Data integration

This ODS aims to facilitate the publication of FAIR genetics/genomics datasets.

We support teams from INRAE's BAP and ECODIV divisions for their data management and integration in Recherche Data Gouv or our Information System GnpIS . To know more about assessment and criteria of eligibility, terms of use or submission modalities, read and fill the following form: ODS_PlantBioinfoPF_DataIntegration.docx . It is a light procedure allowing to build a minimal data management plan including licence and ownership matters. Applications are evaluated about once a month.

For data acquired as part of ongoing funded projects in which URGI is a partner, as well as for BRC genetic resource collections and forestry projects, you can contact us directly or via your usual URGI contact without completing the previous form.

In any cases, datasets must be available at the time of submission and formated by the requesting team in the correct submission format.

Use the following template(s) to submit your datasets in GnpIS:

Genetic resources (taxonomy, germplasms/accessions, collections, passport description, primary phenotypes)

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

Phenotyping data (experimental trial on Genotype X Environment studies)

• 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:
  • Data file :  Submit_Trials_EFPA.xlsx
  • Woody Plant Ontology (to declare your variables): WoodyPlantOntology.xls (ontology tree available here )

Trait Ontology
Many traits/variables are already available in GnpIS ontologies. Search the variables you need to use in GnpIS Ontology Portal .

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

Genotyping, SNP discovery or CNV discovery
Two files must be prepared for each submission: the raw data file (genotyping or CVN calling) and a metadata file describing the experiment, the markers and the plant material.

• Raw data file: a VCF , marker x germplasm matrix or GFF3 are accepted
• Metadata files:  Submit_Genotyping_Array.xlsx for matrixes submissions OR  Submit_NGS_Variants_VCF.xlsx for VCF submissions OR CNV analysis Metadata.xlsx for CNV analysis

Genome

• Genomic Annotation: send us a GFF3 file
• Physical Map: send us a FPC file

Transposable elements
Refer to the documentation dedicated to REPETDB data submission .

Project, contact, institution and publication: Submit_Project.xlsx

Other
For any other data type, contact us .

Data federation

This ODS aims at supporting worldwide teams to build or join federations of information systems.

• If you want to join FAIDARE , see https://urgi.versailles.inrae.fr/faidare/join
• If you want to join WheatIS Data Discovery , see https://urgi.versailles.inrae.fr/wheatis/join
• If you want to join RARe data portal, see https://urgi.versailles.inrae.fr/rare/join

We invite you to contact us as soon as possible so that we can provide help and discuss the best way to go ahead.

Training and Guidelines

URGI Data and Federation team create and provide guidelines to help the Plant community with the best practices for a FAIR data management.

• Guidelines to publish datasets on Recherche Data Gouv : https://doi.org/10.15454/BWJVVG .
• Guidelines in Plant science ( https://rdmkit.elixir-europe.org/plant_sciences ):
  • Germplasm (meta)data collection and sharing
  • Phenotyping (meta)data collection and publication
  • Genotyping (meta)data collection and publication

We also create training courses and materials to disseminate the best practices for a FAIR management of phenotyping data.

You can find our training sessions and materials:

• on ELIXIR training catalog TeSS (Training eSupport System)
• on IFB moodle

If you would like us to provide customized training or support for your community on any of these topics, please  contact us .

---

As stated in our terms of use , our information systems (GnpIS, FAIDARE, WheatIS and RARe) contains personal and professional information on technical and scientific actors involved in the data. This information helps to identify and give recognition to the authors of these datasets for their scientific work.

In accordance with European regulations on the protection of personal data (European Regulation 2016/679), you have the right to access, rectify, oppose and delete any information concerning you. If you wish to exercise this right and obtain the information collected about you by providing proof of your identity, please  contact us .