Demand-Driven Database Integration for Biomolecular Applications

As a member of the consortium for the "Computation and Prediction of Receptor−Ligand Interaction" the Integrated Publication and Information Systems Institute, GMD−IPSI , Darmstadt, participates in the national joint project RELIWE. Docking−D is the part of RELIWE which considers heterogeneous database support and in which GMD−IPSI takes the leading role. In the current situation the receptor and ligand data used within the project, either raw data or data derived during analysis, is extremely heterogeneous. Many of these databases are supported by autonomous systems which employ different data management facilities with heterogeneous data models, in particular dedicated file systems with specialized retrieval and presentation functionality (e.g. PDB [1]) or a relational model (e.g. Whatif [20]). In addition, the information is represented at different levels of detail (e.g. sequence vs. structural data), with mutual inconsistencies in structure, naming, scaling, and behavior, whereby much of this behavior is hidden in the implementation of the autonomous systems. Thus the database system must enable integrated access to the underlying, autonomous, heterogeneous information bases, but also has to allow the integration of new datatypes (e.g. sequence and spatial data) and has to support associative retrieval of the data. Different tools, like receptor−ligand docking algorithms, model building tools for receptors or visualization tools, which are developed or provided by the other partners within the project (e.g. Whatif, LUDI [2]), must be connected to the DBMS.