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Model annotation and discovery with the Physiome Model Repository.

Dewan M Sarwar¹, Reza Kalbasi¹, John H Gennari²

¹Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.

BMC Bioinformatics

|September 8, 2019

Summary

This summary is machine-generated.

Scientists can now discover and reuse biological simulation models more easily. A new web tool and semantic annotations improve model accessibility and reproducibility in research.

Keywords:

CellML Epithelial transport Model discovery Physiome Model Repository Semantic annotation

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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.