Plant Sciences Use Case

The need to cope with population growth and climate change adaptation is a major challenge. We can help address this challenge by publishing genomic and phenomic data as well as integrating this data for analysis. 

Sequencing of the DNA and RNA of crop and forest plants, as well as their pathogens and pests, has generated enormous quantities of data. Much of this data is found in well established repositories and data resources. However, large-scale automated phenotyping is now possible under controlled and field conditions, and there is a lot of classical phenotyping data available outside these resources, in literature and in dispersed databases. This 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.

For this purpose, the Plant Community has collaborated with the European plant phenotyping infrastructure Emphasis and Bioversity of the CGIAR to develop data standards. The most important standards are MIAPPE, which provides a minimum information standard for plant phenotyping, the Crop Ontology, a common framework for describing phenotyping variables, and the Breeding API.

These standards were initiated by the CGIAR community to provide a way to build interoperability among information systems and tools. They provide the foundation of a European, and potentially international, data repositories federation dedicated to plants, which will ultimately allow the exploration of 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. This federation grows following the WheatIS model, and it is therefore easy to join it (Find out more).

Collaboration with EMPHASIS

The Use Case has just published a report with EMPHASIS to clarify the strategies and roles of ELIXIR and EMPHASIS in managing plant phenotyping data across Europe, and to identify opportunities for working together. The report was based on a workshop held on 15 May 2018.

» Read the EMPHASIS and ELIXIR report

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

Cyril Pommier
Cyril Pommier
(ELIXIR France)
Celia Miguel
Celia Miguel
(ELIXIR Portugal)
John Hancock
John Hancock
(ELIXIR Services and Communities Coordinator, ELIXIR Hub)

Find out more