Model annotation and discovery with the Physiome Model Repository

Motivation Mathematics and physics based computational models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models encoded in computable form 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. Biologists and Clinicians can leverage these resources to investigate specific questions and hypotheses. Results We have comprehensively annotated an initial cohort of models with biological semantics, including knowledge of entities such as protein identifiers, anatomical locations and solutes transported. These annotated models are freely available in the Physiome Model Repository. To demonstrate the benefits of this approach, we have developed a web-based tool which enables users to discover models relevant to the questions and hypotheses they are investigating, with a particular focus on epithelial transport. In helping a user to discover relevant models this tool will provide users with suggestions for similar or alternative models they may wish to explore or utilize in their model based on the models they would like to use. The semantic annotation and the web tool we have developed is a new contribution enabling scientists to discover relevant models in the Physiome Model Repository as candidates for reuse in their own scientific endeavours. We believe that this approach demonstrates how semantic web technologies and methodologies can contribute to biomedical and clinical research. Availability and implementation https://github.com/dewancse/model-discovery-tool Contact d.nickerson@auckland.ac.nz