BrAPI - an application programming interface for plant breeding applications

Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar Benites-Alfaro, Clay Birkett, Viana C Calaminos, Pierre Carceller, Guillaume Cornut, Bruno Vasques Costa, Jeremy D Edwards, Richard Finkers, Star Yanxin Gao, Mehmood Ghaffar, Philip Glaser, Valentin Guignon, Puthick Hok, Andrzej Kilian, Patrick KönigJack Elendil B Lagare, Matthias Lange, Marie-Angélique Laporte, Pierre Larmande, David LeBauer, David Lyon, David Marshall, Dave Matthews, Iain Milne, Naymesh Mistry, Nicolas Morales, Lukas Mueller, Pascal Neveu, Evangelia Papoutsoglou, Brian Pearce, Ivan Perez-Masias, Cyril Pommier, Ricardo H Ramirez-Gonzalez, Abhishek Rathore, Angel M Raquel, Sebastian Raubach, Trevor Rife, Kelly Robbins, Mathieu Rouard, Chaitanya Sarma, Uwe Scholz, Guilhem Sempéré, Paul Shaw, Reinhard Simon, Nahuel Soldevilla

Research output: Contribution to journalArticle

12 Citations (Scopus)
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Abstract

MOTIVATION: Modern 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 is 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.

RESULTS: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service Application Programming Interface (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. Â 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 IMPLEMENTATION: More 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.

Original languageEnglish
Article numberbtz190
Pages (from-to)4147-4155
Number of pages9
JournalBioinformatics (Oxford, England)
Volume35
Issue number20
Early online date23 Mar 2019
DOIs
Publication statusPrint publication - 15 Oct 2019

Bibliographical note

© The Author(s) 2019. Published by Oxford University Press.

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    Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O., Birkett, C., Calaminos, V. C., Carceller, P., Cornut, G., Vasques Costa, B., Edwards, J. D., Finkers, R., Gao, S. Y., Ghaffar, M., Glaser, P., Guignon, V., Hok, P., Kilian, A., ... Soldevilla, N. (2019). BrAPI - an application programming interface for plant breeding applications. Bioinformatics (Oxford, England), 35(20), 4147-4155. [btz190]. https://doi.org/10.1093/bioinformatics/btz190