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.
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.