Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Adoption of the Wheat Data Interoperability Guidelines French National Research Institute (INRA) Data sharing in GnpIS

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Data Sharing foundations Metadata and Data – Description data – Discovery data – Depends on data pivot / key ressource Phenotyping data – Germplasm / plant material = Metadata Genbank data – Germplasm = Data

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Data Sharing foundations Compatible identifiers – Scientific Objects Plant Material Genes Markers – Concepts, Observations, Annotations Ontologies Traits / Phenotypes Gene function Process, transformation

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Data Sharing foundations Compatible formats – File format Repository Analysis software input and output – Open APIS Web services

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability WDI Guidelines in GnpIS

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability GnpIS Integrative information system – Plant and bioagressors – Multi thematic Genetic Genomic Phenotyping – Public and private data : partners, international consortium URGI, INRA

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability GnpIS Data discovery Faceted search engine Distributed (Transplant/ EBI)

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability GnpIS dataset building Search Criterion Selection

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability GnpIS dataset building Result visualisation Data and Metadata download

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability GnpIS adopted standards Established Standards for Genomic and Genotyping – Data Formats : VCF, GFF3 – Ontologies : Sequence Ontology, Gene Ontology Germplasms, Plant Material – Multi Crop Passport Descriptor, MCPD, FAO/Bioversity – descriptors descriptors 0. Persistent unique identifier : PUID = URI/DOI 1.Institute code 2.Accession number 5. Genus 6. Species 7. Subspecies : ‘subsp.’ (for subspecies); ‘convar.’ (for convariety); ‘var.’ (for variety); ‘f.’ (for form);‘Group’ (for ‘cultivar group’) … 28. Remarks

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Phenotyping in GnpIS INRA Experimental Network Phenome-FPPN – Infrastructure for high throughput plant phenotyping – Develop and implement new methods Sensors Data management (C. Pommier, P. Neveu) Data analysis – International collaborations (EPPN, Transplant, Australia,...)

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Phenotyping Challenges Field experiments Controlled environment growth chambers Big Data – Variability – Volume – Localised Velocity Data files + metadata (germplasm, variables)

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Phenotyping WDI solutions in GnpIS 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 ? Perspectives – RDA Europe project for model Ontology

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Ontologie Repositories Crop Ontology / GnpIS Crop Ontology and GnpIS websites Dedicated to biologists

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Ontologie Repositories Agroportal Bioportal Instance LIRMM, Montpellier (Clement Jonquet) Expert tools and interfaces – Triple stores – API Breeding API ? – …

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Phenotyping WDI solutions in GnpIS Metadata – MIAPPE (Transplant + EPPN) – ISA Tab Standard for Phenotyping Investigation/Study/Assay Zip Archive Raw data Elaborated data Distributions – Open APIs: Breeding API: – Semantic Web data sharing and exploring AgroLD

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Agronomic Linked Data (AgroLD) RDF/ Triple Store Explore Data Graph navigation

Cyril Pommier et al. / Feedback from the RDA and WheatIS recommendations for Wheat Data Interoperability Aknowledgements