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Semantic optimization of biomolecular queries in object-oriented database systems

Summary: Semantic optimization of biomolecular queries in
object-oriented database systems
Karl Aberer , Klemens Hemm
GMD-IPSI, Dolivostr. 15, D-64293 Darmstadt, GERMANY
email: {aberer,hemm}@darmstadt.gmd.de
Research efforts in molecular biology have led to an explosion both in quantity and quality of
biomolecular data. In particular databases that integrate data from many different, heterogeneous
information resources lead to complex database schemas and large databases. In order to support the
user in creatively exploiting these information resources, flexible and efficient retrieval capabilities are
We sketch in this paper our approach to optimization of declarative queries in object-oriented databases,
that allows to exploit the specific semantic characteristic of datatypes occurring in scientific applications
like molecular biology. These processing capabilities are used within the German national joint project
RELIWE (RELIWE is a research consortium in which EMBL Heidelberg , GMD-IPSI and GMD-SCAI
participate as research institutions, and BASF, Ludwigshafen and E. Merck, Darmstadt participate as
industrial partners; the project is funded by the German "Bundesministerium fuer Bildung und
Wissenschaft" BMBW, grant number 01IB302E.). In RELIWE's subproject Docking-D an integrated
protein/ligand database covering many datasets, that are relevant for drug design [1], including PDB ,
Swissprot, PIR , DSSP, HSSP and PMD, has been developed on top of GMD-IPSI's object-oriented


Source: Aberer, Karl - Faculté Informatique et Communications, Ecole Polytechnique Fédérale de Lausanne


Collections: Computer Technologies and Information Sciences