Breeding programs aim to deliver improved lines or cultivars, the most fundamental input for farming, and are thus foundational for maintaining a productive agricultural system amidst the pressing challenges of climate change. Breeding efforts are time- and resource-intensive, with progress dependent on efficient program logistics and accurate selection decisions. While breeding programs can benefit from modern and emerging breeding techniques like genomic selection, machine learning, and high throughput phenotyping, the successful implementation of these methods depends on the ability to efficiently collect, manage, and analyze large volumes of carefully curated genomic and phenomic data [@doi:10.1007/978-3-030-41866-3_4]. Extracting actionable knowledge from these complex datasets is time-consuming, often prohibiting the adoption of new methods, especially by under-resourced breeding programs. To facilitate the collection, management, and analysis of these datasets, it is essential to transition to digital tools. Historically, independent applications were designed to address specific problems, but in many cases, this led to separate software solutions for each breeding program task and created data silos.
The Breeding Application Programming Interface (BrAPI) is a standardized, representational state transfer (REST), web service, application programming interface (API) specification for breeding and related agricultural data [@doi:10.1093/bioinformatics/btz190]. Since the project inception in 2014, BrAPI has become an essential part of the digital infrastructure for plant breeding, providing a domain-specific open data standard tailored to the needs of plant breeding and genetics projects. BrAPI enables interoperability between breeding software platforms, allowing groups to seamlessly share data and software tools both within and across breeding programs. It eases the merging of datasets of different types and provides access to shared trait ontologies, phenotypic data, genotypes, seed inventories, and other essential components for collaborative breeding efforts.
Since its first publication in 2019 [@doi:10.1093/bioinformatics/btz190], BrAPI has seen a significant increase in community services, compatible tools, and participating organizations. The community has organized numerous hackathons to evolve the specification, resulting in continuous improvements and enhancements. This report includes a short technical description of the standard and a showcase of the applications, services, and tools available from the BrAPI community. It is the intention of this manuscript to demonstrate the value of BrAPI to the wider scientific community as an effective and efficient means to collaborate and exchange data.
An API is a technical connection between two pieces of software. Just as a graphical user interface (GUI) or a command line interface (CLI) allows a human user to interact with a piece of software, an API allows one software application to interact with another. A REST-style (or RESTful) web service is a type of API commonly used in modern web infrastructure. REST is a technical architecture that describes the stateless transmission of data between applications. Typically, RESTful web service APIs are implemented using the standard HTTP protocol that most of the modern internet is built upon. These implementations generally use JavaScript Object Notation (JSON) to represent the data being transferred. Both HTTP and JSON are programming language agnostic, very stable, and highly flexible. This means BrAPI can be implemented in almost any piece of software and can solve a wide range of use cases.
Data repositories and service providers that are BrAPI compatible have mapped their internal data structures to the BrAPI standard models, allowing them to share data with the outside world in a standardized format. Similarly, they can accept new data from external sources and automatically map the new data to their existing database. Client application developers can take advantage of this standardization by building tools and connectors that integrate with all BrAPI-compatible data repositories. Visualization, reporting, analytics, data collection, and quality control tools can be built once and shared with other organizations that follow the standard. This type of BrAPI-compatible, easily sharable tool is often referred to as a BrAPP, meaning BrAPI Application. BrAPPs are simple tools that are entirely reliant on BrAPI for their data requirements, and often fit on a single web page. A single BrAPP can be easily shared and used by many organizations and systems, as long as those organizations have the required BrAPI endpoints available. As the number of BrAPI-compatible databases, tools, and organizations grows, so does the value of implementing the standard into any given application.
Over its lifetime, the BrAPI project has grown and changed substantially. The total size of the specification has almost quadrupled since the release of version v1.0 in 2017, increasing from 51 endpoints in v1.0 to 201 endpoints in v2.1. Because of this growth, the specification documents were reorganized into four modules: BrAPI-Core, BrAPI-Phenotyping, BrAPI-Genotyping, and BrAPI-Germplasm. Figure {@fig:domains} is a simplified domain map of the whole BrAPI data model, showing what kinds of data are defined in each module. While early versions of the specification focused on read-only phenotype data, the specification now has representation from most of the major concepts related to breeding. The newest specification has also been updated to be internally consistent, easier to navigate, and allow for read, write, and update capabilities.
{#fig:domains width="100%"}
As BrAPI has matured, so have the tools, services, and libraries that work with the specification. Each new version is released with a change log to guide developers as they upgrade, an Entity Relationship Diagram (ERD) to visually describe the data model, and a JSON Schema data model to be used for automated development efforts. For groups using Java, Java Script, Python, R, or Drupal, community-maintained libraries are available with full BrAPI implementations ready to be integrated into existing code. The BrAPI Test Server is updated to support every version of the specification for testing purposes. Finally, there are resource pages on the project website that showcase BrAPI-compatible applications and data resources available in the community.
The international BrAPI Community consists of software developers, biologists, and other scientists working on BrAPI related projects and data sources. This community sustains the BrAPI project, builds implementations, maintains development tools, and provides input to enhance the specification. As the project has grown, so too has the community. The BrAPI project started in June 2014 with less than ten people coming together to discuss the idea and has since grown to more than 200 members.
The BrAPI Hackathons are a major staple of the BrAPI community [@doi:10.1101/gr.228460.117]. Twice a year, the community gathers in person or virtually to discuss the specification and collaborate on BrAPI-related projects. These events have proven to be vital to the long-term growth of the community; for some organizations, the hackathon is the only time during the year when they can collaboratively work on BrAPI projects.