Abstract

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.

Keywords

BioconductorEnsemblIdentifierComputer scienceAnnotationDatabaseData miningInformation retrievalBiologyGeneGenomicsGeneticsGenome

MeSH Terms

AlgorithmsDatabase Management SystemsDatabasesProteinGene Expression ProfilingInformation Storage and RetrievalOligonucleotide Array Sequence AnalysisSoftwareSystems Integration

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Publication Info

Year
2005
Type
article
Volume
21
Issue
16
Pages
3439-3440
Citations
2373
Access
Closed

External Links

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2373
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150
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2019
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Cite This

Steffen Durinck, Yves Moreau, A. Kasprzyk et al. (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Computer applications in the biosciences , 21 (16) , 3439-3440. https://doi.org/10.1093/bioinformatics/bti525

Identifiers

DOI
10.1093/bioinformatics/bti525
PMID
16082012

Data Quality

Data completeness: 86%