Using XML technology for the ontology-based semantic integration of life science databases

IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society
Stephan Philippi, Jacob Köhler

Abstract

Several hundred internet accessible life science databases with constantly growing contents and varying areas of specialization are publicly available via the internet. Database integration, consequently, is a fundamental prerequisite to be able to answer complex biological questions. Due to the presence of syntactic, schematic, and semantic heterogeneities, large scale database integration at present takes considerable efforts. As there is a growing apprehension of extensible markup language (XML) as a means for data exchange in the life sciences, this article focuses on the impact of XML technology on database integration in this area. In detail, a general architecture for ontology-driven data integration based on XML technology is introduced, which overcomes some of the traditional problems in this area. As a proof of concept, a prototypical implementation of this architecture based on a native XML database and an expert system shell is described for the realization of a real world integration scenario.

References

Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·V M Markowitz, O Ritter
Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·S B DavidsonP Buneman
Jan 1, 1995·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·P D Karp
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Dec 11, 1999·Nucleic Acids Research·E WingenderF Schacherer
Apr 13, 2000·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·T CritchlowT Slezak
Nov 15, 2000·Biological Chemistry·J van HeldenS J Wodak
Mar 10, 2001·Bioinformatics·F AchardE Barillot
Mar 10, 2001·Bioinformatics·R StevensA Brass
Jul 24, 2001·Briefings in Bioinformatics·R StevensS Bechhofer
Aug 15, 2002·Bioinformatics·Lichun WangAlan Robinson
Jan 10, 2003·Nucleic Acids Research·Andreas D Baxevanis
Jan 10, 2003·Nucleic Acids Research·S MiyazakiY Tateno
Dec 12, 2003·Bioinformatics·Jacob KöhlerMatthias Lange
Dec 25, 2003·Bioinformatics·Stephan Philippi
Jul 17, 2008·Comparative and Functional Genomics·Jennifer Williams, William Andersen

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Citations

Nov 20, 2004·Bioinformatics·Georgios V GkoutosJohn M Hancock
Jan 1, 2013·Health Information Science and Systems·Peng Gong
Mar 20, 2008·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Carl Taswell
Aug 7, 2007·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Alex A T BuiHooshang Kangarloo
Oct 19, 2006·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Stephan Philippi, Jacob Köhler
May 10, 2006·Nature Reviews. Genetics·Stephan Philippi, Jacob Köhler

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