Open Access Software

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

Martijn P van Iersel1*, Alexander R Pico2, Thomas Kelder1, Jianjiong Gao3, Isaac Ho2, Kristina Hanspers2, Bruce R Conklin24 and Chris T Evelo1

Author Affiliations

1 Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, the Netherlands

2 Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA

3 Department of Computer Science, University of Missouri, Columbia, MO 65201, USA

4 Departments of Medicine and Cellular and Molecular Pharmacology, University of California San Francisco CA 94143, USA

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BMC Bioinformatics 2010, 11:5  doi:10.1186/1471-2105-11-5

Published: 4 January 2010



Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services.


Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications.


By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at webcite.