Large-scale open bioinformatics data resources

Abstract

The data explosion in bioinformatics is relentless. More and more genomes are being sequenced and many new types of datasets are being generated in large-scale projects. Integration and true open access to the data are still difficult issues, although they are gradually being addressed. Notably, certain fields have good standardization and interoperability, while others lag behind. This review summarizes the latest developments in genome and sequences databases, transcriptomics data (ESTs, ORESTES, full-length cDNAs), proteomics data (protein databases, protein structures, family and domain classification) as well as loosely integrated fields, such as microarray experiments, mutation databases and databases of regulatory regions and elements. The review attempts to resist simply summarizing what data are available, and aims to provide a critical look at some of the integration and access issues associated with several of these resources.