Abstract
BackgroundSaccharomyces 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.ResultsTo 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.ConclusionsYeastMed 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/.
Highlights
Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be manipulated
We have conducted a usability assessment in order to grade how well biologists can learn and use YeastMed to achieve their goals and how satisfied they are with the system
When the change touches the structure of the flat files or the HTML pages from which YeastMed extracts data, the system will need to reflect this on its components, but only on the modified-source components: the modified-source schema, the mapping rules implying that source, the source-related entities in the ontology and the web service of the source
Summary
Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be manipulated. The yeast Saccharomyces cerevisiae, known popularly as bakers’ or brewers’ yeast, has been used extensively in aging research It is a unicellular organism whose DNA is packaged into chromosomes that are localized in a subcellular structure called the nucleus. They usually perform the following tasks during query formulation and execution: (i) look for appropriate sources where it is possible to find helpful data and specify their location, (ii) identify the focus of each source, (iii) query each convenient source independently using its specific access method and query language, (iv) navigate through the sources to obtain complementary data, and (vi) manuallymerge the results obtained from different sources This is a tedious and time-consuming task for biologists, most of whom are not bioinformatics experts, and reduces the advantage that can be took of the available information
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