title: Bridging biological ontologies and biosimulation: the ontology of physics for biology.
abstract: We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformat-ics modeling of biological structures and the bio-simulation modeling of biological processes. Where-as modeling anatomical entities is relatively well-studied, representing the physics-based semantics of biosimulation and biological processes remains an open research challenge. The OPB bridges this semantic gap-linking the semantics of biosimulation mathematics to structural bio-ontologies. Our design of the OPB is driven both by theory and pragmatics: we have applied systems dynamics theory to build an ontology with pragmatic use for annotating biosimulation models.
authors.affiliation: Departments of Physiology & Biophysics, and Biological Structure,University of Washington, Seattle, WA, USA.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Cook
authors.forename: Jose L  V
authors.initials: JL
authors.lastname: Mejino
authors.forename: Maxwell L
authors.initials: ML
authors.lastname: Neal
authors.forename: John H
authors.initials: JH
authors.lastname: Gennari
mesh_terms: D001703:Biophysics / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008954:Models, Biological; D009626:Terminology as Topic; D018875:Vocabulary, Controlled; D014861:Washington