Enabling FAIR plant phenotyping data submission through the Breeding API

Over the past four years, the ELIXIR Plant Sciences Community has been making large strides towards enabling FAIR plant phenotyping data: the ELIXIR plant data search service FAIDARE (https://urgi.versailles.inra.fr/faidare/) addresses findability by integrating the various BrAPI (https://brapi.org) end-points of ELIXIR Nodes, which address accessibility and ensure compliance with the MIAPPE metadata standard (https://www.miappe.org/) and therefore interoperability. Combined, these resources represent a fully FAIR-compliant data management framework. However, there is one final critical hurdle impeding its broad adoption by plant scientists: there is no standardized user-friendly way to submit a dataset to a BrAPI end-point (or more precisely the database underlying it).

The goal of this project is to develop a web interface for MIAPPE-compliant data submission that can be deployed by any plant phenotyping database. This interface will be modular, including an interactive web form for metadata entry mirroring the organization of MIAPPE, web services for key functionalities such as ontology lookup and validation of MIAPPE compliance, and modules for database entry that upload the data to a database. For the latter, we will develop a module that makes use of BrAPI PUT calls to upload data directly through a BrAPI endpoint, but also a module for uploading the data through FAIRDOM’s SEEK platform, which is already being deployed by some partners.

The project is expected to substantially benefit the sustainability and increase the adoption of the data management framework put together by the ELIXIR Plant Sciences Community, which includes key ELIXIR services such as FAIDARE. Furthermore, the project will both build capacity and increase collaboration between ELIXIR Nodes on data management, and enhance interactions between Node experts contributing to the Plant Sciences Community.


1 November 2019 to 30 April 2020

Nodes involved: 


People involved: 

Daniel Faria
Célia Miguel
Bruno Costa
Marta Silva
Richard Finkers
Evangelia Papoutsoglou
Cyril Pommier
Frederik Coppens
Bert Droesbeke