Biological Databases

Biological databases constitute the data layer of molecular biology and bioinformatics and are becoming a central component of some emerging fields such as clinical bioinformatics, and translational and personalized medicine. The building of biological databases has been conducted either considering the different representations of molecular entities, such as sequences and structures, or more recently by taking into account high-throughput platforms used to investigate cells and organisms, such as microarray and mass spectrometry technologies. This chapter provides an overview of the main biological databases currently available and underlines open problems and future trends. This chapter reports on examples of existing biological databases with information about their use and application for the life sciences. We cover examples in the areas of sequence, interactomics, and proteomics databases. In particular, Sect. 26.1 discusses sequence databases, Sect. 26.2 presents structure databases including protein contact maps, Sect. 26.3 introduces a novel class of databases representing the interactions among proteins, Sect. 26.4 describes proteomics databases, an area of biological databases that is being continuously enriched by proteomics experiments, and finally Sect. 26.5 concludes the chapter by underlining future developments and the evolution of biological databases.