Empowering microarray data analysis with metadata from biological databases through biomaRt.

S. Durinck & W. Huber

biomaRt is a new Bioconductor package that integrates BioMart data resources such as Ensembl, with data analysis in Bioconductor. It can be used to annotate a wide range of gene or gene product identifiers (e.g. Affymetrix, Entrez-Gene, ... ) with information such as gene symbol, chromosomal coordinates, GO and OMIM. Beside it's use for annotation, biomaRt can retrieve a wealth of other information e.g. genomic sequences, SNP information and homologs. Fast and up-to-date data retrieval is possible as biomaRt executes direct SQL queries to the BioMarts. This tight integration of biological databases with data analysis in Bioconductor provides a powerful platform for biological data mining.

Accessing public data sources using BioC

Jianhua Zhang
Dana Farber Cancer Institute

BioC has various means of accessing public genomic data sources. Topics covered include a survey of BioC's metadata and its usage, building annotation data packages, accessing GEO, KEGG, and TIGR data within R using various BioC functions. Attendants are encouraged to bring their own data for annotation purpose.