Plant Sciences Use Case

Sequencing of the DNA and RNA of crop and forest plants, as well as their pathogens and pests, has generated enormous quantities of data. Also, large-scale automated phenotyping is now possible under controlled and field conditions. However, phenotypic data is heterogeneous, described in diverse ways, and difficult to find and re-use.

The Plant Sciences Use Case aims to establish a technical infrastructure and associated social practices to allow plant genotype-phenotype analysis based on the widest available public datasets. By making data interoperable, in accordance with the FAIR principles, plant genotypic and phenotypic data will be easier to find, integrate and analyse.

The Use Case will create a search engine that will allow you to explore plant omics datasets held around Europe. You will then be able to retrieve the data you are interested in or transfer it to an ELIXIR cloud resource where you can store and analyse it.

What the Use Case does

Defines and implements standards for representing phenotypic data and metadata

  • Works with the crop and forest tree research communities to develop, improve or adopt adequate standards.
  • Develops standards for the representation of data and metadata from phenotypic experiments. The Use Case has proposed an extension of the Minimal Information about Plant Phenotyping Experiments (MIAPPE) v1.0 specification. This extension is now out for wider community consultation, and the Use Case is continuing to work on the model.
  • Developed new ontologies to address gaps in existing vocabularies e.g. Woody Plant Ontology, Plant Phenotype Experiment Ontology (PPEO).

Annotates and submits key exemplar datasets

Develops mechanisms for phenotypic/genotypic data access and retrieval

  • The Use Case is currently implementing MIAPPE in a web service using the Breeding API (BrAPI), that will connect participating repositories.

Disseminates best practice and supporting tools

  • The Use Case disseminates best practice to national projects and researchers through workshops and events.
  • Past events have included:
    • Co-organization of PhenoHarmoIS - Semantics for Harmonization and Integration of Phenotypic and Agronomic Data, a community workshop held to agree common ontologies, 9-13 May 2016, Montpellier, France.
    • ELIXIR BrAPI BYOD Hackathon, 30 May-1 June 2017, Ghent, Belgium.

Leadership

Paul Kersey
Paul Kersey
(EMBL-EBI)
Celia Miguel
Celia Miguel
(ELIXIR Portugal)

Find out more