Enhancing the implementation of the Breeding API standard in ELIXIR and semantifying it

As an emerging standard, within the ELIXIR Plant science community, the Plant Breeding API (BrAPI, https://brapi.org) plays a central role in facilitating the exchange of data between plant datasets hosted in different ELIXIR Nodes. The objectives of the project was to integrate Italian and Portuguese ELIXIR Nodes in the development of BrAPI, and facilitate BrAPI's global adoption.

The project transferred existing tools and knowledge to ELIXIR Italy and implemented another BrAPI endpoint maintained by ELIXIR Italy. In addition, the project also disseminated several tools which consume information from BrAPI enabled endpoints to the wider research community in ELIXIR Nodes and the ELIXIR Plant science Community.

To encourage the adoption of BrAPI standard, the project also increased semantic interoperability and machine understandability of BrAPI data by (1) defining a formal vocabulary for properties exposed by BrAP and providing mappings to accepted ontologies, (2) enabling automatic validation via ISA-tools, and (3) adding the appropriate semantics.

The activities in the project were carried out through workshops and open seminars:

  • Distributed Plant Phenotyping data integration: Open seminar by Cyril Pommier (December 2017) given in ELIXIR Netherlands.
  • Two Workshops (December 2017 and April 2018) in Wageningen, The Netherlands, and in Oeiras, Portugal.
  • Latest Developments in the FAIR Data ecosystem: Open seminar by Richard Finkers (April 2018) given in ELIXIR Portugal

Outcomes

  • Significant progress towards the alignment of MIAPPE, BrAPI and ISA and the establishment of a formal and standardized controlled vocabulary for BrAPI
  • A JSON-LD context file, adding semantics to BrAPI (in collaboration with the RDA project RDFENO)
  • Acquisition of critical expertise on BrAPI by the Portuguese and Italian ELIXIR Nodes
  • Implementation of BrAPI by ELIXIR Italy.
  • Training in ontology development between ELIXIR Portugal and Netherlands and the establishment of long-term collaboration in this field between the participating ELIXIR Nodes.

Duration: 

1 October 2017 to 17 April 2018

Nodes involved: