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BioMart: a research data management tool for the biomedical sciences
  • Rolando Garcia-Milian, Yale University

BioMart ( is a freely available open source system that allows complex queries across more than 40 different biological data sets through a single web interface. Originally developed for the Ensembl genome browser, BioMart has been integrated into widely used software such as Galaxy, BioConductor, and Cytoskape. The BioMart interface is also used by data portals such as Ensembl, Wormbase, Gramene, and Reactome. In this workshop we will use simple examples to demonstrate how to navigate, build queries, and save and export the results on BioMart such as: - how to retrieve the Ensembl mouse genes and genomic locations in the first 10 Mbp of chromosome 1 region; - retrieving 1 kb of upstream sequences from a cluster of human genes identified by an expression profile experiment; - obtain a list of the SNPs that have been associated with RB1. For the SNPs, obtain several attributes such as source, rs ID, chromosome location, and pathogenicity

  • data mining
Publication Date
Citation Information
Rolando Garcia-Milian. "BioMart: a research data management tool for the biomedical sciences" (2014)
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