=Paper=
{{Paper
|id=Vol-2137/paper_35.pdf
|storemode=property
|title=Extending the Ontology of Physics for Biology with Thermodynamics
|pdfUrl=https://ceur-ws.org/Vol-2137/paper_35.pdf
|volume=Vol-2137
|authors=Daniel L. Cook,John H. Gennari,Maxwell L. Neal
|dblpUrl=https://dblp.org/rec/conf/icbo/CookGN17
}}
==Extending the Ontology of Physics for Biology with Thermodynamics==
https://ceur-ws.org/Vol-2137/paper_35.pdf
Extending the Ontology of Physics for Biology with Thermodynamics
Daniel L. Cook1 John H. Gennari1 and Maxwell L. Neal2
1
Department
of
Biomedical
Informatics
and
Medical
Education,
University
of
Washington,
Seattle,
WA,
USA
Center
for
Infectious
Disease
Research,
Seattle,
WA,
USA
2
ABSTRACT flows of material, charge, etc. as in chemical reactions, fluid
flows, etc. Third, OPB:Physical properties (Cook, et al,
We
have
extended
the
Ontology
of
Physics
for
Biology
(OPB)
to
rep-‐‑
resent
the
entities
and
relations
of
classical
thermodynamics.
We
de-‐‑ 2011) are the observable or inferrable attributes of entities
scribe
key
subclasses
of
OPB:Thermodynamic
entity
such
as
OPB:
and processes. And fourth, OPB:Physical dependencies
Thermodynamic
property,
and
OPB:Thermodynamic
dependency
in
the
(Cook, et al, 2013) are physical laws (e.g., Ohm’s law) and
context
of
the
OPB’s
overall
representational
schema.
We
are
motivat-‐‑
ed
by
practical
utility
of
energy
bond-‐‑graph
theory,
a
thermodynamics-‐‑
constraints (e.g., conservation of mass).
based
formalism
used
in
the
domain
of
system
dynamical
modeling
and
analysis
of
biological
physical
processes.
We
also
intend
OPB
to
2 NEXT STEP: THERMODYNAMICS
extend
available
upper
biomedical
ontologies
to
encompass
entities
and
theories
of
classical
physics
and
thermodynamics.
To formally represent and constrain models of such dy-
namical phenomena, we have extended OPB to explicitly
1
INTRODUCTION represent thermodynamic entities, properties, and dependen-
cies. Whereas properly derived system dynamical models
The Ontology of Physics for Biology (OPB, 2016) ex-
will constrain models to the universal rules of thermody-
tends available biomedical ontologies to represent the bio-
namics (e.g., conservation of energy, in particular), such
physics of biological entities, their observable physical
constraints are only implicit in model equations. To explicit-
properties and the physical dependencies—the laws of clas-
ly satisfy both dynamical and thermodynamic laws and con-
sical physics—that determine how property values depend
straints, thermodynamics-based energy bond graph model-
upon one another. OPB is based on engineering system dy-
ing was first described for biological systems (Perelson,
namics — the study of stocks and flows of material, charge,
1975), adapted to engineering practice (Karnopp, 1979) and
etc. — used to qualitatively explain and to quantitatively
has been recently formalized by others (Gawthrop and
analyze biological processes over domains such as chemical
Crampin, 2014; Lefèvre, et al., 1999) to model biological
kinetics, fluid dynamics and electrophysiology and spatial
dynamical networks.
scales from molecular to organismal. To our knowledge, no
We have extended OPB to represent the entities and prin-
comparable ontology exists.
ciples of classical thermodynamics in support of thermody-
Our SemGen application1 uses OPB semantics to derive
namic-based computational modeling as well as to extend
and analyze SemSim models (semantic simulation) to input,
the scant representation of physical and thermodynamical
parse, and annotate biosimulation model code. Furthermore,
concepts in prevailing upper biomedical ontologies.
SemGen can decompose SemSim models into reuseable
fragments, merge the fragments as a new SemSim model
and export new computational model code . A SemSim
model is a light-weight OWL ontology that annotates each
variable as an instance of an OPB:Physical property and
each equation as an instance of OPB:Physical dependency
to create a “property dependency graph” (OPB:Property
dependency graph). We have recently applied SWRL rules
to SemSim models and OPB to infer qualitative changes of
model variables on other property values in the model
(Neal, et al., 2016).
OPB parses system dynamical abstractions into 4 high-
level classes. First, OPB:Dynamical entities are energy-
bearing physical continuants such as portions of fluid,
chemical, charge. Second, OPB:Dynamical processes are
* To whom correspondence should be addressed: dcook@uw.edu Fig. 1 OPB:Thermodynamic entity classes.
1
http://sbp.bhi.washington.edu/projects/semgen
1
Doe et al.
2.1 OPB:Thermodynamical entity thermodynamic entities and laws that govern biological pro-
In parallel to OPB system dynamical classes that repre- cesses. OPB is a reference ontology of biophysics that ex-
sent stocks/flow of material, charge, etc., OPB thermody- tends available "upper ontologies" (e.g, BFO, GFO), com-
namic classes represent stocks/flows of energy and entropy plements domain ontologies such as FMA, GO, ChEBI, and
(Figure 1). Thus, an instance of OPB:Mechanical solid has provides a computational resource for annotating biophysi-
(via OPB:hasThermodynamicEntity) a portion of cal models and datasets for reuse and integration.
OPB:Solid potential energy if stretched or compressed
and/or a portion of OPB:Solid kinetic energy if in motion.
2.2 OPB:Thermodynamical property
Thermodynamical entities have OPB:Thermodynamical
properties: (1) rate properties (e.g., OPB:Energy flow rate,
OPB:Entropy flow rate), (2) state properties (e.g.,
OPB:Energy amount, OPB:Entropy amount) and (3) consti-
tutive properties (e.g., OPB:Thermal capacity,
OPB:Thermal conductivity).
2.3 OPB:Thermodynamical dependency
OPB:Thermodynamical dependencies (Fig. 2) define
OPB:Thermodynamical properties in terms of other such
properties or in terms of OPB:Dynamical properties (e.g., Fig. 3. Overview of OPB schema for relating thermody-
fluid volume or pressure). namic classes (left) to observable state and rate dynamical
properties (middle) and the constitutive properties of empir-
ical dependencies (right).
2.5 Acknowledgements
The authors thank Cornelius Rosse and Peter Hunter. This
research was partially supported by the National Institutes
of Health, grant R01LM011969.
REFERENCES
Cook, D. L., F. L. Bookstein and J. H. Gennari (2011). "Physical Properties
of Biological Entities: An Introduction to the Ontology of Physics for
Biology." PLoS ONE 6(12): e28708.
Cook, D. L., M. Neal, F. L. Bookstein and J. H. Gennari (2013). "Ontology
of physics for biology: representing physical dependencies as a basis for
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neering and biology. New York, Pergamon Press.Lefèvre, J., L.
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Real-World Use Cases." PLoS One 10(12): e0145621.
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