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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #355769
Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: BrAPI - An application programming interface for plant breeding applications

Author
item ABBELOOS, RAFAEL - Flanders Institute Of Biotechnology (VIB)
item BAUCHET, GUILLAUME - Boyce Thompson Institute
item BENITES-ALFARO, OMAR - International Potato Center
item Birkett, Clayton
item CARCELLER, PIERRE - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item COSTA, BRUNO - Instituto De Biologia Experimental E Tecnologica
item Edwards, Jeremy
item FINKERS, RICHARD - Wageningen University And Research Center
item GUIGNON, VALENTIN - Bioversity International
item HOK, PUTHICK - Diversity Arrays Technology
item KILIAN, ANDRZEJ - Diversity Arrays Technology
item LAPORTE, MARIE-ANGELIQUE - Bioversity International
item LEBAUER, DAVID - University Of Arizona
item LYON, DAVID - Boyce Thompson Institute
item MARSHALL, DAVID - The James Hutton Institute
item Matthews, David
item MILNE, IAIN - The James Hutton Institute
item MORALES, NICOLAS - Boyce Thompson Institute
item MUELLER, LUKAS - Boyce Thompson Institute
item PAPOUTSOGLOU, EVANGELIA - Wageningen University And Research Center
item PEARCE, BRIAN - Diversity Arrays Technology
item PEREZ-MASIAS, IVAN - International Potato Center
item RAMIREZ-GONZALEZ, RICARDO - John Innes Center
item RAUBACK, SEBASTIAN - The James Hutton Institute
item RIFE, TREVOR - Kansas State University
item ROBBINS, KELLY - Cornell University
item ROUARD, MATHIEU - Bioversity International
item SELBY, PETER - Cornell University
item SEMPERE, GUILHEM - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item SHAW, PAUL - The James Hutton Institute
item GORDON, STEPHEN - The James Hutton Institute
item USZYNSKI, GRZEGORZ - Diversity Arrays Technology
item VEROUDEN, MAIKEL - Wageningen University And Research Center
item BACKLUND, JAN - Dow Agrosciences
item SALIDO, MARTIN - Leibniz Institute Of Plant Genetics And Crop Plant Research
item CORNUT, GUILLAUME - French National Institute For Agricultural Research
item GAO, STAR - Boyce Thompson Institute
item PATRICK, KONIG - Leibniz Institute Of Plant Genetics And Crop Plant Research
item LAGARE, JACK - International Rice Research Institute
item LANGE, MATTHIAS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item LARMANDE, PIERRE - Institute For Research And Development (IRD)
item NEVEU, PASCAL - French National Institute For Agricultural Research
item PROMMIER, CYRIL - French National Institute For Agricultural Research
item TAHORE, ABHISHEK - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SARMA, CHAITANYA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SCHOLZ, UWE - Leibniz Institute Of Plant Genetics And Crop Plant Research
item MISTRY, NAYMESH - Consultant
item SIMON, REINHARD - Consultant
item SOLDEVILLA, NAHUEL - Consultant
item TOVAR, CLARYSABEL - Consultant

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2019
Publication Date: 3/23/2019
Citation: Abbeloos, R., Bauchet, G., Benites-Alfaro, O., Birkett, C.L., Carceller, P., Costa, B.V., Edwards, J., Finkers, R., Guignon, V., Hok, P., Kilian, A., Laporte, M., Lebauer, D., Lyon, D., Marshall, D., Matthews, D.E., Milne, I., Morales, N., Mueller, L., Papoutsoglou, E., Pearce, B., Perez-Masias, I., Ramirez-Gonzalez, R.H., Rauback, S., Rife, T., Robbins, K., Rouard, M., Selby, P., Sempere, G., Shaw, P., Gordon, S., Uszynski, G., Verouden, M., Backlund, J.E., Salido, M.B., Cornut, G., Gao, S.Y., Patrick, K., Lagare, J.E., Lange, M., Larmande, P., Neveu, P., Prommier, C., Tahore, A., Sarma, C., Scholz, U., Mistry, N., Simon, R., Soldevilla, N., Tovar, C. 2019. BrAPI - An application programming interface for plant breeding applications. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz190.
DOI: https://doi.org/10.1093/bioinformatics/btz190

Interpretive Summary: Plant breeding benefits from combining large collections of information including genotyping, field trial observations, and geographic data. There is a need to quickly transfer data between plant breeding databases in a standardized way. To address this need, a community of researchers and computer scientists have developed the plant Breeding Application Programming Interface (BrAPI) to provide interoperability between online plant breeding data resources. BrAPI is a shared, open specification that has been designed and implemented by a global consortium of participants. The focus of the first version of BrAPI on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and molecular 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. More information on BrAPI is available at https://brapi.org/.

Technical 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 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. 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. 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. More information on BrAPI is available at https://brapi.org/.