About COST Action 17111, DATA INTEGRATION TO MAXIMISE THE POWER OF OMICS FOR GRAPEVINE IMPROVEMENT
HOW TO ACKNOWLEDGE OUR COST ACTION
Please use the following text to acknowledge CA17111 INTEGRAPE in all of your future publications related to INTEGRAPE:
This article/publication is based upon work from COST Action CA 17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology).
Description
COST ACTION CA17111 “DATA INTEGRATION TO MAXIMISE THE POWER OF OMICS FOR GRAPEVINE IMPROVEMENT” has officially started in September of 2018.
The COST Action INTEGRAPE will bring together all stakeholders in the grapevine research community (academic, industry, policymakers and consumers) in an open, international, and representative network to develop minimal data standards and good practices in order to integrate data repositories and improve interoperability between datasets. The ultimate objective is to harness and exploit all available data to achieve better management practices and more cost-effective breeding for improved genotypes. Grapevine is grown worldwide to produce fresh berries, processed fruits and wine. The major challenge is to control berry composition and maintain yields while limiting the use of pesticides, water and other inputs, thus adapting the industry to climate change while achieving environmental and economic sustainability. Grapevine research focuses on interactions between the genotype, phenotype and environment, and information must be integrated from heterogeneous datasets including ampelography, environmental biology, genetics, genomics, epigenomics, transcriptomics, proteomics and metabolomics. The data are currently dispersed and difficult to access, hindering meta-analysis (the re-use of grapevine data beyond the original experiments). No institution working in the field of grapevine research has yet taken on the mission to improve data integration and interoperability at the global level, although the grapevine research community is continuously producing large datasets. The concepts described will support stakeholders by developing innovative strategies to integrate grapevine data from existing resources and new experiments in a cost-effective manner, as well as making interoperable grapevine datasets and tools available in a secure and standardised format.
Work is organized in 4 working groups:
- WG1. Data interoperability and definition of minimal contextual data standards
- WG2. Interoperability of infrastructures and web services
- WG3. Data analysis and best practices
- WG4. Dissemination and user community assessment of guidelines and recommendations
Links:
COST Action web page
COST rules and guidelines
COST web site
International Grape Genome Program (IGGP)
Action Documents
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Action’s Memorandum of Understanding (MoU) |
COST ACTION CA17111 “DATA INTEGRATION TO MAXIMISE THE POWER OF OMICS FOR GRAPEVINE IMPROVEMENT” has officially started in September of 2018.
Main Challenge
Establish an open, international, and representative network that integrates data from existing resources in a cost-effective manner, as well as making interoperable grapevine dataset and tools available in a secure and standardized format.
Goals
Grant Period 3
1. Establish a common access point for grapevine data in the existing and well developed platforms in the context of systems biology.
2. Improve the interoperability between Omics data and associated field data (e.g. climatic, agricultural and viticulture data) using data standards, ontologies and common application programming interfaces.
3. Integrate grapevine data with other relevant datasets, such as the metagenomics of microorganisms interacting with grapevine plants and winemaking-related datasets.
4. Provide recommendations and tools for data submission compliant to FAIR principles and data extraction: recommended repositories, standards formats, ontologies and validation tools.
5. Develop a strategy to generate and update shared dictionaries of synonyms for genes and markers to improve the standards and ontologies, in the genetic and genomic domains with the final goal of providing recommendations to the grapevine community for their use based on real datasets.
6. Build a centralized framework for the standard annotation of grapevine genes by integrating and disseminating the IGGP guidelines which propose a standard nomenclature for locus identifiers and define a convention for a gene naming in the context of grapevine genomics
7. Develop guidelines for the processing and analysis of sequence variation, transcriptomics, proteomics, metabolomics, and phenotypic datasets, using whatever information is available about the samples and analytical protocols.
8. Disseminate the recommendations made and train the grapevine community to follow recommendations about guidelines on data standardization and data analysis, providing feedback
9. Organise webinars to demonstrate the scope and use of software tools and information systems
10. Organise hands-on sessions to test the recommendations and tools on real datasets and to train the wider community to comply with the recommended standards.
Establish an open, international, and representative network that integrates data from existing resources in a cost-effective manner, as well as making interoperable grapevine dataset and tools available in a secure and standardized format
Description
Imagine having all of the data about grapevines accessible in a single place
The European network INTEGRAPE seeks the complete integration of information about one of the oldest crop — grapevines — and their main products: wine, table grapes and raisins. In particular, the world grape and wine industries will have access to full and up-to-date information to meet their major challenges: to improve grape berry quality and produce better wines, while limiting the use of pesticides and adapting the wine industry to the threats of climate change.
New techniques allow the study of thousands of grapevine and grape characteristics at once, which generates huge datasets that are only manageable with the support of dedicated informatics tools. These datasets are also usually generated in different non-standardised formats across research laboratories, and stored on researcher laboratory computers or as local databases, which makes them poorly accessible for further use.
What are we doing?
As for the invention of special tools to start to understand the connections of the stars in the constellations, INTEGRAPE will develop and promote tools that are dedicated to harnessing and exploiting all of the available datasets collected by grapevine scientists in the fields of molecular biology, genetics, biochemistry and systems biology.
Where is it going?
Last, but not least, INTEGRAPE will make these data available and usable beyond the original experiments, and they will be interoperable in a secure and standardised format, to develop these grapevine datasets to be available to the public and to private research communities.
Find Out More
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Integrape brochure |