Data Services

Scope of the Service

We provide guidelines to disseminate the best practices for a FAIR data management:

• To publish datasets on Recherche Data Gouv : https://doi.org/10.15454/BWJVVG .
• For 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 support a FAIR data management, particularly for phenotyping data, and to provide guidance on the tools we developed. We already propose the following training courses, but we can customize them:

MIAPPE, Minimum Information About Plant Phenotyping Experiments (MIAPPE)

Description: The Minimal Information About Plant Phenotyping Experiments (MIAPPE, www.miappe.org) standard has been designed by ELIXIR, EMPHASIS and Bioversity international to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking between phenotype and genotype datasets, relevant section of MIAPPE are beginning to be used for genotyping standards.
This formation will cover a general introduction of the MIAPPE principles and some examples to illustrate different use cases on the usage of MIAPPE for plant phenotyping data standardization.

Topics: topic_3572 : Data quality management, topic_0219 : Data curation and archival, topic_3298 : Phenomics, topic_0780 : Plant biology, topic_0625 : Genotype and phenotype

Learning outcomes:

Prerequisites: none

Contacts: Cyril Pommier, Célia Michotey

Training Materials: Plant Data Managment for Phenotyping Experiments - MIAPPE https://hal.inrae.fr/hal-03102944

Events: Training Workshop on Phenotyping Data Management - 2020 MIAPPE 2020 (2020-02-12 to 2020-02-13), Webinar on Plant Data Management - 2020 MIAPPE 2020 (2020-12-17 to 2020-12-17), Webinar on Plant Data Management - 2021 MIAPPE 2020 (2021-04-02 to 2021-04-02), Training Plant Data Management  - 2021 MIAPPE 2021 (2021-09-23 to 2021-09-23)

Gestion des données d’expériences de phénotypage de plantes : standards et cas d’utilisation (FAIR Data Pheno)

Description: Cette formation donnera un aperçu des pratiques et méthodes actuelles pour la standardisation des données de phénotypage des plantes, et ce de manière de traiter la variabilité et l'hétérogénéité inhérentes aux jeux de données de recherche et de sélection.
Le but de cette formation est double : 1) diffuser les bonnes pratiques pour une gestion FAIR des données de phénotypage de plantes, 2) consolider une formation modulaire adaptée à un maximum de besoins, du débutant qui souhaite partager des données standardisées dans Recherche Data Gouv, à l'utilisateur avancé qui souhaite faire de la sémantique ou utiliser des portails de données fédérés. La formation se déroulera avec une alternance de présentations générales et techniques et d'ateliers pratiques.

Topics: topic_3572 : Data quality management, topic_0219 : Data curation and archival, topic_0780 : Plant biology, topic_3571 : Data governance, topic_0625 : Genotype and phenotype

Learning outcomes: A l'issue de cette formation, les participants auront acquis des connaissances théoriques et pratiques sur :
* la gestion des données de phénotypage des plantes selon les principes FAIR
* l'utilisation des standards de (méta)données des communautés végétales
* la standardisation d'un jeu de données au format MIAPPE
* l'identification des moyens à mettre en oeuvre pour améliorer la gestion de leurs données

Prerequisites: none

Contacts: Célia Michotey, Cyril Pommier

Training Materials:

Events: Gestion de données de phénotypage de plantes - 2023 FAIR Data Pheno 2023 (2023-06-15 to 2023-06-16), No event

Soumission de données et métadonnées à EMBL-EBI (FAIR Data Geno)

Description: Processus et outils mis en place dans le cadre des projets AgroDiv et BReIF pour soumettre des données dans les archives EMBL-EBI associées à des descriptions riches des échantillons séquencés dans BioSamples.

Topics: topic_3366 : Data integration and warehousing, topic_0219 : Data curation and archival, topic_0780 : Plant biology, topic_0091 : Bioinformatics, topic_0625 : Genotype and phenotype

Learning outcomes:

Prerequisites: none

Contacts: Vanita Haurheeram, Anne-Françoise Adam-Blondon

Training Materials: Data-brokering script https://forgemia.inra.fr/urgi-is/data-brokering

Events: Soumission de données et métadonnées à EMBL-EBI - 2024 FAIR Data Geno 2024 (2024-05-22 to 2024-05-22), Soumission de données et métadonnées à BioSample et ENA - 2025 FAIR Data EBI 2025 (2025-11-06 to 2025-11-06)

WheatIS data discovery (WheatIS Search)

Description: The WheatIS project aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools. The project is endorsed by the Wheat Initiative.
The WheatIS data discovery tool allows to search data in all the wheat resources around the world.
This training will describe how to use the tool, what data are available, how to join, etc.

Topics: topic_3489 : Database management, topic_3366 : Data integration and warehousing, topic_0780 : Plant biology, topic_0091 : Bioinformatics, topic_0625 : Genotype and phenotype

Learning outcomes:

Prerequisites:

Contacts: Michael Alaux, Raphaël Flores

Training Materials:

Events: WheatIS data discovery - 2020 WheatIS Search 2020 (2020-02-25 to 2020-02-25), WheatIS data discovery - AgBioData WheatIS Search AgBioData (2020-10-07 to 2020-10-07)

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

Criteria of eligibility and Rates

This service is free of charge and open to anyone from the plant community.

Subscription terms

Contact urgi-contact@inrae.fr with the subject line “[ODS_URGI_Training] Project_acronym.” If your need is part of an ongoing funded project in which URGI is a partner, you can get in touch with your usual contact directly.

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 to it.