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Towards an open grapevine information system

View Article: PubMed Central - PubMed

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.

No MeSH data available.


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’.
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fig2: 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’.

Mentions: Looking backward, the grapevine community has been increasingly active in the production of data in the life science area, as shown by a very naive search of recent publications (using query terms ‘grapevine’ OR ‘vitis’) in the PubMed database (Figure 2). The data described in the papers are very diverse covering genomes, genotypes, genomic variation, genetic maps, QTLs, association genetics, transcriptomics, proteomics, metabolomics, phenotype characterizations; and rapidly developing, with the quantity of data produced by a single experiment increasing rapidly over time. The development of a common policy for data standardization has lagged and this gap is impairing progress in grapevine research.


Towards an open grapevine information system
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’.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120350&req=5

fig2: 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’.
Mentions: Looking backward, the grapevine community has been increasingly active in the production of data in the life science area, as shown by a very naive search of recent publications (using query terms ‘grapevine’ OR ‘vitis’) in the PubMed database (Figure 2). The data described in the papers are very diverse covering genomes, genotypes, genomic variation, genetic maps, QTLs, association genetics, transcriptomics, proteomics, metabolomics, phenotype characterizations; and rapidly developing, with the quantity of data produced by a single experiment increasing rapidly over time. The development of a common policy for data standardization has lagged and this gap is impairing progress in grapevine research.

View Article: PubMed Central - PubMed

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.

No MeSH data available.