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Review
. 2016 Nov 23:3:16056.
doi: 10.1038/hortres.2016.56. eCollection 2016.

Towards an open grapevine information system

A-F Adam-Blondon  1 , M Alaux  1 , C Pommier  1 , D Cantu  2 , Z-M Cheng  3 , G R Cramer  4 , C Davies  5 , S Delrot  6 , L Deluc  7 , G Di Gaspero  8 , J Grimplet  9 , A Fennell  10 , J P Londo  11 , P Kersey  12 , F Mattivi  13 , S Naithani  7 , P Neveu  14 , M Nikolski  15 , M Pezzotti  16 , B I Reisch  17 , R Töpfer  18 , M A Vivier  19 , D Ware  20 , H Quesneville  1
Affiliations
Review

Towards an open grapevine information system

A-F Adam-Blondon et al. Hortic Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Conceptual scheme of the grapevine distributed information system (GrapeIS).
Figure 2
Figure 2
Evolution of the number of published papers retrieved from the PubMed database (http://www.ncbi.nlm.nih.gov/pubmed) between 1960 and 2015 with the query ‘grapevine’ OR ‘Vitis’.
Figure 3
Figure 3
Different categories of infrastructures that should contribute to the GrapeIS and their key relationships. Within each category, the list of infrastructures cited is not exhaustive but rather meant to be an illustration of its possible content.
See this image and copyright information in PMC

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