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Representing physiological processes and their participants with PhysioMaps.

Daniel L Cook1, Maxwell L Neal, Robert Hoehndorf

  • 1Biomedical & Health Informatics, Univ, of Washington, USA. dcook@uw.edu.

Journal of Biomedical Semantics
|June 6, 2013
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Summary
This summary is machine-generated.

Researchers developed a formal approach to integrate physiological knowledge using biophysics semantics. This enables semi-automatic parsing of biosimulation models into PhysioMaps for better visualization and analysis.

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Area of Science:

  • Physiology
  • Computational Biology
  • Biophysics

Background:

  • Growing biological knowledge resources necessitate better tools for searching and integrating physiological information.
  • Current resources lack explicit semantics for biological entities and processes, hindering interoperability.

Purpose of the Study:

  • To present a formal approach for integrating physiological knowledge using biophysics semantics.
  • To computationally integrate structural, process, and biophysical knowledge partitions into computable ontologies.

Main Methods:

  • Developed a formal approach based on the Ontology of Physics for Biology.
  • Partitioned physiological knowledge into structural, process, and biophysical components.
  • Computationally integrated these partitions into domain-spanning ontologies.

Main Results:

  • Created computable ontologies for archiving, reusing, and displaying physiological knowledge.
  • Achieved semi-automatic parsing of biosimulation model code into PhysioMaps.
  • PhysioMaps allow visualization and interrogation of model responses to perturbations.

Conclusions:

  • Explicit biophysics semantics offer a formal, computational foundation for integrating physiological knowledge.
  • This approach supports visualization of biosimulation model content across scales and domains.
  • Enables enhanced understanding and reuse of physiological simulation data.