BACKGROUND: Data extraction and integration methods are becoming essential to 
effectively access and take advantage of the huge amounts of heterogeneous 
genomics and clinical data increasingly available. In this work, we focus on The 
Cancer Genome Atlas, a comprehensive archive of tumoral data containing the 
results of high-throughout experiments, mainly Next Generation Sequencing, for 
more than 30 cancer types.
RESULTS: We propose TCGA2BED a software tool to search and retrieve TCGA data, 
and convert them in the structured BED format for their seamless use and 
integration. Additionally, it supports the conversion in CSV, GTF, JSON, and XML 
standard formats. Furthermore, TCGA2BED extends TCGA data with information 
extracted from other genomic databases (i.e., NCBI Entrez Gene, HGNC, UCSC, and 
miRBase). We also provide and maintain an automatically updated data repository 
with publicly available Copy Number Variation, DNA-methylation, DNA-seq, 
miRNA-seq, and RNA-seq (V1,V2) experimental data of TCGA converted into the BED 
format, and their associated clinical and biospecimen meta data in 
attribute-value text format.
CONCLUSIONS: The availability of the valuable TCGA data in BED format reduces 
the time spent in taking advantage of them: it is possible to efficiently and 
effectively deal with huge amounts of cancer genomic data integratively, and to 
search, retrieve and extend them with additional information. The BED format 
facilitates the investigators allowing several knowledge discovery analyses on 
all tumor types in TCGA with the final aim of understanding pathological 
mechanisms and aiding cancer treatments.