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

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/.

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

“…Comments, corrections and/or clarifications regarding PhosphoGRID can be sent to admin@phosphogrid.org. Since its introduction in 2010, PhosphoGRID has become one of the five most visited online databases by the Saccharomyces research community, along with SGD (6), Yeastract (7), CYGD-MIPS (8) and BioGRID (9). …”

IPDS: A semantic mediator‐based system using Spark for the integration of heterogeneous proteomics data sources

“…It uses various technologies for developing Web applications such as SOAP/XML, WSDL, UDDI, XSDL, RDF, and DAML+ OIL. YeastMed 36 is a mediator‐based system for the integration of yeast‐specific data sources such as SGD, YEASTRACT, MIPS‐CYGD, BioGRID, and PhosphoGRID. It has a domain ontology that plays the role of the global schema and supports the user queries.…”

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

“…"Towards Linked Open Gene Mutations Data" by Zappa et al . [ 9 ] presents a prototype implementation of the IARC TP53 Mutation database as Linked Open Data (LOD) that allows to semantically integrate mutation data with information from public molecular biology databases whose content is already available through the LOD and can also serve as a starting point for the development of an ontology on human variation data.…”