The Ontology of Physics for Biology (OPB) is a reference ontology of classical physics as applied to the dynamics of biological systems.

The OPB is designed to encompass the multiple structural scales (“multiscale” — atoms to organisms) and multiple physical domains (“multidomain” — fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. It is a core technology for the Semantics for Biological Processes research group, and contains essential concepts for annotating SemSim models. The formality of the OPB's construction was inspired by the design of the ontology of the Foundational Model of Anatomy, although the two ontologies are orthogonal in coverage. We have published a paper in PLoS ONE that introduces the OPB and have made the OPB source available on BioPortal.

Motivation: Physics-based biosimulation models in a variety model repositories constitute a storehouse of formally-encoded knowledge about biological processes. However, there are major barriers to model reuse and integration because models are encoded in multiple, mutually-incompatible computational languages and are annotated informally, if at all, using domain-specific terminologies. The premise of our work is that whereas there are reference ontologies of physical entities (e.g., molecules, cells, organs), there is no corresponding reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g., Ohm’s law, Ficke’s law) by which the physical meaning of biosimulation models may be annotated

Foundational theory: To satisfy the multiscale and multidomain requirements, the OPB is based on systems dynamics theory, a view of classical physics that recognizes fundamental parallels between physical phenomena at all structural scales and across multiple physical domains. For example, as shown the following two figures, the physical properties of biological entities can be classified in a taxonomy of OPB:Dynamical properties which includes leaf classes for each of seven dynamical domains as in Figure 1.


Figure 1. The multidomain OPB:Dynamical property class hierarchy. Not shown are subclasses of OPB:Constitutive properties and OPB:Thermodynamic properties that also have leaf classes for each dynamical domain (as appropriate).


The classification of OPB:Dynamical properties, OPB:Constitutive properties, and OPB:Thermodynamic properties are defined according to an over-arching, system dynamical theory that has been the basis for physical systems analysis in engineering and biophysics. Redrawn from multiple sources, the figure below shows are dynamical, constitutive, and thermodynamic properties are defined and inter-related by physical definitions and laws of classical physics.


Figure 2.
OPB:Physical dependency classes interrelate OPB:Physical properties according to multidomain system dynamics theory. Ovals represent observable physical properties while rectangles represent quantitative relationships amongst the properties that are either experimentally determined empirical laws (e.g., constitutive laws like Ohm's resistive law) or are dependencies that define one property in terms of another (e.g., the calculus laws that define flow rates in terms of amounts).


Scope: The OPB is based on systems dynamics and thermodynamics. It does not include quantum or relativistic physics, nor is it intended to recapitulate the axiomatic basis of physics as a theoretical framework. Whereas the foundational theory of the OPB encompasses both discrete systems analysis (using ordinary differential equations; ODEs) and continuum systems analysis (using partial differential equations; PDEs), the first version of the OPB is targeted solely to discrete systems analysis. Although our motivating use-cases are drawn from problems in biological systems analysis, the OPB is, in fact, agnostic about biology so that the OPB could be applied to other physics-based domains such as to engineering systems.

Implementation and deployment: The OPB is being developed in the web ontology language (OWL-DL) using the Protege-OWL ontology editing environment. Curatorial authority reside with its current authors.

Contact: Daniel L. Cook, MD, PhD. (dcook@u.washington.edu)