Cyril Pommier, Mathilde Lainé, Raphael Flores, Mikaël Loaec, Célia Michotey, Marie-Angélique Laporte, Claire Guerche, Michael Alaux, G. Merceron, Thomas Letellier, Sophie Durand, Delphine Steinbach, E. Duchêne, Erik Kimmel, Guillaume Cornut, P. Roumet, Hadi Quesneville, A. Lebreton, Elizabeth Arnaud, Anne-Françoise Adam-Blondon, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), CGIAR, Infrastructure Biologie Santé Phenome-FPPN supported by the French National Research Agency (ANR-11-INBS-0012), the H2020 ELIXIR-EXCELERATE project (funded by the European Commission within the Research Infrastructures programme of Horizon 2020, Grant agreement no. 676559), and the Investments for the Future programme (PIA) (ANR-11-INBS-0012). Developments of Wheat, protein crops, rapeseed, and miscanthus ontologies have been supported by the Breedwheat (ANR-10-BTBR- 03), BFF (11-BTBR-0006), Rapsodyn (11-BTBR-0004), and Peamust (11-BTBR-0002) PIA projects. In-kind contribution was made by the Crop Ontology project team supported by the Integrated Breeding Platform and by the CGIAR Platform on Big Data for Agriculture. Some developments were supported by the RDA Europe Project funded by the European Commission, ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), ANR-10-BTBR-0003,BREEDWHEAT,Développer de nouvelles variétés de blé pour une agriculture durable(2010), ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011), ANR-11-BTBR-0004,RAPSODYN,Optimisation de la teneur et du rendement en huile chez le colza cultivé sous contrainte azotée(2011), ANR-11-BTBR-0002,PeaMUST,Adaptation multistress et régulations biologiques pour l'amélioration du rendement et de la stabilité du pois protéagineux(2011), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Pommier, Cyril, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.