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

Cook, Daniel L and Mejino, Jose L V and Neal, Maxwell L and Gennari, John H (2008) Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 136-140, Washington, DC.

Abstract

We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformatics modeling of biological structures and the biosimulation modeling of biological processes. Whereas modeling anatomical entities is relatively wellstudied, 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.