1. Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability
C. Pommier, E.Dzalé Yeumo Kabore, E. Arnaud, P. Larmande, M. Alaux, H. Quesneville

2. International research partnership for wheat improvement
Created in 2011
G20 Agriculture Ministries
Improve food security
International framework
collaborations
wheat improvement
The Wheat Initiative members
Countries: Argentina, Australia, Brazil, Canada, China, France, Germany, Hungary, India, Ireland, Italy, Japan, Spain, Turkey, UK, USA
International organizations: CIMMYT, ICARDA
Private companies: Arvalis, Bayer CropScience, Florimond Desprez V&F, KWS UK, Limagrain, Monsanto Company, RAGT 2n Saateen Union Research, Syngenta Crop Protection

3. Wheat Data Interoperability Group WDI
Wheat related data interoperability improvement
Building a common interoperability framework (metadata, data formats and vocabularies)
Providing guidelines for describing, representing, sharing and linking Wheat related data
Contributors
Sponsors
Active members: Alaux Michael (INRA, France), Aubin Sophie (INRA, France), Arnaud Elizabeth (Bioversity, France), Baumann Ute (Adelaide Uni, Australia), Buche Patrice (INRA, France), Cooper Laurel (Planteome, USA), Fulss Richard (CIMMYT, Mexico), Hologne Odile (INRA, France), Laporte Marie-Angélique (Bioversity, France), Larmand Pierre (IRD, France), Letellier Thomas (INRA, France), Lucas Hélène (INRA, France), Pommier Cyril (INRA, France), Protonotarios Vassilis (Agro-Know, Greece), Quesneville Hadi (INRA, France), Shrestha Rosemary (INRA, France), Subirats Imma (FAO of the United Nations, Italy), Aravind Venkatesan (IBC, France), Whan Alex (CSIRO, Australia)
Co-chairs: Esther Dzalé Yeumo Kaboré (INRA, France), Richard Allan Fulss (CIMMYT, Mexico)

4. WDI Methodology Surveys Workshops Implementation
Landscape of Wheat related standards and their use by the community
Comprehensive overview of Wheat related ontologies and vocabularies
Workshops
Recommendations
Mappings between different data formats
Actions to conduct in order to improve the current level of Wheat related data interoperability
Interoperability use cases
Implementation
Interactive cookbook: recommendations + guidelines
A repository of Wheat related linked vocabularies (Bioportal)

5. WDI Guidelines: wheatis.org

6. The deliverables

7. Scope Metadata Ontologies Tools Formats Use case
Data Types, from WheatIS/RDA survey

8. Data Sharing foundations
Metadata
Description data
Discovery data
Depends on data pivot / key ressource
Phenotyping data
Germplasm / plant material = Metadata
Genbank data
Germplasm = Data

9. Data Sharing foundations
Compatible identifiers
Objects
Plant Material
Genes
Markers
Concepts, Observations, Annotations
Ontologies
Traits / Phenotypes
Gene function
Process, transformation

10. Data Sharing foundations
Compatible formats
File format
Repository
Analysis software input and output
Open APIS
Web services

11. Genomic annotations and variations recommendations
Public and private infrastructure sharing data
Established
Data Formats : VCF, GFF3
Ontologies : Sequence Ontology, Gene Ontology
Tools
Distributed Centralized Repositories
Multiple recognised Autorithies
EBI
NCBI
dbSNP
EBI Variant Archive

12. Gene Expression and Maps
Established standard recommendations, metadata and formats
MIAME
NCBI (GEO)  
EBI Array Express +  ENA
Plant Ontology, Plant Environment Ontology, etc…
Physical Maps
FPC format
Genome browser format : GFF3

13. Germplams Plant Material identification and description
Genebanks and experimental collections
Metadata Format
Multi Crop Passport Descriptors (MCPD)
Slight Evolutions needed (Permanent UID)
Recognized
Adoption in progress
Mapping to genesys and Grin Global
Done in Eurisco ?
Open APIs
Future perspectives

14. Phenotyping Challenges
Field experiments
Controlled environment growth chambers
Big Data
Variability
Heterogenous
Volume
LIDAR, Imaging  PetaBytes
Localised Velocity
Phenomobile, Automated greenhouse, field sensors
Data files + metadata (germplasm, variables)
Emerging Standards

15. Phenotyping WDI solutions
Pivot Object, Key resources identification
Germplasm : MCPD
Trait, Phenotype, Environment Variables: Ontologies
Ontologies
Observation Variable = Trait + Method + unit/scale
Formalized by Crop Ontology
Observation Variables Ontologies
Crop Ontology
INRA Ontologies
Environment Ontologies
XEO to be improved and promoted
Soil ?

16. Ontologie Repositories Crop Ontology / GnpIS
Crop Ontology and GnpIS websites
Dedicated to biologists
Excel Input

17. Crop Ontology / GnpIS widget for portal and search form
Open source :
Example :

18. Ontologie Repositories Agroportal
LIRMM, Montpellier (Clement Jonquet)
Bioportal Instance
Expert tools and interfaces
Ontologies versionning in owl/OBO
Confidentiality
Rich Ontology metadata
Triple stores
API
Breeding API ?

19. Phenotyping data sharing WDI solutions
Metadata
MIAPPE (Transplant + EPPN)
Improvements by a wider audience
File format
ISA Tab Standard for Phenotyping
Investigation/Study/Assay
Zip Archive
Raw data
Elaborated data

20. Data sharing WDI solutions
Open APIs
Breeding API:
Rest Web Services
Json
Easy implementation and integration
Semantic Web data sharing and exploring
AgroLD

21. Data sharing WDI, some tools
Repository data discovery : GnpIS
Faceted search engine
Distributed (Transplant/ EBI)

22. Data sharing WDI, some tools
GnpIS dataset building
Search Criterion Selection

23. Data sharing WDI, some tools
GnpIS dataset building
Result visualisation
Data and Metadata download

24. Data sharing WDI, some tools
Agronomic Linked Data (AgroLD,
RDF/ Triple Store
Explore Data
Graph navigation

25. WDI Perspectives and proposals
Species
Carry on Wheat
Extend to Cereals ( e.g rice, sorghum, maize, millet, …)
Guidelines dissemination (Workshop, trainings, etc…)
Recommended data sharing repositories
Workspace
Dataset publications (metadata, description, DOI)
Recommended Permanent UID providers
datacite, identifiers.org, agora, institutes (INRA) ?
WG pour les besoins de ce slide ?

26. Aknowledgements