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2011

International,  COM (posters) 16 Jan 2011   GnpIS, a portal and information system to bridge genetics and genomics plant and fungi data

Aminah-Olivia Keliet, Erik Kimmel, Michael Alaux, Joelle Amselem, Sophie Durand, Cyril Pommier, Nacer Mohellibi, Nathalie Choisne, Daphné Verdelet, Isabelle Luyten, Nicolas Lapalu, Sébastien Reboux, Hadi Quesneville

Plant & Animal Genome (PAG) XIV Conference , January 15-19, 2011, Town & Country Convention Center in San Diego, California, USA. 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, http://lucene.apache.org,), ii) the other one (“an advanced search tool”) based on Biomart (a query-oriented data management system http://www.biomart.org) and Galaxy (http://galaxy.psu.edu). They are freely available at this url: https://urgi.versailles.inra.fr/gnpis, (D. Steinbach & al. paper in prep). These tools are developed according to user needs, genetists 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.

Update: 20 Dec 2013
Creation date: 07 Jun 2011