BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

TLDR

biomaRt is a Bioconductor package that links BioMart data resources to Bioconductor analysis tools, enabling annotation of gene identifiers with symbols, chromosomal coordinates, Gene Ontology, OMIM, and retrieval of genomic sequences and SNPs. It achieves fast, up‑to‑date data retrieval by executing direct SQL queries against BioMart databases such as Ensembl. This tight integration creates a powerful environment for mining biological data within Bioconductor. The package is available at http://www.bioconductor.org under LGPL; contact [e-mail].

Abstract

Summary:biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining. Availability:http://www.bioconductor.org. LGPL Contact:[e-mail]