abstract
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.