Using a Rule-System as Mediator for Heterogeneous Databases, exemplified in a Bioinformatics Use Case

Abstract: Databases nowadays used in all kinds of application areas often differ greatly in a number of properties. These varieties add complexity to the handling of databases, especially when two or more different databases are dependent. The approach described here to propagate updates in an application scenario with heterogeneous, dependent databases is the use of a rule-based mediator. The system EruS (ECA rules updating SCOP) applies active database technologies in a bioinformatics scenario. Reactive behaviour based on rules is used for databases holding protein structures. The inherent heterogeneities of the Structural Classification of Proteins (SCOP) database and the Protein Data Bank (PDB) cause inconsistencies in the SCOP data derived from PDB. This complicates research on protein structures. EruS solves this problem by establishing rule-based interaction between the two databases. The system is built on the rule engine ruleCore with Event-Condition-Action rules to process PDB updates. It is complemented with wrappers accessing the databases to generate the events, which are executed as actions. The resulting system processes deletes and modifications of existing PDB entries and updates SCOP flatfiles with the relevant information. This is the first step in the development of EruS, which is to be extended in future work. The project improves bioinformatics research by providing easy access to up-to-date information from PDB to SCOP users. The system can also be considered as a model for rule-based mediators in other application areas.