Download Beverley John C. Beverley IE 500/PHI 598: Ontological Engineering

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John C. Beverley
IE 500/PHI 598: Ontological Engineering
30 November 2013
Thermodynamic Equilibrium Ontology
I.
Introduction
Thermodynamics is the study of energy, state systems, work, and path systems. This
physical science branch is often bifurcated into classical and statistical fields of study where the
former focuses on macroscopic behavior, while the latter focuses on microscopic behavior.
While both of these branches deserve the attention of an ontologist, for the purpose of this
project only the macroscopic tree will be considered in what follows. The field of
thermodynamics is rife with terminological confusion and antiquated definitions. This
observation is supported by cursory glance in any introductory textbook concerning the field.1 A
prime example of antiquated use is the term latent heat that is sometimes considered synonymous
with enthalpy and other times not (Cengel & Boles). While it is not the job of the ontologist to
clarify these uses and abuses, awareness of these issues might bring needed terminological
clarity to the field. Moreover, it is clear that a well-developed ontology must begin with the
foundations of the field of inquiry. It is with that in mind, and the lofty goals of terminological
clarity, appropriate characterization of thermodynamic systems, and potential extensions into
For instance, the phrase ‘reversible’ has a precise definition in the literature: a microscopic
change of energy state, which can be restored by infinitesimal alterations. Yet it is often used
interchangeably with the meaning, ‘able to be reversed,’ even by physicists! Consider the typical
example of a reversible piston under constant pressure. Here the use of reversible is applied to a
macroscopic object. This misuse is even more apparent when it is noted that on a microscopic
scale, all chemical reactions in a thermodynamic system are considered reversible.
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existing chemical ontologies, on the distant horizon, that the following Thermodynamic
Equilibrium Ontology was designed.
As indicated above, Thermodynamics is the study of energy, but more specifically, it is
the study of energy inhering in a Thermodynamic System. Such systems will be formally defined
below in the Classes section, but the intuition underlying the concept is easily grasped: they are
arbitrary regions of space. Systems have accompanying properties, and it is from consideration
of properties in a system, some held constant while others vary, that the famous Thermodynamic
Laws are derived.2 Indeed, when certain properties are assumed constant then various
thermodynamic equilibria can be established in a thermodynamic state. From these latter
considerations derive chemical, thermal, and mechanical equilibria, as well as the broader,
inclusive, thermodynamic equilibrium, which is the focus of this ontology. These aspects of
thermodynamic systems are the foundation of thermodynamics as practiced. While several
features of thermodynamic systems were not included in the current ontology, every attempt was
made to create a baseline thermodynamic ontology amenable to additions. That is, while certain,
perhaps more complicated, aspects of thermodynamic systems were not included in the present
ontology, additions can be made to accommodate greater breadth. Areas for extension will be
noted when applicable in what follows.
II.
Scope and Methodology
The Thermodynamic Equilibrium Ontology focuses on Thermodynamic Systems for various
Thermodynamic Properties and Thermodynamic States. The Buffalo Formal Ontology 1.0 was
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Zeroth Law: If two systems have the same temperature as a third, then they have the same
temperature as each other; First Law: the total energy of an isolated system is constant; Second
Law: an isolated system spontaneously evolves towards a state of higher entropy; Third law:
establishment of absolute zero.
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employed as the framework for this ontology following similar use by other chemical
ontologies.3 Properties and States inhere in Thermodynamic Systems. Thermodynamic Reactions
are included as well for comprehensiveness, as processes inhering in Thermodynamic Systems.
The goal of this ontology is to design, in Protégé, an appropriate ontology that brings these
concepts together while specifying relations among the classes and subclasses. Before turning to
the definitions of each class and subclass, and taking a cue from thermodynamics textbooks, a
few diagrams will help solidify the meanings of these terms. Consider the following:
Figure 1.1
Figure 1.1 represents a Thermodynamic System with associated Thermodynamic System
Boundary and Thermodynamic Surroundings. A system is simply an area under investigation
and is demarcated by the boundary, which shields it from the surroundings. On the right hand
side of the above photo, we have a raging fire demarcated as the system, with the boundary
arbitrarily chosen encompassing the flames and the surroundings represented by everything else
in the photo. The Thermodynamic System Boundary was included in the Thermodynamic
Dumontier Labs, for instance, employs BFO in several of its ontologies. Dumontier’s Complex
Chemical Composition Ontology will be discussed in depth below.
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Equilibrium Ontology, the Thermodynamic Surroundings not included in the final version. This
is due to the lack of specification of the System boundary in various textbooks considered. For
instance, some defined the Surroundings as merely the adjacent environment of the System
Boundary, while others included the entire universe (Cengel & Boles). To be sure,
Thermodynamic Surroundings should be included in the ontology, but at present, it is unclear
precisely what the phrase means.
The following diagram specifies the focus of the Thermodynamic System further into
Open Systems, Closed Systems, and Isolated Systems:
Figure 1.2
Open Systems are those that allow Free Energy or Mass to flow through the
Thermodynamic Boundaries. A Closed System has a Thermodynamic Boundary that is
impermeable to Mass transfer, while an Isolated System is impermeable to Free Energy and
Mass transfer.
Thermodynamics texts often focus on Isolated Systems since they are more amenable to
idealization. This ontology has included Thermodynamic Reactions as inhering in
Thermodynamic Systems in general, however, rather than simply in Isolated Systems. This is
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due to the fact that the Systems considered above may undergo chemical, mechanical, and
thermal reactions, as well as may reach chemical, mechanical, and thermal equilibrium. The
focus on Isolated Systems, while helpful in calculation, can be treated as any other System in this
ontology, as long as the transfer restrictions are maintained. One final note must be made before
moving to the Classes section. While the above Systems involve Free Energy and Mass transfers,
the transfer of energy and mass is not included in this ontology. Physicists studying
thermodynamics typically use these concepts while Chemists tend to focus on the Mass and
Energy inhering in a system. Energy transfer and Mass transfer can be included, however, in
later designs, to better approximate the Physicist’s understanding of thermodynamic processes. 4
Classes
As mentioned above, the Basic Formal Ontology was chosen as the skeleton for this
project. Thus, basic classes included Thing, entity, continuant, occurrent, independent
continuant, spatial region, processural entity, etc. Most classes were not pertinent for the purpose
of this ontology. The major division in BFO, between occurrent and continuant, was the first
major obstacle however. Thermodynamic Equilibrium, and its component equilibria, are
continuants. That is, when such equilibrium occurs it is wholly present at that time. Moreover,
Thermodynamic Equilibrium is a dependent continuant since it inheres in other entities, namely,
Thermodynamic States. Thermodynamic Properties and Thermodynamic Disposition States
inhere in Thermodynamic States as well.
The upper-level classes of the Thermodynamic Equilibrium Ontology follow:
Class
Genus
Description
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The Helmholtz Free Energy was included for just this purpose. Thermochemistry tends to use
Gibbs Free Energy (also included) as a measure of Thermodynamic System’s capacity to do
work while Helmholtz Free Energy is the bread and butter of Thermal Physics.
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Quality
Dependent continuant
Thermodynamic System
Quality
Quality
Thermodynamic Property
Thermodynamic System
Quality
Extensive Property
Thermodynamic Property
Intensive Property
Thermodynamic Property
Thermodynamic System
Disposition
disposition
Object
Independent_continuant
Thermodynamic System
Object
Object_boundary
Independent_continuant
Thermodynamic System
Boundary
Object_boundary
Thermodynamic Reaction
Process
Chemical Reaction
Thermodynamic Reaction
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Exhibited if it inheres in an
entity at all
A dependent_continuant
quality that inheres in a
Thermodynamic System.
A Thermodynamic System
Quality inhering in a
thermodynamic system that
does not solely determine the
global properties of the
system.
Properties of a
thermodynamic system that
are dependent on the size of
the system
Properties of a
thermodynamic system that
are independent of the size of
the system.
A Thermodynamic System
has the disposition to reach
equilibrium under various
constant conditions.
Spatially extended
independent continuant
Any arbitrary region of space
currently under inspection.
Surface of some sort (whether
inside or outside of a thing)
Object that is the real or
imagined surface that
separates a Thermodynamic
System from its surroundings.
Process inhering in a
Thermodynamic System in
which equilibrium is not
sustained and Free Energy,
Pressure, Temperature, and
Enthalpy are dynamic.
Thermodynamic Reaction
Process of varying chemical
movements in
Thermodynamic System
leading to transformations in
Free Energy.
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Mechanical Reaction
Thermodynamic Reaction
Thermal Reaction
Thermodynamic Reaction
Thermodynamic Reaction
Process of varying Pressure in
Thermodynamic System
leading to transformations in
Free Energy.
Thermodynamic Reaction
Process of varying Enthalpy,
Temperature, and Entropy in
Thermodynamic System
leading to transformations in
Free Energy
The largest class, Extensive Property, is listed below, as it comprises a significant portion of the
ontology, and almost all of the Thermodynamic Properties superclass.
Class
Enthalpy
Genus
Thermodynamic Property
Entropy
Thermodynamic Property
Free Energy
Thermodynamic Property
Gibbs Free Energy
Free Energy
Helmholtz Free Energy
Free Energy
Internal Energy
Thermodynamic Property
Thermodynamic System Mass
Thermodynamic Property
Volume
Thermodynamic Property
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Description
An extensive thermodynamic
property that is energy
supplied to a thermodynamic
system as heat under constant
pressure.
Measure of molecular
disorder or randomness in a
thermodynamic system.
Energy of a Thermodynamic
System under specific
constant conditions. .
Energy of a Thermodynamic
System under constant
pressure.
Energy of a Thermodynamic
System under constant
temperature.
Sum of all microscopic forms
of energy in a thermodynamic
system.
Extensive Thermodynamic
Property that gives rise to the
phenomenon of resistance to
force by the system.
Measure of space occurrent
occupies in three dimensions
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The following section will detail the Object Properties used in this ontology, as well as several
relevant relations among the above classes.
Object Properties
The following table outlines the object properties associated with the Thermodynamic
Equilibrium classes described.
Domain
Relation
Range
Thermodynamic System
Bearer of
Thermodynamic Property
Thermodynamic Reaction
Depends on
Thermodynamic Equilibrium
Has proper part
Thermodynamic Disposition
State
Chemical Equilibrium
Thermodynamic Property
Inheres in
Thermodynamic System
Mechanical Equilibrium
Is proper part of
Thermodynamic Equilibrium
This is a relatively small number of examples, but they should be adequate to explain the
role these Object Properties play in the ontology. The goal, to reiterate, is to connect the various
properties and states to the Thermodynamic System. Thus, relations such as ‘bearer of’ were
crucial, as well as inverses such as ‘inheres in.’ The ‘is proper part of’ relation was also
important in describing the complicated combination of equilibria which result in
Thermodynamic Equilibrium. That is, Thermodynamic Equilibrium is composed of various other
equilibria, which must obtain. With that in mind, the relation seemed to require Asymmetry, as
well as an Irreflexive restriction. This followed since X ‘is proper part of’ Y does not mean either
that Y ‘is proper part of X’ or that X ‘is proper part of’ X. Indeed, the typical definition of proper
part precludes this, as nothing can be a proper part of itself.
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Data Properties
Thermodynamic as practiced by the chemist is a predominantly numerical enterprise. It
should be no surprise then that there are a large number of Data Properties in this ontology.
These serve the purpose of relating numerical quantities to Thermodynamic States, Properties,
and Reactions, as well as the Thermodynamic System in general. The following section will
outline the various Data Properties by giving examples of their respective use within the
ontology.
Domain
Chemical Reaction
Internal Energy
Non-Spontaneous Reaction
Mechanical Reaction
Spontaneous Reaction
Enthalpy
Open System
Mechanical Reaction
Thermal Equilibrium
Enthalpy
Volume
Relation
Has Enthalpy value
Has Kinetic Energy value
has Entropy value
Has Gibbs value
Has Helmholtz value
Has Internal Energy value
Has Mass value
Has Pressure value
Has Temperature value
Has Thermodynamic
Potential value
Has Volume value
Range
Real number
Integer
Real number
Real number
Real number
Integer
Positive Integer
Real number
Positive Integer
Integer
Real number
The calculations resulting from assessment of a Thermodynamic System allow values to be
associated with Properties of the system. Unfortunately, BFO 1.0 does not seem to have a
framework into which generically_dependent_continuants can be placed, though later versions of
BFO allow for the inclusion of Information Artifacts of this nature. Moreover, since later
versions of BFO are backward compatible, it should be able to accommodate actual calculations
resulting in values for the Data Properties given above. It should be noted that Professor
Rudnicki who noted that, for instance, the Gibbs Free Energy is measurement of the
Thermodynamic System rather than a genuine part of the system itself brought this to the
author’s attention.
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III.
Thermodynamic Equilibrium Ontology
With the classes specified, it is now time to turn to the Thermodynamic Equilibrium
Ontology itself.
Features of the Ontology
Several features of the Thermodynamic Equilibrium Ontology have already been
mentioned. In the following section, the heart of the ontology will be discussed in detail.
Figure 3.1
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Figure 3.1 is a snippet of the Class hierarchy with Thermodynamic Property highlighted.
This property is composed of Intensive and Extensive properties, which are themselves divided
into several subclasses. Figure 3.2 below elaborates on one of the Extensive properties:
Enthalpy. As indicated below, Enthalpy takes Internal Energy and Thermodynamic Potential
values and is disjoint with the other Extensive properties. Figure 3.3 further indicates that
Enthalpy inheres in Thermodynamic System and is a subclass of Thermodynamic Property.
Figure 3.2
Figure 3.3
These class relations represent how chemists employ enthalpy in calculations. Enthalpy is a
feature of Thermodynamic Systems, which relies on the Internal Energy and Thermodynamic
Potential of the system. Indeed, it is a rather interesting property in that it is often determined by
holding temperature constant. That is, when temperature is held constant and energy enters a
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system, there is a measurable increase in Internal Energy that cannot be accounted for by
common means, i.e. via temperature. This is enthalpy.
Figure 3.4 below highlights the Thermodynamic System class. As shown in Figure 3.5,
this class has three subclasses: Closed, Open, and Isolated.
Figure 3.4
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Figure 3.4
Figure 3.5
Figure 3.5 presents several interesting features of the Thermodynamic System class. For
instance, a Thermodynamic System has a Thermodynamic System Boundary as a proper part.
Moreover, a Thermodynamic System is the bearer of some Thermodynamic Property and some
Thermodynamic System Disposition. This latter feature is perhaps the most important as it
includes Thermodynamic Equilibrium to which we now turn.
A final feature, which we will consider in this section, is the Thermodynamic
Equilibrium class. Figure 3.6 indicates its place in the Class hierarchy as a subclass of
Thermodynamic Disposition State. It should be noted that Thermodynamic Equilibrium has
several sibling classes: Chemical Equilibrium, Mechanical Equilibrium, and Thermal
Equilibrium. Figure 3.7 shows the interesting relationship which Thermodynamic Equilibrium
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has with its siblings. Each of the siblings is a proper part of Thermodynamic Equilibrium. That
is, when a Thermodynamic System has reached a state in which Chemical Equilibrium,
Mechanical Equilibrium, and Thermal Equilibrium obtain, then it is in a state of Thermodynamic
Equilibrium.
Figure 3.6
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Figure 3.7
Figure 3.8
Moreover, though not indicated in Figure 3.8, the fact that Thermodynamic Equilibrium inheres
in some Thermodynamic System while each of the Chemical, Mechanical, and Thermal
Equilibrium’s are related to Thermodynamic Equilibrium as proper parts of should be reiterated.
True Path Testing
Any ontology worthy of BFO should follow the basic True Path Rule. Several examples of
true path tests follow. Italicized classes were added to the BFO frame:
I.
II.
III.
Gibbs Free Energy is_a Free Energy is_a Extensive Property is_ a Thermodynamic
Property is_a Thermodynamic System Quality is_a quality is_a dependent_quality
is_a continuant is_a entity is_a Thing
Temperature is_a Intensive Property is_a Thermodynamic Property is_a
Thermodynamic System Quality
Closed System is_a Thermodynamic System is_a object is_a independent_continuant
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IV.
Spontaneous Reaction is_a Thermal Reaction is_a Thermodynamic Reaction is_a
process is_a processural_entity is_a occurrent
Each of these entities follows a true path from the bottom of the class hierarchy to the upper level
ontology.
IV.
Comparison with Existing Ontology
Relatively few chemistry ontologies account for the thermodynamic properties developed in
this ontology. The extensive labor involved in relating classes associated with specific variables
to thermodynamic systems is perhaps a deterring aspect of these ontologies. Nevertheless, there
have been attempts to characterize the upper-level domain of the field of chemistry, which have
included aspects of Thermodynamic Equilibrium. The following is an example of just this sort
from Dumontier Labs. Pertinent differences with the Dumontier ontology will be discussed as
they arise in the discussion.
Dumontier Labs
An Ontology was located that attempts to accommodate thermodynamic systems by an
alternative method. The Dumontier Labs chemistry ontology varies in significant detail from the
ontology developed above. In the following section, several relevant differences will be
examined. Differences include:



While the Dumontier Complex Chemistry Ontology includes classes describing various
reactions it has no Thermodynamic System Class. States are characterized by various
thermodynamic systems, and are incompletely described without them. This ontology
includes Thermodynamic System as a subclass of object, which is a continuant.
Moreover, Thermodynamic System has subclasses: Isolated System, Closed System, and
Open System. Again, without an appropriate way to describe the underlying
thermodynamic system, descriptions of chemical processes are moot.
Dumontier Labs does not boundaries for their represented reactions. Thermodynamic
Equilibria are boundary states for reactions and so create the starting and finish lines
necessary for said reactions. The Thermodynamic Equilibrium Ontology obviously
includes this framework.
Dumontier includes separate classes for Group Elements. These classes are defined with
disjunction. For instance, the Group 10 Elements are defined by extension with:
Darmstadtium, Nickel, Palladium, or Platinum. None of the Group Element classes,
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

however, includes Hydrogen. Hydrogen is typically included in either the Group 1
Elements or the Group 17 Elements due to its unique properties. The Dumontier Labs
ontology, however excludes the element. Thus, a disjoint union of the Group Element
classes would be not be exhaustive of the periodic table, though this is precisely what one
should expect from such a union. For comprehensiveness, the Thermodynamic
Equilibrium Ontology includes up-to-date Atoms, Elements, Compounds, and Molecules.
Regardless, Group designations are unnecessary for the Thermodynamic Equilibrium,
and so this ontology avoided having to make a choice as to where Hydrogen should be
placed.
Dumontier Labs has the element with atomic number114 incorrectly listed as
Ununquadium. IUPAC adopted the name Flerovium for this element in 2012. A similar
oversight was made with Ununhexium, which was named Livermorium in 2012. There is
also no Copernicum element listed in the ontology. These have been corrected in the
present ontology.
Finally, Dumontier Labs includes 18 Group Element classes corresponding to ‘group
element’ extension classes. This appears to be a redundancy in the ontology, as deletion
of any of the separate Group Elements, or all of the seemingly redundant classes, seems
to effect no relevant alteration in the ontology. Indeed, the 18 Group Elements are
sibling classes of the continuant and occurrent class though they are clearly continuant
entities.
The major issues with the Dumontier Labs chemistry ontology have been avoided in the
construction of the current ontology. The major complaint with Dumontier is the absence of a
framework within which thermochemical reactions, or any reaction, could take place. If the
Dumontier ontology were employed, for instance, to account for the various calculated data
acquired from thermodynamic research it would be unable to do so without significant overhaul.
Indeed, several of the classes seem haphazardly organized with island classes unrelated to the
rest of the ontology prevailing. This is rather surprising as Dumontier Labs hosts several rather
impressive ontologies on its website. These range from various aspects of the Biological
Sciences to Physics and Metric measurement ontologies. Again, many of these ontologies are
well designed and capable of handling quantitative development. This cannot be said, however,
for the Complex Chemical Ontology.
V.
Areas for Further Research
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The next step in the development of this ontology is to update it to BFO 2.0 and include the
generically dependent continuant class to allow for information artifact definitions. Following
this step, the inclusion of physics related thermodynamic information would expand the ontology
exponentially. This would include classes that covered Work, Heat transfer, various phase
transitions, and associated values. Again, this includes a great deal of data as can be seen from
Figure 5.1 and Figure 5.2 below.
Figure 5.1
Figure 5.2
Figure 5.1 and Figure 5.2 are the beginning and ending of a Saturated Water Table at
varying Temperature. Saturation in this table indicates that water is midway between a gas and
liquid, or liquid and solid. Given increasing temperature in such a state associated properties of
the molecule change. Thus, specific volume (volume divided by mass), Internal energy,
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Enthalpy, and Entropy change according to the amount of temperature change. It is hoped that in
the future this information can be accessed via an appropriate ontological framework. It should
be noted, however, that this is a rather tall order due to the number of molecules available for
study, and the number of variables, which can be held constant when obtaining such information.
Nevertheless, the water table above relies on a Thermodynamic System with Thermodynamic
Properties already defined. Thus, significant ground has been broken in the development of an
ontology that can accommodate substantial data in this field.
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Work Cited
Cengel, Y., Boles, M. (2010). Thermodynamics: An Engineering Approach. Fifth Edition.
Prentice Hall Publishing.
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