Tools

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research.  It is regularly improved and released several times per year.

GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.

References:

• Delphine Steinbach, Michael Alaux, Joelle Amselem, Nathalie Choisne, Sophie Durand, Raphae ̈l Flores, Aminah-Olivia Keliet, Erik Kimmel, Nicolas Lapalu, Isabelle Luyten, Célia Michotey, Nacer Mohellibi, Cyril Pommier, Sébastien Reboux, Dorothée Valdenaire, Daphné Verdelet and Hadi Quesneville : Database, Vol. 2013, Article ID bat058, doi:10.1093/database/bat058

• Samson-Steinbach Delphine, Legeai Fabrice, Karsenty Emmanuelle et al. (2003) GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics. Nucleic Acids Res., 31, 179–182.

Funding : 

This work is supported by the INRA Plant Biology and Breeding department, the French National Research Agency, the Genoplante programme, the TransPLANT project (EU 7th Framework Programme, contract number 283496) and the ELIXIR-Excelerate project (EU H2020 project of the ELIXIR ESFRI).

Contact: urgi-contact@versailles.inra.fr

This information system is currently used to manage the data of many projects at national or international level :

• SIREGAL INRA project: management of INRA plant genetic resources
• Phenome-FPPN French National infrastructure: management of INRA plant phenotyping data in different environments
• IWGSC: management of the data produced by the International Wheat Genome Sequencing Consortium
• WheatIS: GnpIS is a node of the international Wheat distributed information system in the frame of the Wheat Initiative
• Whealbi European project: management of Wheat data
• Breedwheat French National project: management of Wheat data
• PeaMUST French National project: management of Pea data
• Rapsodyn French National project: management of rapeseed data
• AKER French National project: transfert of the GnpIS software for the management of the sugar beet data
• Amaizing French National project: management of Maize data

It is developed by INRA URGI GnpIS information system team

Access mode(s):