The design and analysis of genetic and genomic studies usually involve the retrieval of large amounts of genomic data available in public databases and repositories.
BioMart is a freely available online service that allows the easy retrieval of genomic data from several databases (Ensembl Genes, Homology and Variations, among many others). The user needs to select the Datasets of interest, choose the respective Filters (to get specific queries) and Attributes (to select the outputs of interest).
BioMart can generate results in several output formats (.html, .csv, .xls, among others). Some examples of queries that can be processed in question of minutes and with few mouse clicks are: retrieval of the coding sequences or homologs of genes located in large genomic intervals or to recover the non-synonymous SNPs from specific genomic regions, among many others.
BioMart and other freely available computational tools (such as Galaxy and Taverna) allow experimentalists with little programming experience to mine and extract relevant information from very large genomic datasets. BioMart can also be incorporated through MartService into more sophisticated mining platforms developed by bioinformaticians.
Contact: Professor Arek Kasprzyk, MD, PhD, Ontario Institute for Cancer Research, Canada. Email: Arek.Kasprzyk@oicr.on.ca
"We are currently upgrading the BioMart software so that it may be used tomanage International Cancer Genome Consortium (ICGC) data.The ICGC(www.icgc.org) is the biggest data management challenge in biology to date.To cope with this challenge, the BioMart team is: -Developing new web interfaces; -Improving the scalability of the system; -Improving the security features; -Improving the web portal support"
Professor Arek Kasprzyk, MD, PhD
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart--biological queries made easy. BMC Genomics. 2009 Jan 14;10:22.
Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A. BioMart Central Portal--unified access to biological data. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W23-7.
Message posted by: Diego Forero