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BMC Bioinformatics. 2019 Sep 6;20(1):457. doi: 10.1186/s12859-019-2987-y.

Model annotation and discovery with the Physiome Model Repository.

Author information

Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA.
Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA.
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA.
Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.



Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models help to ensure that such models are accessible, discoverable, and reusable. To this end, researchers have developed tools and standards to encode mathematical models of biological systems enabling reproducibility and reuse, tools and guidelines to facilitate semantic description of mathematical models, and repositories in which to archive, share, and discover models. Scientists can leverage these resources to investigate specific questions and hypotheses in a more efficient manner.


We have comprehensively annotated a cohort of models with biological semantics. These annotated models are freely available in the Physiome Model Repository (PMR). To demonstrate the benefits of this approach, we have developed a web-based tool which enables users to discover models relevant to their work, with a particular focus on epithelial transport. Based on a semantic query, this tool will help users discover relevant models, suggesting similar or alternative models that the user may wish to explore or use.


The semantic annotation and the web tool we have developed is a new contribution enabling scientists to discover relevant models in the PMR as candidates for reuse in their own scientific endeavours. This approach demonstrates how semantic web technologies and methodologies can contribute to biomedical and clinical research. The source code and links to the web tool are available at


CellML; Epithelial transport; Model discovery; Physiome Model Repository; Semantic annotation

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