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Description:
The work presented in this thesis is outlined in the following. The state of the art in the relevant disciplines is introduced and reviewed in chapter 2. This includes on the one hand the current state of molecular biological databases, their heterogeneity and the integration of molecular biological databases. On the other hand the current usage of ontologies in general and with special regard to database integration is described. The principles of semantic database integration as introduced in this thesis are new and suitable to be used also in other database integration systems, which have to deal with a high number of semantically heterogeneous databases. Therefore in Chapter 3 the newly introduced principles for ontology based semantic database integration are presented independent of their implementation. Chapter 4 introduces the requirements for the implementation of a semantic database integration system (SEMEDA). Several general requirements for the integration of molecular biological systems from the scientific literature are discussed with regard to the feasibility of their implementation in general and in SEMEDA. In addition, the requirements specific to semantic database integration are introduced. In addition how the BioDataServer is used to overcome "technical" heterogeneity, so that SEMEDA only has to deal with semantic heterogeneity is analysed. In chapter 5, an appropriate data structure for storing ontologies, database metadata and the semantic definitions as described in Chapter 3 is developed. Subsequently, it is discussed how this data structure can be edited and queried. In Chapter 6, SEMEDAs software design, implementation and system architecture is given. Chapter 7 describes the use of SEMEDA and its interfaces. The user interface SEMEDA-edit is used to collaboratively edit ontologies and to semantically define databases using ontologies. SEMEDA-query is the query interface that provides uniform access to heterogeneous databases. In addition, a set of procedures exists which can be used ...