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Combining applications and remote databases view in a common SQL distributed genomic database

Authors:

Pierre-Emmanuel Gros ,

Bioinformatics team, LIMSI-CNRS, Université Paris-Sud, BP 133, F-91403 Orsay Cedex, France, FR
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Joan Hérisson,

Bioinformatics team, LIMSI-CNRS, Université Paris-Sud, BP 133, F-91403 Orsay Cedex, France, FR
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Nicolas Ferey,

Bioinformatics team, LIMSI-CNRS, Université Paris-Sud, BP 133, F-91403 Orsay Cedex, France, FR
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Rachid Gherbi

Bioinformatics team, LIMSI-CNRS, Université Paris-Sud, BP 133, F-91403 Orsay Cedex, France, FR
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Abstract

Huge volumes of bioinformatics data are emerging from sequencing efforts, gene expression assays, X-ray crystallography of proteins, and many other activities. High-throughput experimental methods produce masses of data, so that the whole of biology has changed from a data-light science into a data-driven science. Currently there are a lot of databases and software tools dealing with these genomic data. In general, each tool and database uses a different type of data in exchange protocols, and usually they offer specific services. These Databases are design with different languages and run on different operating systems. Therefore biologists are in a difficult situation where they have to use, process and store heterogeneous data when using heterogeneous software tools and databases. Our framework, GenoMEDIA provides two main middleware to help for this integration, Lydia and Antje. On the one hand, the Lydia middleware offers us facilities for working simultaneously with a variety of Services and Databases. On the other hand, the Antje one ,with the concept of remote view, is designed to allow users to manage multiple heterogeneous remote databases in a uniform vision. The aim of this paper is to present GenoMEDIA and how heterogeneous databases and remote services are integrated, in particular how Antje was designed, implemented and tested with various genomic

DOI: http://doi.org/10.2481/dsj.4.244
How to Cite: Gros, P.-E. et al., (2006). Combining applications and remote databases view in a common SQL distributed genomic database. Data Science Journal. 4, pp.244–254. DOI: http://doi.org/10.2481/dsj.4.244
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Published on 25 Jan 2006.
Peer Reviewed

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