Towards an open grapevine information system

Anne-Françoise Adam-Blondon (1) , Michael Alaux (1) , Cyril Pommier (1) , D Cantu (2) , Z-M Cheng (3) , Gr Cramer (4) , C Davies (5) , Serge Delrot (6) , L Deluc (7) , G Di Gaspero (8) , J Grimplet (9) , A Fennell (10) , Jp Londo (11) , P Kersey (12) , F Mattivi (13) , S Naithani (7) , Pascal Neveu (14) , M Nikolski (15, 16) , M Pezzotti (17) , Bi Reisch (18) , R Töpfer (19) , Ma Vivier (20) , D Ware (21, 18) , Hadi Quesneville (1)

1 URGI - Unité de Recherche Génomique Info
2 UC - University of California
3 The University of Tennessee [Knoxville]
4 University of Nevada [Reno]
5 CSIRO - Commonwealth Scientific and Industrial Research Organisation [Canberra]
6 UMR EGFV - Ecophysiologie et Génomique Fonctionnelle de la Vigne
7 OSU - Oregon State University
8 IGA - Istituto di Genomica Applicata
9 UR - Universidad de La Rioja
10 SDSTATE - South Dakota State University
11 USDA - United States Department of Agriculture
12 European Bioinformatics Institute [Cambridge, UK]
13 FEM - Fondazione Edmund Mach - Edmund Mach Foundation [Italie]
14 MISTEA - Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie
15 CBIB - Centre de Bioinformatique de Bordeaux
16 LaBRI - Laboratoire Bordelais de Recherche en Informatique
17 UNIVR - Università degli studi di Verona = University of Verona
18 Cornell University [New York]
19 IRZ - Institute for grapevine breeding Geilweilerhof
20 Stellenbosch University
21 CSHL - Cold Spring Harbor Laboratory

Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.

Mots clés: analyse de génome; vitis vinifera; viticulture

Domaines: Bio-informatique [q-bio.QM]

Anne-Françoise Adam-Blondon, Michael Alaux, Cyril Pommier, D Cantu, Z-M Cheng, et al.. Towards an open grapevine information system. Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩. ⟨hal-01404714⟩