# Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA

Sophie Durand, Windpouire Esther Dzale Yeumo, Cyril Pommier, Michael Alaux, Guillaume Cornut, Raphaël Flores, Erik Kimmel, Thomas Letellier, Célia Michotey, Nacer Mohellibi, et al.

► To cite this version:

Sophie Durand, Windpouire Esther Dzale Yeumo, Cyril Pommier, Michael Alaux, Guillaume Cornut, et al.. Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA. 4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides. hal-02791168

HAL Id: hal-02791168

https://hal.inrae.fr/hal-02791168

Submitted on 5 Jun 2020

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INRA
SCIENCE & IMPACT

# Findable, Accessible, Interoperable and
Reusable data linked to genetic resources for
plant biology and breeding

Anne-Françoise Adam-Blondon
Sophie Durand

Unit of Research in Genomic-Info (URGI), INRA

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# Aknowledgements

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URGI team

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Coord P. Kersey
EMBL-EBI (GB)

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BrAPI

Bill & Melinda Gtaes
foundation; CassavaBase;
T3; IBP; JHI; Bioversity;
CIRAD; IRRI; GOBII;
Wageningen; CIP; DaRT;
Cornell; iPlant

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Bioversity
International

Elisabeth Arnaud

Wheat Initiative

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Esther Dzalé Kaboré
Odile Hologne

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RESEARCH DATA ALLIANCE

WheatIS Expert Working
Group

Mario Caccamo
Dave Edwards
Gerard Lazo...

H. Quesneville M. Loaec
C. Pommier C. Guerche
M. Alaux F. Philippe
R. Flores T. Letellier
E. Kimmel C. Michotey
G. Cornut N. Mohellibi

## Financial supports

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INRA

SCIENCE & IMPACT

ANR

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RESEARCH DATA ALLIANCE

BILL & MELINDA
GATES foundation

TransPLANT funded by EC FP7 Infrastructures, contract n° 283496.
ELIXIR-EXCELERATE funded by EC H2020, contract n° 676559.
ARCAD-FEDER is funded by EC FEDER

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INRA
Context
# Plant Genetic resources managed by the Plant Biology and Breeding division of INRA

Priority to biological resources connected to research activities at INRA

## Genomic resources

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307 libraries for 65 plant species

## Model species

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75,100 accessions

## Crops and forage

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55,938 accessions

## Vegetables

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## Fruit species and rose

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## Conservation of :

- Patrimonial resources

- Resources related to specific research projects

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37,796 accessions

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28,752 accessions
Managed by a network of 15 Biological Resource Centers

* Better share and use resources while Accumulating useful information about it

• Sustain their maintenance

* Professionalize their management and their exchange with regard to international legal and sanitary rules

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INRA's catalogs and Information systems

* Genomic resources: http://cnrgv.toulouse.inra.fr/fr

- Genetic ressources: https://urgi.versailles.inra.fr/siregal/siregal/grc.do

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# INRA's BRC catalog is included in the GnpIS information system for plant genetics and genomics

https://urgi.versailles.inra.fr/gnpis/

Steinbach et al. 2013, Database, doi:10.1093/database/bat058

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# GnPIS has to be interoperable with the information systems of an « ecosystem » of networks on PGRs and related data

## French Networks

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Ministère de l'agriculture, de l'agroalimentaire et de la forêt

MINISTÈRE
DE L'AGRICULTURE
DE L'AGROALIMENTAIRE
ET DE LA FORêt

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GEVES

Expertise & Performance

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FRB

FONDATION
POUR LA RECHERCHE
SUR LA BIODIVERSITE

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AgroBRC

## Global Networks

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FAO

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Traité International

SUR LES RÉSOURCES PHYTOGENÉTIQUES
POUR L'ALIMENTATION ET L'AGRICULTURE

Genesys
DivSeek.org

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GBIF

## European Networks

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European
Cooperative
Programme for Plant
Genetic
Resources

ECP/GR

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eurisco

Finding seeds for the future

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EMBL-EBI

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## International exchange data standards

BrAPI

Web
services

doi®

PUID

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Crop Ontology

for agricultural data

Controled
vocabulary

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Biology
International

MCPD

Minimal Info

elixir

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isatools

Data format
# FAIR principles and guidelines

Wilkinson et al., 2016, The FAIR Guiding Principles for scientific data management and stewardship. DOI: 10.1038/sdata.2016.18

**Facilitate knowledge discovery** for humans and machines in their **discovery** of, **access** to, **integration** and **analysis** of, scientific data.

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**Findable** – Easy to find by both humans and computer systems and based on mandatory description of the metadata that allow the discovery of interesting datasets

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**Accessible** – Stored for long term such that they can be easily accessed and/or downloaded with well-defined license and access conditions, whether at the level of metadata, or at the level of the actual data content

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**Interoperable** – Ready to be combined with other datasets by humans as well as computer systems

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**Reusable** – Ready to be used for future research and to be processed further using computational methods
Achievements
# Working on standards with the international research community

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Alignment of the specifications of the **BioSample EMBL** database with the **MCPD standard** for the **identification of the plant material** used in genomic experiments

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Wheat Initiative

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transPLANT

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EPPN

Community recommendations for data standardisation: [wheatis.org](http://wheatis.org)

Data standard for phenotyping experiment [www.miappe.org](http://www.miappe.org)

Crop specific ontologies (e.g. Vitis, Woody Trees) : [www.cropontology.org](http://www.cropontology.org)

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DOI assigned to all genetic resources according to the FAO standard

DOI assigned to some phenotyping experiment datasets (e.g Wheat phenotyping DOI:10.15454/1.4489666216568333E12)

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INRA
SCIENCE & IMPACT
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## Data interoperability/integration: identification of key objects

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### Challenges:

* Demonstrations of knowledge gain through data integration

* Key object for connecting with other disciplinary data (GPS, variety, ...)
# Integration of GnPLS with other international data portals for plant biology and genetics

## 1- Exchange of standardized information (data interoperability)

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# Integration of GnpIS with other international data portals for plant biology and genetics

## 1- Standardized protocols for the exchange of standardized data (machine interoperability)

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# FAIR assessment of GnpIS

★ FAIR indicators calculated on the best dataset in each thematic

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Conclusions
Making data FAIR is a lot about community management (within and between):

- Developpers

- Specialists of ontologies and standards

- Data managers

- Biologists (data producers)

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(Global)

Infrastructure

projects

Crop
projects

Need for identification and long term maintainance of:

- Searchable central repositories of standards and ontologies for agriculture (e.g. agroportal.lirmm.fr, biosharing.org)

- FAIR tools for data managers/developers for automatic formatting or format validation (BioSchemas, ...)
Thank you!