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Open Access Highly Accessed Software

BioMart – biological queries made easy

Damian Smedley1, Syed Haider1, Benoit Ballester1, Richard Holland1, Darin London2, Gudmundur Thorisson3 and Arek Kasprzyk4*

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

2 Institute for Genome Sciences & Policy (IGSP), Duke University CIEMAS, 101 Science Drive, DUMC Box 3382, Durham, NC 27708, USA

3 Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK

4 Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto, Ontario, M5G 0A3, Canada

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BMC Genomics 2009, 10:22  doi:10.1186/1471-2164-10-22

Published: 14 January 2009

Abstract

Background

Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. Frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming. Therefore, many groups rely on local bioinformatics support to process queries by accessing the resource's programmatic interfaces if they exist. This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution.

Results

BioMart enables scientists to perform advanced querying of biological data sources through a single web interface. The power of the system comes from integrated querying of data sources regardless of their geographical locations. Once these queries have been defined, they may be automated with its "scripting at the click of a button" functionality. BioMart's capabilities are extended by integration with several widely used software packages such as BioConductor, DAS, Galaxy, Cytoscape, Taverna. In this paper, we describe all aspects of BioMart from a user's perspective and demonstrate how it can be used to solve real biological use cases such as SNP selection for candidate gene screening or annotation of microarray results.

Conclusion

BioMart is an easy to use, generic and scalable system and therefore, has become an integral part of large data resources including Ensembl, UniProt, HapMap, Wormbase, Gramene, Dictybase, PRIDE, MSD and Reactome. BioMart is freely accessible to use at http://www.biomart.org webcite.