Abstract
BioMart is a freely available, open source, federated database system that provides a unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects between different research groups. BioMart contains several levels of query optimization to efficiently manage large data sets and offers a diverse selection of graphical user interfaces and application programming interfaces to ensure that queries can be performed in whatever manner is most convenient for the user. The software has now been adopted by a large number of different biological databases spanning a wide range of data types and providing a rich source of annotation available to bioinformaticians and biologists alike.Database URL: http://www.biomart.org
Highlights
Biological data are complex and require specialized expertise for their collection, analysis and interpretation
As a consequence of this, different biological data sources are distributed around the world, clustered around centres of such expertise
Large-scale collaborative efforts have been established to comprehensively study cancer genomes [1, 2]. This can result in the data for a single project being stored in different locations
Summary
Biological data are complex and require specialized expertise for their collection, analysis and interpretation. As a consequence of this, different biological data sources are distributed around the world, clustered around centres of such expertise Each of these centres has its own solution for storing and presenting its data. This can result in the data for a single project being stored in different locations To facilitate such collaborations, technology is required that enables data at multiple sites to be interlinked and presented as a unified source, allowing researchers to perform integrative analyses. BioMart has a flexible data model, so that it can be used with a wide range of biological data types, and built-in query optimizations make it suitable for use with very large data sets Due to these features, members of collaborative groups are able to maintain their own data sources independently, while providing a unified access point for all of the data generated by their project. Data transfer can optionally be performed using the secure HTTPS protocol, both between servers and to and from clients
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