title: Transparent mediation-based access to multiple yeast data sources using an ontology driven interface.
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/.
authors.forename: Abdelaali
authors.initials: A
authors.lastname: Briache
authors.forename: Kamar
authors.initials: K
authors.lastname: Marrakchi
authors.forename: Amine
authors.initials: A
authors.lastname: Kerzazi
authors.forename: Ismael
authors.initials: I
authors.lastname: Navas-Delgado
authors.forename: Badr D
authors.initials: BD
authors.lastname: Rossi Hassani
authors.forename: Khalid
authors.initials: K
authors.lastname: Lairini
authors.forename: José F
authors.initials: JF
authors.lastname: Aldana-Montes
mesh_terms: D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D020407:Internet; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface