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.