Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #337639
Title: Towards an open grapevine information system

Author
item ADAM-BLONDON, ANNE-FRANCOISE - French National Institute For Agricultural Research
item ALAUX, MICHAEL - French National Institute For Agricultural Research
item POMMIER, CYRIL - French National Institute For Agricultural Research
item CANTU, DARIO - University Of California
item CHENG, ZONG-MING - University Of Tennessee
item CRAMER, GRANT - University Of Nevada
item DAVIES, CHRISTOPHER - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item DELROT, SERGE - French National Institute For Agricultural Research
item DELUC, LAURENT - Oregon State University
item DI GASPERO, GABRIELE - Applied Genomics Laboratory
item GRIMPLET, JEROME - Instituto Aragone' S De Ciencias De La Salud
item FENNELL, ANNE - South Dakota State University
item Londo, Jason
item KERSEY, PAUL - European Bioinformatics Institute
item MATTIVI, FULVIO - Fondazione Edmund Mach
item NAITHANI, SUSHMA - Oregon State University
item NEVEU, PASCAL - French National Institute For Agricultural Research
item NIKOLSKI, MACHA - University Of Bordeaux
item PEZZOTTI, MARIO - University Of Verona
item REISCH, BRUCE - Cornell University
item TOPFER, REINHARD - Julius Kuhn Institute
item VIVIER, MELANE - Stellenbosch University
item Ware, Doreen
item QUESNEVILLE, HADI - French National Institute For Agricultural Research

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2016
Publication Date: 11/23/2016
Citation: Adam-Blondon, A., Alaux, M., Pommier, C., Cantu, D., Cheng, Z., Cramer, G.R., Davies, C., Delrot, S., Deluc, L., Di Gaspero, G., Grimplet, J., Fennell, A., Londo, J.P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B., Topfer, R., Vivier, M., Ware, D., Quesneville, H. 2016. Towards an open grapevine information system. Horticulture Research. doi: 10.1038/hortres.2016.56.

Interpretive Summary: This manuscript is the outcome of a grapevine experts meeting that took place in the fall of 2015. The objective was to create a coordinated federation of information systems holding grape data distributed around the world that provides an integrated set of interfaces supporting advanced data modelling, rich semantic integration and the next generation of data mining tools. Such system is called GrapeIS, and it aims to link genotypes to phenotypes, and scientific research to agronomical and oeneological data, thus providing new insights into grape biology, and allowing new varieties of grape to be developed meeting existing challenges such as biotic stressors which include living disturbances like fungi or harmful insects, and abiotic stress factors such as heavy rain, intense sunlight or wind that may cause harm to the grapevines, climate change, and consumer demand. For this, the authors claim that it is critical to develop, implement and adopt appropriate standards for data annotation and formatting.

Technical Abstract: Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. While the methods used in biology have evolved tremendously in recent years and now involve the routine production of large datasets 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 frame 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 modelling, 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.