Middleware Support to the Specification and Execution of Active Rules for Biological Database Constraint Management

Constraints are important to ensure consistency and validity of biological data to computerize biological findings. Incorrect data could lead to serious scientific problems when conducting further biology research and experiments. We propose an XML-based active rule system named BioRule to enforce constraints on top of existing data sources. The BioRule system serves as a middleware to filter inconsistent data before populating or updating data sources. Biological semantics are specified in active rules, while the validation can be enforced by the BioRule system automatically according to the defined rules. To facilitate and simplify the specification of active rules, we developed a web-based user-friendly tool to guide end-users. Rule examples, over an existing biology application, are also provided in this paper to illustrate the specification of active rules though web-based interfaces for constraint validation.