- Article -
| In Silico Biology 2, 0021 (2002); ©2002, Bioinformation Systems e.V. |
The Semantic Metadatabase (SEMEDA): Ontology based integration of federated molecular biological data sources
Jacob Köhler1 and Steffen Schulze-Kremer2
1University Bielefeld, Germany
E-mail: jacob.koehler@uni-bielefeld.de
2Resource Center DHGP, Berlin, Germany
E-mail: steffen@rzpd.de
Edited by E. Wingender; received November 30, 2001; revised and accepted February 3, 2002; published March 19, 2002
Abstract
A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [Ashburner et al., 2000]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg.de/semeda/.
We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration.
Keywords: Semantic database integration, molecular biology, meta-database, ontology, knowledge representation, controlled vocabulary