer 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.
Transformer dependency
Portion of liquid suspension
Volume dimension
Activity of chemical of a solute that is a cation
p-cation
Decimal cologarithm of chemical activity
p-anion
Activity of anion for univalent protons
pH
Activity of anion for divalent calcium cations
pCa
A physics dependency that relates an occurrence of a physics process to the physics condition(s) of its participants.
Occurrence dependency
Ionic chemical bond
1
1
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 )
Transducer dependency that couples a chemical reaction potential times flow rate to the vectorial transport diffusible particles across a diffusion barrier.
Chemo-diffusional transducer 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
Diffusive transformer dependency
Hydrophobic chemical bond
1
Capacitive force dependency by which the diffusional potential of a portion of particles depends the amount of particles that it contains.
Diffusional capacitive dependency
1
Nernst potential
equilibrium potential
reversal 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.
Electrochemical capacitance dependency
Activity of cation for univalent chloride ions
pCl
Hydrogen bond
Van der waals bond
1
Fluid energy flow dependency
Atomic amount that is the relative atomic mass (of elements from natural, stable, terrestrial sources.
Atomic weight
"Molar charge" is the amount of electrical charge per mole of a substance and thus provides a parametric value for scaling a molecular or molar flow rate into an ionic or electrical flow rate.
A physical constant that is the number of electrical charges carried by a mole of an atoms or molecules
Molar charge
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.
Network domain
1
1
1
Ohm's law
Ohms law
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)
A constitutive dependency by which a flow rate of a process depends on the difference in force properties of the process participants.
Resistive dependency
Property event dependency
An process dependency that relates a physical state event to changes of continuant state of participants during an occurrence of a process.
Physical event dependency
A constitutive dependency of a flow rate property of one dynamical entity depends on the force property of another dynamical entity
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.
Convective transport dependency
1
Chemical energy flow dependency
G
Gibbs free energy
Gibbs function
free enthalpy
https://en.wikipedia.org/wiki/Gibbs_free_energy
Joule SI-unit
A thermodynamic potential that is the amount work that may be performed by a dynamical entity at a constant temperature and pressure.
Gibbs energy
A
F
https://en.wikipedia.org/wiki/Helmholtz_free_energy
Joule SI-unit
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.
A thermodynamic potential that is amount of energy of dynamical entity that is available for doing useful work at a constant temperature and volume.
Helmholtz free energy
Equilibrium potential
ionic 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.
Nernst reversal potential
start time
time zero
zero time
A temporal instant that is the origin of a temporal coordinate system.
Temporal coordinate origin
Dynamical event dependency
U
https://en.wikipedia.org/wiki/Internal_energy
Joule SI-unit
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.
Internal energy
1
1
Entropy SI-unit
3.14159
Archimedes' constant
pi
π
A mathematical constant that is that is the ratio of a circle's circumference to its diameter.
pi
2.71828
Euler's number
exponential decay constant
exponential growth constant
A mathematical constant that is the limit of (1 + 1/n)n as n approaches infinity.
e
1
1
An energy state dependency of the energy of a material entity on its rate of motion or flow
Kinetic energy dependency
1
Solid kinetic energy dependency
1
Fluid kinetic energy dependency
1
Areal density of mass
1
A dependency of the potential energy of an electrically charged entity due to its displacement in an electrical field.
Electrical potential energy dependency
1
A dependency of the potential energy stored in an elastic entity due to changes of its shape
Elastic potential energy dependency
1
Lineal density of mass
A maathematical entity that is a real or imaginary scalar quantity.
Mathematical constant
Solid displacement
1
https://en.wikipedia.org/wiki/Entropy
per Lambert, 2002:
1) 'entropy is the spreading and sharing of energy"; i.e., dispersal of energy amongst microstates.
2) 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.
3) "entropy change = quantity of energy dispersed at a temperature T"
_________
Information entropy is related to thermodynamic entropy but its representation is deferred pending development of an "information ontoloty" that has suitable classes for representing the ties to thermodynamic entropy.
Thermodynamic entity that is the portion of energy dispersed into a portion of substance at a given absolute temperature.
Portion of entropy
Lambert, Frank L., "Entropy is Simple, Qualitatively", JChemEd.chem.wisc.edu. Vol 79, No. 10, October 2002
Rotational displacement
Solid displacement rate
A thermodynamical dependency that defines a physical property of a dynamical entity whose value is temporally and/or spatially invariant.
Thermodynamical constraint
1
A thermodynamic constraint that the fluid pressure within a dynamical entity is invariant both spatially and temporally.
Isobaric constraint
1
A thermodynamic constraint that the temperature within a dynamical entity is invariant both spatially and temporally.
Isothermal constraint
1
A thermodynamic constraint that there is no change in the volume of a dynamical entity
Isovolumetric 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.
Isentropic constraint
1
A thermodynamic constraint that there is no flow of energy or matter across the dynamical boundary of a dynamical entity
Adiabatic constraint
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.
Solid translational acceleration
A thermodynamic constraint that the sum of potential energy plus kinetic energy of a dynamical entity is temporally invariant.
Lagrangian constraint
1
1
The dependence of heat energy flow rate on values of a thermodynamical state property and a constitutive property
Heat flow dependency
A physics modeling entity that is a geometrical form used to represent physics continuants, process or modelting entities.
Geometrical entity
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.
Solid angular acceleration
H
Energy dimension
Torque dimension
Joule SI-unit
A portion of energy that is the difference in the amounts of kinetic and of potential energy that inhers in a dynamical entity
Lagrangian energy
Solid distortion velocity
1
Volumnal density of matter
A physical quality that is a constitutive scalar that defines the ratio of a dynamical property to a property of a different type.
Physical constant
NA
https://en.wikipedia.org/wiki/Avogadro_constant
Avogadro constant is 6.022140857(74)×10**23 per mole in the International System of Units (SI).
A physical constant that is the number of constituent particles, usually atoms or molecules, in one mole of a substance.
Avogadro constant
1
An amount property that is the diifference between the number of protons and the number of electrons composing a material dynamic entity
Ionic charge
k
https://en.wikipedia.org/wiki/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.
A physical constant that is the ratio of the energy of a particle to its temperature.
Boltzmann constant
Atomic mass unit
https://en.wikipedia.org/wiki/Atomic_mass_constant
Atomic amount that is one twelfth of the mass of an unbound atom of carbon-12 at rest and in its ground state
Atomic mass constant
https://en.wikipedia.org/wiki/Atmosphere_(unit)
A physical constant that is the standard atmospheric pressure defined as 101325 Pa (1.01325 bar) as used as a reference or standard pressure.
Standard atmosperic pressure
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.
Thermodynamical potential dependency
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.
Cotransport domain
Enthalpic energy dependency
Pump counter transport
Pump cotransport
Gibbs free energy dependency
0-junction
Kirchhoff's first rule
Kirchhoff's junction 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
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
Junctional rate constraint
A loop rate constraint for flow rate properties
Flow loop rate constraint
A loop rate constraint for force properties.
Force loop rate constraint
Helmholtz free energy dependency
Shear distortion velocity
Lagrangian energy dependency
Internal energy dependency
1
Constitutive rate dependency by which energy is exchanged between solid mechanical entities.
Mechanical transformer dependency
Tensile distortion velocity
An amount property that is the amount of dynamical entity distributed over a spatial region normalized to the size of the region
Amount density
1
Lineal mechanical capacity dependency
lever
Lineal mechanical transformer
gear
Rotational mechanical transformer
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.
Total energy dependency
1
1
Entropy-driven heat flow
1
1
Temperature-driven heat flow
A mechanical velocity that is the rate of angular displacement around one axes
Joint velocity
Joint angular velocity
Joint rotational velocity
A mechanical velocity that is the rate of displacement of solid entity,
Solid velocity
A physics network model in which nodes are dynamical entities node-node arcs are physical processes.
Physiomap graph model
A spatial property that is the rotation required to superimpose two straight lines by rotation about an intersection of the lines
Spatial angle
A physics occurrent that is the flow or exchange of matter and/or energy amongst dynamical entities that are partcipants in the process.
Dynamical process
Thermodynamical domain in which physics continuants have, exchange adn transform thermodynamic energy.
Energy domain
Portion of positive charge
1
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.
A constitutive dependency of dynamical properties of a portion of an hypothetical ideal gas.
Gas law dependency
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.
Charles gas law
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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.
Boyle gas law
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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.
Guy-Lussac gas law
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1
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.
A gas law that relates the values of volume and amount of gas when its pressure and temperature are unchanged.
Avogadro gas law
1
1
1
universal gas law
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
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.
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A gas law that relates the values of pressure, volume, amount and temperature of a portion of an ideal gas.
Ideal gas law
A constitutive state property of continuum that relates state properties of a portion of ideal gas
Gas law constant
A physics event whose occurrence is sufficient to initiate or terminate an occurrence of a process
Process occurrence event
1
A physics change that is a change of physical state of a process participant at a instant in time.
Physics event
A physics change that is the time-course of changes, either discrete or continuous, in a physics process or in the physical state of a process participant.
Physics trajectory
A physics trajectory that is a temporally ordered series of values of a physical property of a physics process
Process trajectory
lineal density
A property spatial scope of a physical property whose value is expressed on per length basis.
Lineal scope
areal density
A property spatial scope of a physical property whose value is expressed on per area basis.
Areal scope
volumetric density
A property spatial scope of a physical property whose value is expressed on per volume basis.
Volumnal scope
A spatial scope of a property whose value applies to an entire physical entity.
Discrete spatial scope
Correlative value
Correlation coefficient
Standard error of mean
1
Solid acceleration
1
A dynamical acceleration property that is the temporal rate of change of a fluid flow rate.
Fluid acceleration
A gas law constant for Boyle's gas law
Boyle gas constant
A gas law constant for Avogadro's gas law
Avogadro gas constant
A gas law constant for Charles' gas law
Charles gas constant
A gas law constant for Guy-Lussac's gas law
Guy-Lussac gas constant
1
A material amount of a portion of gas
Amount of gas
A constitutive process whose rates are determined by a transformer dependency.
Transformer process
2
A constitutive process whose rates are determined by a transducer dependency.
Transducer process
Transport flow process
Chemo-diffusional transducer process
Chemo-mechanical transducer process
Fluid-mechanical transducer process
Advective transport process
Convective transport process
Pump transport process