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Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology

Dan Cook University of Washington, Seattle, WA

Authors

Daniel L. Cook, Maxwell L. Neal, Michal, Galdzicki, John H. Gennari

Abstract

The behavior--the dynamic processes--of biological systems have been encoded as physics-based biosimulations using a variety of mathematical languages (e.g., CellML, SBML, JSim, MATLAB). Recent efforts to annotate the biological content of such models have leveraged available structural ontologies such as Foundational Model of Anatomy (FMA), Gene Ontology (GO), and ChEBI. As an ontological resource for the biophysical content of biosimulation models, we are developing the Ontology of Physics for Biology (OPB) as a reference ontology that encodes concepts for the physical properties (e.g., fluid volume, electrical potential) and the physical laws (e.g., Ohm's law, conservation laws). that are encoded as variables and computations in physics-based biosimulations. The OPB is based on textbook principles of classical physics and engineering systems dynamics, and is consistent with high-level ontologies such as Basic Formal Ontology (BFO). Its organizing schema and main classes (Physical entities, Physical properties, Physical dependencies, Physical processes, and Process manifestations) generalize across those physical domains relevant to biology (e.g., electrochemistry, biochemical kinetics, solid mechanics). It is implemented in the web ontology language (OWL), follows the ontologic principles of Open Biomedical Ontologies (OBO), and is available in preliminary form on the BioPortal site (http://bioportal.bioontology.org/).