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The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units
Bernard de Bono1, Soroush Safaei2, Pierre Grenon3
1Centre for Health Informatics and Multiprofessional Education, University College London London, UK ; Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand.
Frontiers in Physiology
|March 12, 2015
Summary
This study introduces a workflow for modularizing physiology simulations, enabling semantic interoperability of tissue models and data. This facilitates objective comparison and reuse of physiological models and associated data.
Area of Science:
- Physiology
- Computational Biology
- Systems Biology
Background:
- Interoperability of physiological models and data is crucial for comparison and reuse.
- Current models lack semantic interoperability, hindering objective analysis.
- Tissue-level simulations require a standardized approach for modularity.
Purpose of the Study:
- To develop a workflow for modularizing tissue-level physiology simulations.
- To ensure semantic interoperability of functional tissue units.
- To enable modeling of molecular exchange across scales.
Main Methods:
- Systematic extraction, parcellation, and annotation of tissue histology data.
- Development of a circuitboard representation for fluid flow routes.
- Integration of physiology-based pharmacokinetic and pharmacodynamic models.
Main Results:
- Created semantically interoperable functional tissue units.
- Established interoperability between units and a fluid flow model.
- Demonstrated quantitative depiction of biological mechanisms across scales.
Conclusions:
- The developed workflow enhances the reusability and comparability of physiology models.
- Semantic interoperability of tissue models is achievable through systematic data annotation.
- This approach supports multi-scale modeling of physiological processes.
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