Model annotation and discovery with the Physiome Model Repository.

Area of Science:

• Computational Biology
• Biomedical Informatics

Background:

• Mathematical and physics-based simulation models offer computable and reproducible ways to understand biological phenomena.
• Standardized descriptions and repositories enhance model accessibility, discoverability, and reusability.
• Existing tools facilitate model encoding, semantic description, and archiving for efficient scientific investigation.

Purpose of the Study:

• To enhance the discoverability and reusability of biological simulation models.
• To demonstrate the utility of semantic annotation and web-based tools for model exploration.

Main Methods:

• Comprehensive annotation of biological models with semantic information.
• Development of a web-based tool for semantic querying and model discovery.
• Inclusion of annotated models in the Physiome Model Repository (PMR).

Main Results:

• A cohort of biological models has been comprehensively annotated with biological semantics.
• Annotated models are accessible through the Physiome Model Repository (PMR).
• A web-based tool facilitates discovery of relevant models, including those for epithelial transport, via semantic queries.

Conclusions:

• Semantic annotation and the developed web tool enable scientists to discover reusable models in the PMR.
• This approach highlights the contribution of semantic web technologies to biomedical and clinical research.
• Source code and links to the discovery tool are publicly available for reuse.