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 König & 30 others Jack 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, Maikel Verouden

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

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 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
Pages (from-to)4147-4155
JournalBioinformatics (Oxford, England)
Volume35
Issue number20
DOIs
Publication statusPublished - 15 Oct 2019

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Application programming interfaces (API)
Breeding
Programming
Specifications
Specification
Plant Breeding
Specification Test
Data integration
Data Exchange
Data Integration
Electronic data interchange
Data Management
Information Storage and Retrieval
Interoperability
Open Source
Information management
Web services
Telecommunication links
Web Services
Genomics

Cite this

Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O. E., ... Verouden, M. (2019). BrAPI-an application programming interface for plant breeding applications. Bioinformatics (Oxford, England), 35(20), 4147-4155. https://doi.org/10.1093/bioinformatics/btz190
Selby, Peter ; Abbeloos, Rafael ; Backlund, Jan Erik ; Basterrechea Salido, Martin ; Bauchet, Guillaume ; Benites-Alfaro, Omar E. ; Birkett, Clay ; Calaminos, Viana C. ; Carceller, Pierre ; Cornut, Guillaume ; Vasques Costa, Bruno ; Edwards, Jeremy D. ; Finkers, Richard ; Yanxin Gao, Star ; Ghaffar, Mehmood ; Glaser, Philip ; Guignon, Valentin ; Hok, Puthick ; Kilian, Andrzej ; König, Patrick ; Lagare, Jack Elendil B. ; Lange, Matthias ; Laporte, Marie Angélique ; Larmande, Pierre ; LeBauer, David S. ; Lyon, David A. ; Marshall, David S. ; Matthews, Dave ; Milne, Iain ; Mistry, Naymesh ; Morales, Nicolas ; Mueller, Lukas A. ; Neveu, Pascal ; Papoutsoglou, Evangelia ; Pearce, Brian ; Perez-Masias, Ivan ; Pommier, Cyril ; Ramírez-González, Ricardo H. ; Rathore, Abhishek ; Raquel, Angel Manica ; Raubach, Sebastian ; Rife, Trevor ; Robbins, Kelly ; Rouard, Mathieu ; Sarma, Chaitanya ; Scholz, Uwe ; Sempéré, Guilhem ; Shaw, Paul D. ; Simon, Reinhard ; Verouden, Maikel. / BrAPI-an application programming interface for plant breeding applications. In: Bioinformatics (Oxford, England). 2019 ; Vol. 35, No. 20. pp. 4147-4155.
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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 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.",
author = "Peter Selby and Rafael Abbeloos and Backlund, {Jan Erik} and {Basterrechea Salido}, Martin and Guillaume Bauchet and Benites-Alfaro, {Omar E.} and Clay Birkett and Calaminos, {Viana C.} and Pierre Carceller and Guillaume Cornut and {Vasques Costa}, Bruno and Edwards, {Jeremy D.} and Richard Finkers and {Yanxin Gao}, Star and Mehmood Ghaffar and Philip Glaser and Valentin Guignon and Puthick Hok and Andrzej Kilian and Patrick K{\"o}nig and Lagare, {Jack Elendil B.} and Matthias Lange and Laporte, {Marie Ang{\'e}lique} and Pierre Larmande and LeBauer, {David S.} and Lyon, {David A.} and Marshall, {David S.} and Dave Matthews and Iain Milne and Naymesh Mistry and Nicolas Morales and Mueller, {Lukas A.} and Pascal Neveu and Evangelia Papoutsoglou and Brian Pearce and Ivan Perez-Masias and Cyril Pommier and Ram{\'i}rez-Gonz{\'a}lez, {Ricardo H.} and Abhishek Rathore and Raquel, {Angel Manica} and Sebastian Raubach and Trevor Rife and Kelly Robbins and Mathieu Rouard and Chaitanya Sarma and Uwe Scholz and Guilhem Semp{\'e}r{\'e} and Shaw, {Paul D.} and Reinhard Simon and Maikel Verouden",
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Selby, P, Abbeloos, R, Backlund, JE, Basterrechea Salido, M, Bauchet, G, Benites-Alfaro, OE, Birkett, C, Calaminos, VC, Carceller, P, Cornut, G, Vasques Costa, B, Edwards, JD, Finkers, R, Yanxin Gao, S, Ghaffar, M, Glaser, P, Guignon, V, Hok, P, Kilian, A, König, P, Lagare, JEB, Lange, M, Laporte, MA, Larmande, P, LeBauer, DS, Lyon, DA, Marshall, DS, Matthews, D, Milne, I, Mistry, N, Morales, N, Mueller, LA, Neveu, P, Papoutsoglou, E, Pearce, B, Perez-Masias, I, Pommier, C, Ramírez-González, RH, Rathore, A, Raquel, AM, Raubach, S, Rife, T, Robbins, K, Rouard, M, Sarma, C, Scholz, U, Sempéré, G, Shaw, PD, Simon, R & Verouden, M 2019, 'BrAPI-an application programming interface for plant breeding applications', Bioinformatics (Oxford, England), vol. 35, no. 20, pp. 4147-4155. https://doi.org/10.1093/bioinformatics/btz190

BrAPI-an application programming interface for plant breeding applications. / Selby, Peter; Abbeloos, Rafael; Backlund, Jan Erik; Basterrechea Salido, Martin; Bauchet, Guillaume; Benites-Alfaro, Omar E.; Birkett, Clay; Calaminos, Viana C.; Carceller, Pierre; Cornut, Guillaume; Vasques Costa, Bruno; Edwards, Jeremy D.; Finkers, Richard; Yanxin Gao, Star; Ghaffar, Mehmood; Glaser, Philip; Guignon, Valentin; Hok, Puthick; Kilian, Andrzej; König, Patrick; Lagare, Jack Elendil B.; Lange, Matthias; Laporte, Marie Angélique; Larmande, Pierre; LeBauer, David S.; Lyon, David A.; Marshall, David S.; Matthews, Dave; Milne, Iain; Mistry, Naymesh; Morales, Nicolas; Mueller, Lukas A.; Neveu, Pascal; Papoutsoglou, Evangelia; Pearce, Brian; Perez-Masias, Ivan; Pommier, Cyril; Ramírez-González, Ricardo H.; Rathore, Abhishek; Raquel, Angel Manica; Raubach, Sebastian; Rife, Trevor; Robbins, Kelly; Rouard, Mathieu; Sarma, Chaitanya; Scholz, Uwe; Sempéré, Guilhem; Shaw, Paul D.; Simon, Reinhard; Verouden, Maikel.

In: Bioinformatics (Oxford, England), Vol. 35, No. 20, 15.10.2019, p. 4147-4155.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - BrAPI-an application programming interface for plant breeding applications

AU - Selby, Peter

AU - Abbeloos, Rafael

AU - Backlund, Jan Erik

AU - Basterrechea Salido, Martin

AU - Bauchet, Guillaume

AU - Benites-Alfaro, Omar E.

AU - Birkett, Clay

AU - Calaminos, Viana C.

AU - Carceller, Pierre

AU - Cornut, Guillaume

AU - Vasques Costa, Bruno

AU - Edwards, Jeremy D.

AU - Finkers, Richard

AU - Yanxin Gao, Star

AU - Ghaffar, Mehmood

AU - Glaser, Philip

AU - Guignon, Valentin

AU - Hok, Puthick

AU - Kilian, Andrzej

AU - König, Patrick

AU - Lagare, Jack Elendil B.

AU - Lange, Matthias

AU - Laporte, Marie Angélique

AU - Larmande, Pierre

AU - LeBauer, David S.

AU - Lyon, David A.

AU - Marshall, David S.

AU - Matthews, Dave

AU - Milne, Iain

AU - Mistry, Naymesh

AU - Morales, Nicolas

AU - Mueller, Lukas A.

AU - Neveu, Pascal

AU - Papoutsoglou, Evangelia

AU - Pearce, Brian

AU - Perez-Masias, Ivan

AU - Pommier, Cyril

AU - Ramírez-González, Ricardo H.

AU - Rathore, Abhishek

AU - Raquel, Angel Manica

AU - Raubach, Sebastian

AU - Rife, Trevor

AU - Robbins, Kelly

AU - Rouard, Mathieu

AU - Sarma, Chaitanya

AU - Scholz, Uwe

AU - Sempéré, Guilhem

AU - Shaw, Paul D.

AU - Simon, Reinhard

AU - Verouden, Maikel

PY - 2019/10/15

Y1 - 2019/10/15

N2 - 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 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.

AB - 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 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.

U2 - 10.1093/bioinformatics/btz190

DO - 10.1093/bioinformatics/btz190

M3 - Article

VL - 35

SP - 4147

EP - 4155

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 20

ER -

Selby P, Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet G, Benites-Alfaro OE et al. BrAPI-an application programming interface for plant breeding applications. Bioinformatics (Oxford, England). 2019 Oct 15;35(20):4147-4155. https://doi.org/10.1093/bioinformatics/btz190