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 Community 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).
2019 AGM Report
The Community has met during the 2019 ELIXIR All Hands in Lisbon. The report of the discussions is publicly available and gives an overview of the most up to date activities and objectives of the community.
Collaboration with EMPHASIS
The Community has 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.
Goals of the Community
To define and implement 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 Community has collaborated with Emphasis and the international community to publish the Minimal Information about Plant Phenotyping Experiments (MIAPPE) v1.1 specification. The MIAPPE description is available both as pdf and xls format.
- Developed new ontologies to address gaps in existing vocabularies e.g. Woody Plant Ontology, Plant Phenotype Experiment Ontology (PPEO).
To develop database federations and web portals for phenotypic, genotypic or generic data discovery
- The Community is elaborating on the results from the wheatis and transplant to propose a generic data discovery federations. It will be available for any database soon. Contact us to join, see below for contact informations.
- The Community is currently implementing MIAPPE in a web service using the Breeding API (BrAPI), that will connect participating repositories. It will be accessible through a web portal publicly available in early 2019. Contact us to join or directly propose a configuration in the indexing tool.
To annotate and submit key exemplar datasets
- The Community submits datasets to relevant public archives according to defined standards. This includes data from the following species:
To disseminate best practice and supporting tools
- The Community disseminates best practice to national projects and researchers through workshops and events.
- Past events have included:
The Plant Community has been involved in a number of short-term, technical projects called Commissioned Services. The current projects it is involved in are:
- FONDUE - FAIR-ification of Plant Genotyping Data and its linking to Phenotyping using ELIXIR Platforms
For completed projects the Community has been involved in see the Commissioned Services page.
Find out more
- Contact the plant community list (plant-community [at] elixir-europe.org) to learn how you can get involved.
- Contact Cyril Pommier (cyril.pommier [at] inra.fr).