Forest tree GnpIS: an information system dedicated to ... · PDF fileForest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics ... (crop ontology)

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

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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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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

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GnpIS Portal: https://urgi.versailles.inra.fr/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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DATA INTEROPERABILITY

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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

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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

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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

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DEMONSTRATION

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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

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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

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Genomic annotation to Genetic maps

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Genomic annotation to Genetic maps

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Genomic annotation to Genetic maps

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Genomic annotation to Genetic maps

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Genomic annotation to Genetic maps

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Genetic maps to Phenotypes

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Genetic maps to Phenotypes

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Genetic maps to Phenotypes

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Genetic maps to Phenotypes

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Genetic maps to Phenotypes

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Genetic maps to Phenotypes

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Genetic maps to Phenotypes

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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Phenotypes to Genetic resources

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CONCLUSION

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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

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Conclusion & Perspectives New developments

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• Geolocation tool • Data flow improvement

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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

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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

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