File:PAG2011 URGI GnpIS DS poster final.pdf

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PAG2011_URGI_GnpIS_DS_poster_final.pdf(file size: 6.04 MB, MIME type: application/pdf)

Gnpis, A Portal And Information System To Bridge Genetics And Genomics Plant And Fungi Data

A poster by Delphine P Steinbach, Aminah-Olivia Keliet, Erik Kimmel, Michael Alaux, Joelle Amselem, Sophie Durand, Cyril Pommier, Nacer Mohellibi, Nathalie Choisne, Daphné Verdelet, Isabelle Luyten, Nicolas Lapalu, Sebastien Reboux, and Hadi Quesneville, all of INRA URGI.

Presented at PAG 2011.


URGI (Unité de Recherche Génomique-Info) is an INRA bioinformatics unit dedicated to plants and pest genomics. Its mission is to develop and host a genomic and genetic information system called GnpIS, for plants of agronomical interest and their bioagressors. It hosts a bioinformatics platform labeled and state-approved at institute and national level. URGI maintains an efficient computing environment and offers services covering database conception, software engineering, and bioinformatics. A focus is done on doing an interoperability between both the tools (a set of Oracle, PostGreSql, MySql databases and their interfaces in Java, Perl) and the data located in all these databases (for example on Wheat and Grapevine data). 2 new tools were developed to cross query these data, i) one tool ("a quick search tool") based on Lucene (a high-performance, full-featured text search engine library), ii) the other one ("an advanced search tool") based on Biomart (a query-oriented data management system and Galaxy ( They are freely available at this url:, (D. Steinbach & al. paper in prep). These tools are developed according to user needs, geneticists or breeders in the frame of partnership through scientific projects. The goal of this portal and this information system GnpIS, is to help scientists in their research on finding genes responsible for traits of agronomical interest (QTLs), to explore diversity (SNPs) and to select the best allele for breeding, for example to resist to bioagressors or to adapt plant to climate variations.

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