Cyril Pommier, Pierre Larmande / IGAD

Goup 2 : Increase data access and availability

(formats, research objects identification, users)

Cyril Pommier, Pierre Larmande / IGAD

Wheat Data Interoperability Group• Data sharing Guidelines

– http://wheatis.org/

Cyril Pommier, Pierre Larmande / IGAD

Scope

• Metadata• Ontologies• Tools• Formats• Use case• Data Types, from WheatIS/RDA survey

Cyril Pommier, Pierre Larmande / IGAD

Genomic annotations and variations

• 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

Cyril Pommier, Pierre Larmande / IGAD

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

Cyril Pommier, Pierre Larmande / IGAD

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

Cyril Pommier, Pierre Larmande / IGAD

Phenotyping

• Field experiments• Controlled environment growth chambers• Big Data

– Variability – Volume– Localised Velocity

• Data files + metadata (germplasm, variables)• Ontologies

– Observation Variables Ontologies : Crop Ontology, INRA Ontologies– Environment Ontologies

• XEO to be improved and promoted• Soil ?

• Metadata– MIAPPE (Transplant): Evolution, improvement by a wider audience– Crop Research Ontology : Implementation of MIAPPE ?

• Distributions– Open APIs: Breeding API– ISA Tab for Phenotyping

Cyril Pommier, Pierre Larmande / IGAD

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 ?

• MCPD to Include PUID/DOI for germplasms– Joint activity with Divseek, others ?– Funding needed for workshop ?

Cyril Pommier, Pierre Larmande / IGAD

Perspectives and proposals

• Environment Variables ontologies– Improve XEO Environment Ontology (Dedicated Workshop ?)– Disseminate and Adopt

• MIAPPE recommendations– Validated in Transplant, EPPN– Validate at a wider audience: US, Australia, Europe, CGIARs, …– Dedicated Workshop or Working group ?