Data Services

Scope of the Service

The service covers 4 types of datasets describe below.

Genetic resources
This service offer aims to facilitate the publication of FAIR genetic resources and their associated metadata (taxonomy, germplasm/accessions, collections, passport descriptions, primary phenotypes) into GnpIS  and reference repositories, such as Florilège, RARe, EURISCO, FAIDARE and WheatIS.
To ensure the richness of the associated metadata and the URGI's ability to integrate this data, the dataset must be submitted in the appropriate format. The URGI can provide support during this stage.

• Crops datasets: Submit_GeneticResources.xlsx
• Forest datasets: Submit_GeneticResources_ECODIV.xlsx

Phenotyping data
This service offer aims to facilitate the publication of FAIR phenotyping datasets (Genotype X Environment experimental trials) into  GnpIS  and reference repositories, such as FAIDARE and WheatIS, Recherche Data Gouv.
To ensure the richness of the associated metadata and the URGI's ability to integrate this data, the dataset must be submitted in the appropriate format. The URGI can provide support during this stage.

• Crops trial and experimental data: 
  • Single observations:  Submit_Ephesis.xlsx
  • Time series: Submit_Ephesis_time_serie.xlsx
  • Full documentation available here in french:  README-FR.pdf
  • Example of Multi year Vitis Trial: Excel file year 1 , Excel file year 2 -> Preview in GnpIS here
• Forest trial and experimental data:
  • Dataset file: Submit_Trials_ECODIV.xlsx
  • Woody Plant Ontology (to declare your variables): WoodyPlantOntology.xls (ontology tree available here )

Many traits and variables are already available in GnpIS ontologies. Search for the variables you need to use in GnpIS Ontology Portal  before submitting your dataset:

• If your species does not have an ontology yet, you can create one by following the Crop Ontology Trait Dictionary Template and its guidelines .
• If your species has an ontology, but some variables are missing, download the existing ontology and add the missing terms before sending us the updated version.

Genomic data
This service offer aims to facilitates the integration of FAIR genomic datasets into  GnpIS  by providing genome annotations in JBrowse 2 or Intermine or BLAST banks.
To ensure the richness of the associated metadata and the URGI's ability to integrate this data, the dataset must be submitted in the appropriate format:

• Genomic Annotation: GFF3 file
• Physical Map: FPC file
• Transposable elements: Refer to the documentation dedicated to REPETDB data submission

Other data
This service offer aims to facilitate the publication of FAIR datasets in Recherche Data Gouv reference repository.
URGI provides support for metadata completion and publication of standardized data to ensure the dataset's richness.

Criteria of eligibility and Rates

This service is free of charge and open primarily to INRAE staff from the departments contributing to the platform: BAP and ECODIV.
Prestation payante pour d’autres départements/instituts ou pour des projets ?

The data to be published must be available at the time of submission of the request. An embargo is possible (by default, set at 2 years after the end of the project) but the data must eventually be made public.
The data must be submitted by the requesting team in the appropriate format (described above in the scope of the offer). This ensures the richness of the associated metadata (in line with the FAIR principles) and the ability to integrate the data into GnpIS. The URGI team can provide support during this stage.

Subscription terms

The ODS_URGI_DataPublication.docx (1.27 MB) request form must be completed and sent as a PDF to urgi-contact@inrae.fr with the subject line “[ODS_URGI_DataPublication] Project_acronym.” This simple procedure allows you to create a minimal data management plan including license and ownership matters.

If your data was acquired as part of an ongoing funded project in which URGI is a partner, or if your data is part of a CRB collection or a forest project, you can directly get in touch with your usual contact without filling out the form.

Requests can be made throughout the year. They will be reviewed within one month at most.
After the review, you may need to discuss the request with the platform, particularly to validate your objectives and needs and URGI's capacity to respond.

Any publication citing the integrated dataset(s) must cite the URGI platform , and possibly GnpIS references .