Bridging biological ontologies and biosimulation: the ontology of physics for biology.
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.
Cook
Daniel L
DL
Departments of Physiology & Biophysics, and Biological Structure,University of Washington, Seattle, WA, USA.
Mejino
Jose L  V
JL
Neal
Maxwell L
ML
Gennari
John H
JH
D001703:Biophysics / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008954:Models, Biological; D009626:Terminology as Topic; D018875:Vocabulary, Controlled; D014861:Washington