Using XML technology for the ontology-based semantic integration of life science databases

Several hundred internet accessible life science databases with constantly growing contents and varying areas of specialization are publicly available via the internet. Database integration, consequently, is a fundamental prerequisite to be able to answer complex biological questions. Due to the presence of syntactic, schematic, and semantic heterogeneities, large scale database integration at present takes considerable efforts. As there is a growing apprehension of extensible markup language (XML) as a means for data exchange in the life sciences, this article focuses on the impact of XML technology on database integration in this area. In detail, a general architecture for ontology-driven data integration based on XML technology is introduced, which overcomes some of the traditional problems in this area. As a proof of concept, a prototypical implementation of this architecture based on a native XML database and an expert system shell is described for the realization of a real world integration scenario.