BioMart--biological queries made easy. Export

@article{citeulike:3886758, 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.}, author = {Smedley, Damian and Haider, Syed and Ballester, Benoit and Holland, Richard and London, Darin and Thorisson, Gudmundur and Kasprzyk, Arek}, citeulike-article-id = {3886758}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-10-22}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19144180}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19144180}, doi = {10.1186/1471-2164-10-22}, issn = {1471-2164}, journal = {BMC genomics}, keywords = {biomart, software}, number = {1}, pages = {22+}, posted-at = {2009-01-15 09:10:12}, priority = {2}, title = {BioMart--biological queries made easy.}, url = {http://dx.doi.org/10.1186/1471-2164-10-22}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:3886758 L3 - citeulike-article-id:3886758 N2 - 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. IS - 1 JF - BMC genomics SN - 1471-2164 TI - BioMart--biological queries made easy. VL - 10 SP - 22 KW - biomart KW - software AU - Smedley, Damian AU - Haider, Syed AU - Ballester, Benoit AU - Holland, Richard AU - London, Darin AU - Thorisson, Gudmundur AU - Kasprzyk, Arek PY - 2009/// UR - http://dx.doi.org/10.1186/1471-2164-10-22 ER -