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

Steffen Durinck1, Yves Moreau, Arek Kasprzyk

  • 1Department of Electronical Engineering, ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium. steffen.durinck@esat.kuleuven.ac.be

Bioinformatics (Oxford, England)
|August 6, 2005
PubMed
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The biomaRt package integrates BioMart databases with Bioconductor for gene annotation and data retrieval. This tool facilitates biological data mining by providing access to gene symbols, sequences, and SNP information.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • BioMart provides access to diverse biological databases.
  • Bioconductor is a popular platform for bioinformatics analysis.
  • Integrating these resources is crucial for efficient biological data mining.

Purpose of the Study:

  • To introduce biomaRt, a Bioconductor package.
  • To enable seamless integration of BioMart data resources with Bioconductor.
  • To facilitate annotation and retrieval of biological data for analysis.

Main Methods:

  • Developed a Bioconductor package named biomaRt.
  • Implemented direct SQL queries to BioMart databases (e.g., Ensembl).
  • Enabled annotation of gene identifiers with various biological attributes.

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Main Results:

  • biomaRt annotates gene identifiers (e.g., Entrez-Gene, Affymetrix probes) with gene symbols, chromosomal coordinates, Gene Ontology, and OMIM information.
  • The package allows retrieval of genomic sequences and single nucleotide polymorphism (SNP) data.
  • Fast and up-to-date data retrieval is achieved through direct SQL queries.

Conclusions:

  • biomaRt offers a powerful environment for biological data mining.
  • The package tightly integrates large BioMart databases with Bioconductor data analysis.
  • Facilitates efficient access to comprehensive biological information for research.