Title: A case study of integrating protein interaction data using semantic web technology

Authors: Lavanya Dhanapalan, Jake Yue Chen

Addresses: Department of Computer and Information Science, Purdue University School of Science, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana 46202-5132, USA. ' Indiana University School of Informatics, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana 46202-5132, USA

Abstract: We describe a new ontology-driven semantic data integration approach for post-genome biology studies. Here, a view-based global schema can be automatically generated by merging RDF schemas from local databases. The semantic inconsistency of the merged schema is resolved by the creation of |RDF ontology maps|. Data querying capability is accomplished with a virtual data repository, in which a D2RQ-based |relational-to-RDF| map is developed to link schema to the relational database backend. With sample RDQL queries, we demonstrate that our approach significantly simplifies the retrieval of human protein interaction data from different databases containing hundreds of thousands of records.

Keywords: semantic web; semantic data integration; resource description framework; RDF schema; ontology maps; protein–protein interactions; post-genome biology; relational databases; protein interaction data.

DOI: 10.1504/IJBRA.2007.015004

International Journal of Bioinformatics Research and Applications, 2007 Vol.3 No.3, pp.286 - 302

Published online: 04 Sep 2007 *

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