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 König & 30 others Jack 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 journalArticleResearchpeer-review

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)1-9
JournalBioinformatics (Oxford, England)
Early online date23 Mar 2019
DOIs
Publication statusFirst published - 23 Mar 2019

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

Bibliographical note

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

Cite this

Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O., ... Soldevilla, N. (2019). BrAPI - an application programming interface for plant breeding applications. Bioinformatics (Oxford, England), 1-9. [btz190]. https://doi.org/10.1093/bioinformatics/btz190
Selby, Peter ; Abbeloos, Rafael ; Backlund, Jan Erik ; Basterrechea Salido, Martin ; Bauchet, Guillaume ; Benites-Alfaro, Omar ; Birkett, Clay ; Calaminos, Viana C ; Carceller, Pierre ; Cornut, Guillaume ; Vasques Costa, Bruno ; Edwards, Jeremy D ; Finkers, Richard ; Gao, Star Yanxin ; 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 ; Lyon, David ; Marshall, David ; Matthews, Dave ; Milne, Iain ; Mistry, Naymesh ; Morales, Nicolas ; Mueller, Lukas ; Neveu, Pascal ; Papoutsoglou, Evangelia ; Pearce, Brian ; Perez-Masias, Ivan ; Pommier, Cyril ; Ramirez-Gonzalez, Ricardo H ; Rathore, Abhishek ; Raquel, Angel M ; Raubach, Sebastian ; Rife, Trevor ; Robbins, Kelly ; Rouard, Mathieu ; Sarma, Chaitanya ; Scholz, Uwe ; Sempéré, Guilhem ; Shaw, Paul ; Simon, Reinhard ; Soldevilla, Nahuel. / BrAPI - an application programming interface for plant breeding applications. In: Bioinformatics (Oxford, England). 2019 ; pp. 1-9.
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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. {\^A} 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 Omar Benites-Alfaro 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 Gao, {Star Yanxin} 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 Marie-Ang{\'e}lique Laporte and Pierre Larmande and David LeBauer and David Lyon and David Marshall and Dave Matthews and Iain Milne and Naymesh Mistry and Nicolas Morales and Lukas Mueller and Pascal Neveu and Evangelia Papoutsoglou and Brian Pearce and Ivan Perez-Masias and Cyril Pommier and Ramirez-Gonzalez, {Ricardo H} and Abhishek Rathore and Raquel, {Angel M} 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 Paul Shaw and Reinhard Simon and Nahuel Soldevilla",
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Selby, P, Abbeloos, R, Backlund, JE, Basterrechea Salido, M, Bauchet, G, Benites-Alfaro, O, Birkett, C, Calaminos, VC, Carceller, P, Cornut, G, Vasques Costa, B, Edwards, JD, Finkers, R, Gao, SY, Ghaffar, M, Glaser, P, Guignon, V, Hok, P, Kilian, A, König, P, Lagare, JEB, Lange, M, Laporte, M-A, Larmande, P, LeBauer, D, Lyon, D, Marshall, D, Matthews, D, Milne, I, Mistry, N, Morales, N, Mueller, L, Neveu, P, Papoutsoglou, E, Pearce, B, Perez-Masias, I, Pommier, C, Ramirez-Gonzalez, RH, Rathore, A, Raquel, AM, Raubach, S, Rife, T, Robbins, K, Rouard, M, Sarma, C, Scholz, U, Sempéré, G, Shaw, P, Simon, R & Soldevilla, N 2019, 'BrAPI - an application programming interface for plant breeding applications', Bioinformatics (Oxford, England), pp. 1-9. 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; Birkett, Clay; Calaminos, Viana C; Carceller, Pierre; Cornut, Guillaume; Vasques Costa, Bruno; Edwards, Jeremy D; Finkers, Richard; Gao, Star Yanxin; 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; Lyon, David; Marshall, David; Matthews, Dave; Milne, Iain; Mistry, Naymesh; Morales, Nicolas; Mueller, Lukas; Neveu, Pascal; Papoutsoglou, Evangelia; Pearce, Brian; Perez-Masias, Ivan; Pommier, Cyril; Ramirez-Gonzalez, Ricardo H; Rathore, Abhishek; Raquel, Angel M; Raubach, Sebastian; Rife, Trevor; Robbins, Kelly; Rouard, Mathieu; Sarma, Chaitanya; Scholz, Uwe; Sempéré, Guilhem; Shaw, Paul; Simon, Reinhard; Soldevilla, Nahuel.

In: Bioinformatics (Oxford, England), 23.03.2019, p. 1-9.

Research output: Contribution to journalArticleResearchpeer-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

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 - Gao, Star Yanxin

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

AU - Lyon, David

AU - Marshall, David

AU - Matthews, Dave

AU - Milne, Iain

AU - Mistry, Naymesh

AU - Morales, Nicolas

AU - Mueller, Lukas

AU - Neveu, Pascal

AU - Papoutsoglou, Evangelia

AU - Pearce, Brian

AU - Perez-Masias, Ivan

AU - Pommier, Cyril

AU - Ramirez-Gonzalez, Ricardo H

AU - Rathore, Abhishek

AU - Raquel, Angel M

AU - Raubach, Sebastian

AU - Rife, Trevor

AU - Robbins, Kelly

AU - Rouard, Mathieu

AU - Sarma, Chaitanya

AU - Scholz, Uwe

AU - Sempéré, Guilhem

AU - Shaw, Paul

AU - Simon, Reinhard

AU - Soldevilla, Nahuel

N1 - © The Author(s) 2019. Published by Oxford University Press.

PY - 2019/3/23

Y1 - 2019/3/23

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 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.

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 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.

U2 - 10.1093/bioinformatics/btz190

DO - 10.1093/bioinformatics/btz190

M3 - Article

SP - 1

EP - 9

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

M1 - btz190

ER -

Selby P, Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet G, Benites-Alfaro O et al. BrAPI - an application programming interface for plant breeding applications. Bioinformatics (Oxford, England). 2019 Mar 23;1-9. btz190. https://doi.org/10.1093/bioinformatics/btz190