# Developping grapevine FAIR data

Anne-Francoise Adam-Blondon

► To cite this version:

Anne-Francoise Adam-Blondon. Developping grapevine FAIR data. 27. Plant and Animal Genome Conference (PAG) 2018, Jan 2018, San Diego, CA, United States. pp.16. hal-02786779

HAL Id: hal-02786779

https://hal.inrae.fr/hal-02786779v1

Submitted on 5 Jun 2020

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Distributed under a Creative Commons CC BY 4.0 - Attribution - International License
# Developing Grapevine FAIR data

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

Anne-Françoise Adam-Blondon

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# GnpIS: INRA IS for crops, forest trees and pathogens

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GnpIS

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Phenotypes

• GxE

• QTL maps

• GWAS, GS

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Genetics

• Genetic maps

• Genetic markers

• Genetic resources

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Genome

• Annotation (TE, genes)

• Transcriptome

• SNP / Structural variant
# Main global objectives

* Be a robust and sustainable repository of FAIR data
(Findable, Accessible, Interoperable, Reusable)

* Integrate GnpIS in sustainable and robust federations of information systems because data is highly dispersed and likely to stay so

* Facilitate knowledge development and data analysis

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# Acknowledgements

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URGI team

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H. Quesneville
C. Pommier
M. Alaux

D. Charruaud

G. Cornut

S. Durand

R. Flores

N. Francillonne

C. Guerche

E. Kimmel

M. Lainé

T. Letellier

M. Loaec

C. Michotey

N. Mohellibi

F. Philippe

## Financial supports

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INRA
SCIENCE & IMPACT

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ANR

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RDA
RESEARCH DATA ALLIANCE

International
infrastructures
/initiatives
transPLANT

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Analysis and Experimentation on Ecosystems

France

AnaEE

openM1N7ED
Open Mining Infrastructure for Text & Data

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WHEAT
INITIATIVE

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BrAPI

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Bioversity
International

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Planteome

## National and international
crop projects

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Betterave2020

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Breed

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wheat

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PeaMUST

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BFF

Biomass For the Future

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WheatBI

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GENTREE

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International
Wheat Genome
Sequencing
Consortium
# Making data and Information systems FAIR has a lot to do with community management

## Within and between:

- Developers

- Specialists of ontologies and standards

- Data managers

- Biologists (data producers)

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(Global)

Infrastructure
projects

Crop/biology
focused
projects

## And clarifying what is under the responsibility of each community

Example of what is currently done to develop international federation of FAIR information systems for:

- the wheat community

- phenotyping data
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# Metadata : data about the phenotyping experiment

* MIAPPE: Minimum Information About Phenotyping Experiment

* Developed and maintained by an international community interested in plant phenotyping: large community of breeders and biologists, European infrastructure for Plant Phenotyping (EPPN/EMPHASIS), European infrastructure of Bioinformatics (ELIXIR), Planteome, Excellence in Breeding Plateform...

* www.miappe.org

* Steering committee Emphasis, Elixir CGIARs
Interoperable

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Reusable

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# Metadata : data about the phenotyping experiment

Crop Ontology

Variable=trait + method + scale

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Identification : MultiCrop

Passport Data
Standard

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Phenotype 1 = measurement on a cultivar in an environment-GPS1-time1

Phenotype 2 = measurement on a cultivar in an environment-GPS2-time2

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Genotype = observed marker's alleles on a cultivar

Climate 1 = climatic data at GPS1-time1

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MIAPPE standard aligned with
MCPD and Crop Ontology
standards

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Inspire EU directive?
# Who provides the metadata – e.g. phenotyping data at INRA

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**Data managers:** important role in facilitating flows between registries of identifiers, data set repositories and data producers
Develop a sustainable and robust
federation of plant information systems

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Data is scattered in many different information systems
# Findability: Data discovery through a common portal

Spannagl et al 2016, doi: 10.3835/plantgenome2015.06.0038

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## Challenges:

* Synchronize technical updates of the infrastructure

* Synchronize improvements of the data model

* Searching with increasingly natural language (e.g. for traits)

**Opportunity:** great tool to build a community of developers, data managers and specialist of ontologies that work together
# Federation of Plant Information systems

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# Federation(s) of plant information sytems

Development of a consistent and robust suite of open source tools based on common internationally agreed standards : one of the key elements of a sustainable federation

Durinx C, et al. Identifying ELIXIR Core Data Resources

F1000Research 2016, doi: 10.12688/f1000research.9656.1

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Conclusions

* Survey of the background in the grapevine community in the frame of the IGGP

* A-F Adam-Blondon et al. (2016) Towards an open grapevine information system. Hort Res, 3, 16056. https://doi.org/10.1038/hortres.2016.56
One implementation of a plant federation we could start playing with: https://urgi.versailles.inra.fr/ifb/

IFB

Database

☐ GRAMENE (272)

☐ GNPSI (115)

☐ TRITICEAE TOOLBOX (10)

☐ WHEAT PANGENOME (8)

☐ GRAINGENES (2)

Type

☐ GENE (259)

☐ SEQUENCE FEATURE (120)

☐ EXPERIMENT (10)

☐ INTERPRO FAMILY (7)

☐ GO PROCESS (6)

☐ PHENOTYPE (3)

☐ QTL (2)

Species

☐ TRITICUM AESTIVUM (81)

☐ BRACHYPODIUM DISTACHYON (74)

☐ TRITICUM URARTU (66)

☐ AEGILOPS TAUSCHII (62)

☐ HORDEUM VULGARE SUBSP. VULGARE (60)

☐ ARABIDOPSIS THALIANA (49)

☐ SOLANUM LYCOPERSICUM (25)

☐ VITIS VINIFERA (18)

☐ BRASSICA NAPUS (15)

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Thank you!