BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
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.
Durinck
Steffen
S
Department of Electronical Engineering, ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium. steffen.durinck@esat.kuleuven.ac.be
Moreau
Yves
Y
Kasprzyk
Arek
A
Davis
Sean
S
De Moor
Bart
B
Brazma
Alvis
A
Huber
Wolfgang
W
D000465:Algorithms; D003628:Database Management Systems; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D018511:Systems Integration