title: Representing physiological processes and their participants with PhysioMaps.
abstract: BACKGROUND
  As the number and size of biological knowledge resources for physiology grows, researchers need improved tools for searching and integrating knowledge and physiological models. Unfortunately, current resources-databases, simulation models, and knowledge bases, for example-are only occasionally and idiosyncratically explicit about the semantics of the biological entities and processes that they describe.
  
  
  RESULTS
  We present a formal approach, based on the semantics of biophysics as represented in the Ontology of Physics for Biology, that divides physiological knowledge into three partitions: structural knowledge, process knowledge and biophysical knowledge. We then computationally integrate these partitions across multiple structural and biophysical domains as computable ontologies by which such knowledge can be archived, reused, and displayed. Our key result is the semi-automatic parsing of biosimulation model code into PhysioMaps that can be displayed and interrogated for qualitative responses to hypothetical perturbations.
  
  
  CONCLUSIONS
  Strong, explicit semantics of biophysics can provide a formal, computational basis for integrating physiological knowledge in a manner that supports visualization of the physiological content of biosimulation models across spatial scales and biophysical domains.
authors.affiliation: Biomedical & Health Informatics, Univ, of Washington, USA. dcook@uw.edu.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Cook
authors.forename: Maxwell L
authors.initials: ML
authors.lastname: Neal
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.forename: Georgios V
authors.initials: GV
authors.lastname: Gkoutos
authors.forename: John H
authors.initials: JH
authors.lastname: Gennari