Light-weight integration of molecular biological databases.

Abstract

Due to the increasing number of molecular biological databases and the exponential growth of their contents, database integration is an important topic of research in bioinformatics. Existing approaches in this area have in common that considerable efforts are needed to provide integrated access to heterogeneous data sources. This article describes the LIMBO architecture as a light-weight approach to molecular biological database integration. By building systems upon this architecture, the efforts needed for database integration can be significantly lowered. As an illustration of the principle usefulness of the underlying ideas, a prototypical implementation based upon the LIMBO architecture is described. This implementation is exclusively based on freely available open source components like the PostgreSQL database management system and the BioRuby project. Additional files and modified components are available upon request from the author.