As public sector breeding has modernized, it has become a more data intensive enterprise. Numerous applications and databases have been created for a wide variety of tasks from collecting field observations to analyzing genetics. However, this data still has to be manually passed and translated from one system to another. As a result, breeders have less time to unleash the power of data to develop better varieties.
The Breeding API (BrAPI) project is solving this issue by developing an open data standard and automated sharing protocols to connect the landscape of software tools available to breeders. The project mobilizes a global community of software developers, with a Cornell University-based coordinator funded by EiB.
Peter Selby presents the BrAPI Project, in a webinar recorded for the EIB Virtual Meeting 2020.
"BrAPI provides a common language that all breeding applications can speak when transferring information," said Peter Selby, BrAPI project coordinator. "This means that we can share data between many types of applications to solve many different use cases."
For example, when the University of Queensland assessed breeding programs at the Ethiopian Institute of Agricultural Research (EIAR), they found that inventory management was a key area for improvement. Through BrAPI, they were able to easily connect one of their own inventory management tools to the existing EIAR breeding data management system.
Selby gave an overview of the key use cases enabled so far at CGIAR Excellence in Breeding’s Virtual meeting 2020. It is now possible to download a database of field layouts and traits of interest into mobile apps that allow field researchers to quickly collect crop phenotype data, and then upload their observations back into the system. Popular genotype databases are integrated with tools to manage the process of sending new samples to outside genotyping laboratories, with the laboratory results being automatically pulled back for use by the breeding program. Finally, these two databases of phenotype and genotype information can be connected to perform powerful analyses that accelerate the speed and accuracy of crop improvement.
BrAPI also creates an open platform for developers to share innovation through the development of BrAPPs, or breeding applications. The idea of BrAPPs is to create standalone tools that can be integrated with any BrAPI-compliant system, all of which are available through the BrAPI website.
Mariano Crimi (IBP) presents on the power of BrAPPS at the EiB Virtual Meeting 2020.
The Breeding Management System (BMS), developed by the Integrated Breeding Platform (IBP), offers a broad suite of breeding tools to over 675 users around the world, but lacked some important data visualization features. As the BMS is BrAPI compliant, the team was easily able to adapt BrAPPS made for this purpose by the Breedbase software team at the Boyce Thompson Institute (BTI).
Inspired by this experience, IBP applied for an EiB grant to send senior developer Nahuel Soldevilla on sabbatical to collaborate with the BTI team on a new BrAPP. The result was the BrAPI Fieldmap tool, now used by BMS users – and potentially by any BrAPI-compliant application – to draw field outlines on to satellite images and keep a database of this geographic data.
The EiB sabbatical project aims to enable cross-institution collaborations of this type, while the team was also able to advance the BrAPI standard. "The BrAPI standard has been instrumental to providing the technical bridge that different development teams needed," said Mariano Crimi, BMS project manager.
"The BrAPI community is the true heart and soul of the project," said Selby. "We gather regularly for international hackathons to develop tools and enhance the BrAPI standard." From a small group that first gathered in 2015, the community has grown to over 150 collaborators and 30 partners, uniting formerly disparate breeding software and data management efforts behind a single collaboration.
In March 2020, the project met an important milestone with the release of BrAPI version 2.0. This version connects applications for setting up breeding trials, managing genetic resources, collecting field data and performing genetic analysis, connecting crucial components of the breeding workflow.
For more information, visit: www.brapi.org.
Written by Sam Storr, Communications Consultant.