Representing physiological processes and their participants with PhysioMaps

Daniel L. Cook*, Maxwell L. Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


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.

Original languageEnglish (US)
Article numberS2
JournalJournal of biomedical semantics
Issue number1
StatePublished - Apr 15 2013
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2013 Cook et al; licensee BioMed Central Ltd.

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications


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