Abstract
MotivationModern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge.ResultsTo facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases.Availability and implementationMore information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
Highlights
Plant breeding is widely recognized as crucial to feeding a rapidly growing population, especially in developing countries (Flavell 2017)
A complete list of contributors is given in the consortium description and a continuously updated list can be found on the Breeding Application Programming Interface (BrAPI) website
We have defined a first version of a plant breeding Application Programming Interface (API) that defines the key calls needed to exchange information about germplasm, phenotypes, experiments, studies, geographic locations, samples, and genetic markers
Summary
The Breeding API is a practical tool to help solve problems in accessing, exchanging, and integrating data across systems and applications. BrAPI calls are organized into categories that reflect the major domains needed for exchanging data between plant breeding information management systems and client applications. An important role in the community is played by the BrAPI coordinator, who helps to organizes the hackathons and workshops, reviews and coordinate proposals for new or updated calls, provides support for implementers, and maintains the documentation and the BrAPIbrapi website. Description: This site contains information about a collection composed of ~7000 domesticated (S. lycopersicum) lines, along with representative wild species, collected with the scope of the european project EU-SOL The scheduled and public resource test reports are stored for future assessment
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