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. But both technical and sociological progress in data definition and sharing are lagging behind data generation.

Structural variation in most crop plants is enormous (more so than in humans), and phenotypic data is often:

  • inaccessible
  • diverse and non-standard
  • lacking any unified route of access.

The Plant Sciences Use Case is harnessing the domain-specific expertise and data held across the ELIXIR Nodes that have an interest in plants and agriculture. The Use Case is establishing a technical infrastructure and associated social practices to define an open model for the publication and sharing of plant genotype-phenotype data.

The Use Case will also provide a search engine to allow users to explore plant omics datasets held around Europe, and to download data of interest to a local or cloud compute facility for analysis.

What the Use Case does

  • Designs, implements and recommends standards (minimum information, vocabularies, and  file formats) for the representation of genotypic and phenotypic data, through coordination with the crop and forest tree research communities.
  • Encourage the availability of FAIR data through the provision of a search engine and open APIs, through which any researcher can disseminate and access relevant data.
  • Annotates and submits key exemplar datasets to relevant public archives.
  • Develops re-usable modules for the visualisation of these datasets.
  • Disseminates best practice and supporting tools to national projects and researchers.

How the Use Case is organised

The work of the Plant Sciences Use Case is defined in Work Package 7 of the ELIXIR-EXCELERATE project. The Work Package is led by Paul Kersey and Celia Miguel.

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