Currently more than 850 biological databases exist. The majority of biological knowledge is not in these databases but rather contained as free text in scientific literature. For systems biology tasks it is often necessary to integrate and extract data from heterogeneous databases and free text as well as to analyse the information in the context of experimental data. ONDEX is an integration framework which aims to address these challenges by combining features of database integration, text mining and sequence analysis with methods for graph-based data analysis and visualisation. The main topics of this diploma thesis are the redesign of the ONDEX backend, the development of a data exchange format, the development of a query environment and the allocation of Web services for data integration, data exchange and queries. These Web services allow backend workflow control from both local and remote workstations.
We aim to demonstrate that automated deduction techniques, in particular those following the model computation paradigm, are very well suited for database schema/query reasoning. Specifically, we present an approach to compute completed paths for database or XPath queries. The database schema and a query are transformed to disjunctive logic programs with default negation, using a description logic as an intermediate language. Our underlying deduction system, KRHyper, then detects if a query is satisfiable or not. In case of a satisfiable query, all completed paths -- those that fulfill all given constraints -- are returned as part of the computed models. The purpose of our approach is to dramatically reduce the workload on the query processor. Without the path completion, a usual XML query processor would search the database for solutions to the query. In the paper we describe the transformation in detail and explain how to extract the solution to the original task from the computed models. We understand this paper as a first step, that covers a basic schema/query reaÂsoning task by model-based deduction. Due to the underlying expressive logic formalism we expect our approach to easily adapt to more sophisticated problem settings, like type hierarchies as they evolve within the XML world.