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Forest tree GnpIS: an information system dedicated to forest tree
genetics, genomics and phenomics
Célia Michotey
Genomics and Forest Tree Genetics - IUFRO 30 May – 03 June 2016, Arcachon
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Célia Michotey / Forest tree GnpIS
03/06/2016
Context
• Needs • manage forest tree data
• share this knowledge in a lasting way
Many tools developed
• Challenges • Data dispersed and inconsistent
• Lack of visibility
• Difficulty to maintain tools
Interest to set up a central tool
• Opportunities • make datasets interoperable
• enhance data reuse and enrichment
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Célia Michotey / Forest tree GnpIS
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Genomic
Genetic
Phenomic
• Annotation
• Transcriptome
• Polymorphism
• Genetic maps
• Genetic markers
• Genetic resources
• GxE
• QTL maps
• GWAS
GnpIS Information System (IS) for plants and crop parasites
Célia Michotey / Forest tree GnpIS
03/06/2016
GnpIS Portal: https://urgi.versailles.inra.fr/gnpis
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Célia Michotey / Forest tree GnpIS
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GnpIS Information System (IS) for plants and crop parasites
• National, European and International partnerships • Projects
Ex: ANR GenOak
Ex: EU H2020 GenTree
• Networks Ex: INRA PlantaComp
Ex: EU H2020 Elixir
• Evolution • Perpetual developments
• Projects and users feedbacks
• References • Publication : GnpIS: an information system to integrate genetic and genomic
data from plants and fungi. D. Steinbach et al., Database Journal 2013
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Célia Michotey / Forest tree GnpIS
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Data flow between IS
• Benefits • unique entry point
• ensure interoperability
• ensure data quality and consistency
• facilitate data integration
GnpIS
National IS
Inter-national
IS
Local
IS 2
Local
IS 1
Célia Michotey / Forest tree GnpIS
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Data flow between IS
Automated flow
Set up
To set up
National portals International networks
GnpIS Institutional IS
Local databases
Vénik PlantaExp (+ BaseNancy)
Pl@ntNet
SAMPLE, Echantillons
Files
Célia Michotey / Forest tree GnpIS
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Standards for interoperability
• Key scientific objects • Accession
• Marker
• Trait
• Need terms definitions • Accession ?
• Variable ?
• Need standards • Data formats
• Ontology
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Genomic
Genetic
Phenomic
Célia Michotey / Forest tree GnpIS
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Genomic annotation to Genetic maps
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https://urgi.versailles.inra.fr/jbrowse/gmod_jbrowse/?data=myData%2FForestTrees%2FPoplar&loc=Chr07%3A6491961..6501870
Célia Michotey / Forest tree GnpIS
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Genomic annotation to Genetic maps
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https://urgi.versailles.inra.fr/jbrowse/gmod_jbrowse/?data=myData%2FForestTrees%2FPoplar&loc=Chr07%3A6491961..6501870
Célia Michotey / Forest tree GnpIS
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Conclusion & Perspectives Data in GnpIS
• Available • Oak
• Poplar
• Pine
• Spruce
• Willow
• To integrate • Ash
• Douglas fir
• French Common Garden
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https://urgi.versailles.inra.fr/Species/ Forest-trees/Database-overview
Célia Michotey / Forest tree GnpIS
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Conclusion & Perspectives New developments
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• Geolocation tool • Data flow improvement
Célia Michotey / Forest tree GnpIS
03/06/2016
Conclusion & Perspectives Ontology
• Available • “Tree trait ontology”
(in house)
• In progress • “woody plant ontology”
(crop ontology) http://www.cropontology.org/
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https://urgi.versailles.inra.fr/ephesis/ephesis/ontologyportal.do
Célia Michotey / Forest tree GnpIS
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Acknowledgments
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Christel Anger
« Information System and Data Integration » Team
Nicolas Francillonne Joëlle Amselem
Anne-Françoise Adam-Blondon Hadi Quesneville
François Ehrenmann Christophe Plomion
URFM Christian Pichot
Catherine Bastien Véronique Jorge
Odile Rogier
GenOak