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Updated: Jun 28, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Bridging biological ontologies and biosimulation: the ontology of physics for biology
Daniel L Cook1, Jose L V Mejino, Maxwell L Neal
1Departments of Physiology & Biophysics, and Biological Structure,University of Washington, Seattle, WA, USA.
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.
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