This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010

Open Access Open Badges Research

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

Abdelaali Briache1, Kamar Marrakchi1, Amine Kerzazi2, Ismael Navas-Delgado2, Badr D Rossi Hassani1, Khalid Lairini1 and José F Aldana-Montes2*

Author Affiliations

1 Department of Biology, Faculty of Sciences and Techniques, University Abdelmalek Essaâdi, Tangier, BP: 416, 90000, Morocco

2 Department of Computer Languages and Computing Science, Higher Technical School of Computer Science Engineering, University of Malaga, Malaga, 29071, Spain

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BMC Bioinformatics 2012, 13(Suppl 1):S7  doi:10.1186/1471-2105-13-S1-S7

Published: 25 January 2012



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.


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.


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 webcite.