2016
IUFRO Genomics and Forest Tree Genetics (2016-05-30-2016-06-03) Arcachon (FRA). In : IUFRO Genomics and Forest Tree Genetics. Book of Abstract. 2016.
21 Jun 2016 Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomicsMichotey, C. ; Anger, C. ; Ehrenmann, F. ; Rogier, O. ; Jorge, V. ; Bastien, C. ; Plomion, C. ; Pichot, C. ; Quesneville, H. ; Adam-Blondon, A.-F.
Due to the major technological advances both in genomics and phenomics, it is now possible to quickly obtain large amounts of data at low cost. One of the consequences is the critical need for data management, with the opportunity to make these datasets interoperable, thus enhancing their reuse and enrichment. GnpIS[1] is an original information system (IS) able to manage these data. It was designed to integrate and link genetic, genomic, phenomic and environmental data into a single environment, allowing plant (crops and forest trees) and fungi researchers to store, query and explore information from different angles.
Here I will present the “Forest tree GnpIS”, a GnpIS focused on forest tree data. The forest tree resources are accessible through a web portal (https://urgi.versailles.inra.fr/gnpis/). This main entry point is a google-like search, a tool using keywords for data discovery. The bird’s eye view obtained allows navigation through the data with dedicated tools facilitating more specific queries and data retrieval. Cards were developed to gather all representative information on major elements (accession, markers, trials …).
This IS is regularly improved with new functionalities answering specific needs raised by scientists and released several times a year. Data are supplied by local sources (files and databases) produced and managed by research teams. In order to make data submission easier, workflows are implemented to automate data flow: 1) extraction from local sources and insertion in GnpIS, 2) extraction from GnpIS and insertion into international IS (such as Evoltree eLab). Ash, pine, spruce, willow, poplar and oak data (genetic resources, phenotypes, genotypes, polymorphisms and genetic maps) have been integrated into this forest IS (https://urgi.versailles.inra.fr/Species/Forest-trees/Database-overview). It is possible from a genome browser and its annotation to access genetic maps results (via markers and QTL) and from a QTL for a trait of interest to get the phenotyping results of this trait and to select the accessions with the most interesting results. To refine your selection, you can study the accessions pedigree and genotyping results. Integration of the data produced within the French Common Garden network (over 1,000 trials with genotypes gathered from ~15 species) is in progress and data from other species are expected soon.
Creation date: 11 Oct 2016
eZ PublishPublication supervisor: A-F. Adam-Blondon
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