Agricultural Ontologies in Use: the Breeding API Project

The Ontologies Community of Practice is engaged in the development of ontologies for agricultural research. In a series of blog posts, we’ll take a look at ongoing ontologies projects and developments.

The Breeding API (BrAPI) specifies a standard interface for plant phenotype/genotype databases to serve their data to crop breeding applications. It is a shared, open API, which can be used by all data providers and data consumers who wish to participate. The Crop Ontology server is BrAPI compliant, and the two communities have been successfully collaborating for many years.

Release of Version 1.3 and Progress on Version 2.0

Over the past year, the BrAPI project has made significant progress. Looking at development of the specification, the latest stable release is Version 1.3, and work has begun on Version 2.0.

Version 1.3 introduced the move to fully adopt OpenAPI 3 as the documentation standard, along with a new set of documentation hosted on SwggerHub. The version was assessed by the BrAPI community during the last community hackathon, and it contains the basic models and methods for controlling phenotypic data in a variety of use cases, as well as a new paradigm for search queries and a variety of smaller bug fixes.

Version 2.0 will expand on that basic functionality and include a rewrite of the genotyping specification.

Community Hackathons

There have been two successful BrAPI community hackathons in the past year. The first was hosted at the International Maize and Wheat Improvement Center (CIMMYT) in Texcoco, Mexico, and the second was hosted by Wageningen University and Research in Wageningen, Netherlands.

Participants at the BrAPI community hackathon held in Texcoco, Mexico.

 

Participants at the BrAPI community hackathon held in Wageningen, Netherlands.

The hackathons have grown in productivity and popularity. At the most recent hackathon, about one third of attendees were new to the community, and everyone was able to show progress from the week of hacking.

The Automated Sample Submission Project

A focused group within the BrAPI community has been working hard over the past year on the Automated Sample Submission project. The project is an effort to automate the process of submitting samples to a genotyping vendor and obtaining the resulting data.

Currently this process is slow and prone to human error, but with BrAPI, we were able to show that the data flow process can be automated and passed electronically via API. Although there is still work to be done on this project before it is ready for production, several groups have already begun implementing their own versions of this automated data flow.

Publication of a Paper

Last but not least, in May 2019, the BrAPI community manuscript was accepted for publishing in Bioinformatics. The manuscript was a long time coming and a lot of effort by members of the BrAPI community. We are proud to see it accepted.

For more detailed updates from the BrAPI community, visit the “News” section on our website.

August 27, 2019

Peter Selby

BrAPI Coordinator
Cornell University
Ithaca New York
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