A step towards the greater use of computational models in biology was taken when the world's first database of annotated biological models went online on 11 April 2005.
The BioModels Database has been designed to allow biologists to store, search and retrieve published mathematical models of biological systems. The free-to-use database aims to provide access to published, peer-reviewed, quantitative models of biochemical and cellular systems.
Until now, there has been no 'official' way for biologists to readily share such models, but they can now produce and freely distribute their models using the widely accepted, open-source Systems Biology Markup Language (SBML). Once entered into the database, models are annotated and linked to relevant data sources, such as publications or other databases, by human curators.
The database is the result of a collaboration led by the European Bioinformatics Institute in the United Kingdom (which is part of the European Molecular Biology Laboratory) and the SBML team from the United States. Other contributors come from the United States, Japan and South Africa.
The developers' hope is that, ultimately, scientists will be encouraged to deposit their published models in the BioModels Database, making them freely available to all.
The database is currently open to the submission of models — the curators will pick them up for syntax and semantic curation and then submit them to the database itself. At present, they accept only SBML Level 2 Version 1, but say that they will soon expand to Level 1, then CellML, and eventually to other formats.
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Stevens, D. Model resource. Nat Rev Genet 6, 429 (2005). https://doi.org/10.1038/nrg1646
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DOI: https://doi.org/10.1038/nrg1646
