Data Services

Accessible via a public web portal , GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools (such as URGI’s dataverse on Recherche Data Gouv, BLAST, JBrowse and Intermine instances) and web services . Data hosted in GnpIS is also indexed in FAIDARE and WheatIS Data Discovery .

GnpIS curates and adds value its datasets by enabling their interoperability and reusability through the use of internationally agreed standards and ontologies ( MIAPPE  and Crop Ontology  for phenotyping data, MultiCropPassportData for genetic resources, NCBI/EMBL recommendations for genomic data). It is continuously improving its compliance with the FAIR principles (Findable, Accessible, Interoperable, Reusable). To enhance the findability and accessibility of the submitted datasets, we collaborate with Data INRAE to assign a DOI (Digital Object Identifier) to your dataset and integrate it into GnpIS.

Finally, GnpIS gives access to curated genome annotations, with a strong expertise of URGI’s staff on transposable elements annotation.

GnpIS is used by INRAE and its partners in major national and international projects. For instance, GnpIS is the repository for the global community working on wheat genomics (International Wheat Genome Sequencing Consortium; IWGSC; https://wheat-urgi.versailles.inra.fr ). GnpIS is also INRAE’s repository for crops and forest trees catalogs of genetic resources, their phenotyping data and genetic data, as no central archive exists for such data, and support their linkage with genomic data, feed the catalog of the French infrastructure of Resources for Research in Agriculture ( www.agrobrc-rare.org ).

It is a major player for data management of the French national node of the ESFRI EMPHASIS for plant phenotyping and its staff has been very active in linking the ELIXIR and EMPHASIS European infrastructures ( https://www.elixir-europe.org/use-cases/plant-sciences ).

DATA OVERVIEW ?

Services

Data can be accessed through GnpIS web portal, which is freely accessible at https://urgi.versailles.inrae.fr/gnpis .

Data producers can publish new datasets in GnpIS using the dedicated  Data publication service. 

We also offer help with FAIR data management and create  Training and Guidelines .

Description of the data life cycle in GnpIS is included in URGI Data Management Plan (DOI : 10.15454/9HM5UI ).

Terms of Use are described in our dedicated page .

References

GnpIS

• Adam-Blondon et al. Mining Plant Genomic and Genetic Data Using the GnpIS Information System. Methods Mol Biol. 2017;1533:103-117. https://doi.org/10.1007/978-1-4939-6658-5_5
• Steinbach et al. GnpIS: an information system to integrate genetic and genomic data from plants and fungi. Database (Oxford). 2013;2013:bat058.  https://doi.org/10.1093/database/bat058

Focus on wheat data

Alaux et al. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol. 2018;19(1):111.  https://doi.org/10.1186/s13059-018-1491-4

Focus on phenotyping data  

Pommier et al. Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. Plant Phenomics. 2019;2019:1671403. https://doi.org/10.34133/2019/1671403