BrAPI - An application programming interface for plant breeding applications

Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar E. 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 S. Lebauer, David A. Lyon, David S. Marshall, Dave Matthews, Iain Milne, Naymesh Mistry, Nicolas Morales, Lukas A. Mueller, Pascal Neveu, Evangelia Papoutsoglou, Brian Pearce, Ivan Perez-Masias, Cyril Pommier, Ricardo H. Ramírez-González, Abhishek Rathore, Angel Manica Raquel, Sebastian Raubach, Trevor Rife, Kelly Robbins, Mathieu Rouard, Chaitanya Sarma, Uwe Scholz, Guilhem Sempéré, Paul D. Shaw, Reinhard Simon, Nahuel Soldevilla, Gordon Stephen, Qi Sun, Clarysabel Tovar, Grzegorz Uszynski, Maikel Verouden, Jonathan Wren

Research output: Contribution to journalArticle

Abstract

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 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. Results: To 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 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 (US)
Pages (from-to)4147-4155
Number of pages9
JournalBioinformatics
Volume35
Issue number20
DOIs
StatePublished - Oct 15 2019

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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  • Cite this

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