igad discussion group 2: increase data access and availability
TRANSCRIPT
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Cyril Pommier, Pierre Larmande / IGAD
Goup 2 : Increase data access and availability
(formats, research objects identification, users)
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Cyril Pommier, Pierre Larmande / IGAD
Wheat Data Interoperability Group• Data sharing Guidelines
– http://wheatis.org/
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Cyril Pommier, Pierre Larmande / IGAD
Scope
• Metadata• Ontologies• Tools• Formats• Use case• Data Types, from WheatIS/RDA survey
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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
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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
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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
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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
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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 ?
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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 ?