“DATA INTEGRATION TO MAXIMISE THE POWER OF OMICS FOR GRAPEVINE IMPROVEMENT”
From September 2018 to September 2022
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.
DESCRIPTION
The European network INTEGRAPE seeks to completely integrate all information regarding one of the world’s oldest crops — grapevine — and their main products: wine, table grapes and raisins. In particular, the world’s grape and wine industries will have full access to up-to-date information to meet their major challenges: to improve grape berry quality and produce better wines, whilst 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 generate huge datasets manageable only with the support of dedicated informatic tools. These datasets are often generated in different non-standardised formats across research laboratories, stored on a researcher’s lab computer or on a local database, which makes them poorly accessible for further use.
INTEGRAPE developed and promoted tools dedicated to harnessing and exploiting all available datasets collected by grapevine scientists in the fields of molecular biology, genetics, biochemistry and systems biology.
INTEGRAPE has made this data available and usable beyond the original experiments, interoperable in a secure and standardised format, developing grapevine datasets in order to be made available to public and private research communities.
The following are amongst the most significant deliverables of INTEGRAPE:
(1) the elaboration of Guideline ‘cookbooks’ and Dictionary of unified grape-sample ontologies (some of which have already being published; e.g., Savoi et al., 2021), providing recommendations for genomic and metabolomic data acquisition, repository submission and handling of datasets, together with recommended repositories and standard formats for organ naming.
(2) the release of the PN40024 fourth genome assembly and its annotation (Velt et al., in preparation), serving as a platform for researchers to discuss and promote the diverse genomic tools associated to this reference genome.
(3) the creation of the Gene Reference Catalogue (Navarro-Payá et al., 2022), building a repository for the standard annotation of grape genes and their functions, based on past and current gene/ gene family characterizations.
(4) the enlisting of Online repositories and tools for omics data exploration and visualization, which to date are not yet interoperable among them.
HOW TO ACKNOWLEDGE COST ACTION CA17111 INTEGRAPE
Please use the following text to acknowledge CA 17111 INTEGRAPE in all of your future publications related to INTEGRAPE:
This article/publication is based upon work from COST Action CA17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology).
