BioRL: An XML-based Active Rule Language for Biological Database Constraint Management

High throughput biological experiments produce a large amount of biological data that can be updated by time. Inconsistent data stored in the same or different databases may lead to serious biological research problems. Constraint management is important to ensure biological data integrity. Some existing databases were built for the easy use for biologists; however the database management system (DBMS) may not have a sufficient constraint management system. In this paper, we propose an XML-based active rule language, named BioRL, to enforce constraints on existing databases without changing the original system structures or the underlying databases. In BioRL language, biological semantics are represented declaratively in active rules by using XQuery expressions and functions. This paper presents the syntax of the BioRL language, with examples that illustrate the use of BioRL in an application environment. This paper also presents the BioRule system to support the specification and execution of BioRL, focusing on the architectural components of the BioRL parser and the BioRL repository.