Transparent mediation-based access to multiple yeast data sources using an ontology driven interface |
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Authors: | Briache Abdelaali Marrakchi Kamar Kerzazi Amine Navas-Delgado Ismael Rossi Hassani Badr D Lairini Khalid Aldana-Montes José F |
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Affiliation: | Department of Computer Languages and Computing Science, Higher Technical School of Computer Science Engineering, University of Malaga, Malaga, 29071, Spain. jfam@lcc.uma.es. |
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Abstract: | BACKGROUND: Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RNAs...) is scattered within several data sources like SGD, Yeastract, CYGD-MIPS, BioGrid, PhosphoGrid, etc. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned results is a complex and time-consuming task for biologists most of whom are not bioinformatics expert. It also reduces and limits the use that can be made on the available data. RESULTS: To provide transparent and simultaneous access to yeast sources, we have developed YeastMed: an XML and mediator-based system. In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources. The system is composed of a set of modules that depend heavily on XML and Semantic Web technologies. User queries are expressed in terms of a domain ontology through a simple form-based web interface. CONCLUSIONS: YeastMed is the first mediation-based system specific for integrating yeast data sources. It was conceived mainly to help biologists to find simultaneously relevant data from multiple data sources. It has a biologist-friendly interface easy to use. The system is available at http://www.khaos.uma.es/yeastmed/. |
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