Enhancing the implementation of the plant Breeding API standard within ELIXIR

The ELIXIR Staff Exchange project ‘Enhancing the implementation of the Breeding API standard in ELIXIR and semantifying it’ has been completed.

“The plant breeding API (BrAPI) is a global effort to enable interoperability among plant breeding databases. BrAPI is also used to achieve interoperability of plant datasets between ELIXIR nodes,” says Dr Richard Finkers. He is a scientist in the Wageningen UR Plant Breeding group and the coordinator of ELIXIR’s plant use case in the Netherlands. Finkers: “In a June 2017 BrAPI workshop, BrAPI was aligned with the metadata standard adopted by ELIXIR’s plant use case. This is the Minimal Information About Plant Phenotyping Experiment (MIAPPE). BrAPI can now be considered an implementation of MIAPPE.”

Involving Italy
The plant-oriented partners of the ELIXIR-Excelerate project are all implementing BrAPI endpoints to expose phenotypic data following the MIAPPE standard. However, the Italian node is not involved in the Excelerate project because Italy previously was not a member of ELIXIR. Therefore, the first objective of the Staff Exchange project was to transfer the tools and knowledge to the Italian node in order to

  • implement another European BrAPI endpoint,
  • include Italy in the community involved in BrAPI and MIAPPE developments.

Finkers: “In addition, several tools have been developed by third parties, which are able to consume information from BrAPI-enabled endpoints. We have disseminated this information to the ELIXIR plant community.”

Improving BrAPI
The second objective of the project was to improve BrAPI and facilitate the global adoption of the standard. To this end, several actions were taken:

  • define a formal vocabulary for properties exposed by BrAPI, to disambiguate meaning and, where possible, provide mappings to accepted ontologies,
  • define the proper semantic type of each property, to enable automatic validation via tools such as ISA-tools,
  • add the semantics defined above to BrAPI, by defining the appropriate JSON-LD context.

Finkers: “These actions have led to an improved description of BrAPI, for both humans and machines. The improved semantics will also lead to clearer specifications, facilitating the adoption of BrAPI by third parties, and further establishing it as the standard to make plant breeding data interoperable.”

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