BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community

Peter Selby¹, Rafael Abbeloos², Anne-Francoise Adam-Blondon^{3

4}, Francisco J Agosto-Pérez¹, Michael Alaux⁴, Isabelle Alic⁵, Khaled Al-Shamaa⁶, Johan Steven Aparicio⁷, Jan Erik Backlund⁸, Aldrin Batac^{8

9}, Sebastian Beier^{10

11}, Gabriel Besombes⁵, Alice Boizet^{12

13}, Matthijs Brouwer¹⁴, Terry Casstevens¹⁵, Arnaud Charleroy⁵, Keo Corak¹⁶, Chaney Courtney¹⁷, Mariano Crimi⁸, Gouripriya Davuluri¹⁸, Kauê de Sousa¹⁹, Jeremy Destin⁴, Stijn Dhondt², Ajay Dhungana²⁰, Bert Droesbeke²¹, Manuel Feser^{18

22}, Mirella Flores-Gonzalez²³, Valentin Guignon¹⁹, Corina Habito⁸, Asis Hallab^{10

24}, Jenna Hershberger¹⁷, Puthick Hok²⁵, Amanda M Hulse-Kemp¹⁶, Lynn Carol Johnson¹⁵, Sook Jung²⁶, Paul Kersey²⁷, Andrzej Kilian²⁵, Patrick König¹⁸, Suman Kumar¹⁸, Josh Lamos-Sweeney¹, Laszlo Lang²⁴, Matthias Lange¹⁸, Marie-Angélique Laporte¹⁹, Taein Lee²⁶, Erwan Le Floch⁴, Francisco López²⁸, Brandon Madriz²⁹, Dorrie Main²⁶, Marco Marsella²⁸, Maud Marty⁴, Célia Michotey⁴, Zachary Miller¹⁵, Iain Milne³⁰, Lukas A Mueller²³, Moses Nderitu³¹, Pascal Neveu⁵, Nick Palladino³², Tim Parsons³², Cyril Pommier⁴, Jean-François Rami^{12

13}, Sebastian Raubach³⁰, Trevor Rife¹⁷, Kelly Robbins¹, Mathieu Rouard¹⁹, Joseph Ruff²⁷, Guilhem Sempéré^{33

34}, Romil Mayank Shah³⁵, Paul Shaw³⁰, Becky Smith³⁰, Nahuel Soldevilla^{8

9}, Anne Tireau⁵, Clarysabel Tovar^{8

9}, Grzegorz Uszynski²⁵, Vivian Bass Vega²⁴, Stephan Weise¹⁸, Shawn C Yarnes³², The BrAPI Consortium³⁶

Affiliations

¹ Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
² VIB Agro-incubator, Vlaams Instituut voor Biotechnologie (VIB), 9850 Nevele, Belgium.
³ IFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA, 91057 Evry, France.
⁴ Université Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.
⁵ MISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.
⁶ International Center for Agricultural Research in the Dry Areas (ICARDA), Dalia Bldg, Bashir El Kassar Street, VFPM+GJW, Bayrut, Lebanon.
⁷ International Center for Tropical Agriculture (CIAT), Cali, Valle del Cauca, Colombia.
⁸ Integrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
⁹ Leafnode LLC, 56237 El Batán, Texcoco, México, México.
¹⁰ Institute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, Forschungszentrum Jülich GmbH, Wilhelm Johnen Straße, 52428 Jülich, Germany.
¹¹ Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.
¹² CIRAD, UMR AGAP Institut, 34980, Montpellier, France.
¹³ AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, 34980, France.
¹⁴ Wageningen University and Research, Droevendaalsesteeg, Wageningen, 2, 6708 PB, Netherlands.
¹⁵ Buckler Lab and Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.
¹⁶ USDA-ARS Genomics and Bioinformatics Research Unit, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA.
¹⁷ Department of Plant and Environmental Sciences, Clemson University, 16 N Clemson Ave, Clemson, SC 29631, USA.
¹⁸ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.
¹⁹ Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.
²⁰ College of Agriculture, Louisiana State University (LSU), 106 Martin D. Woodin Hall Baton Rouge, LA 70803, USA.
²¹ VIB Data Core, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.
²² Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Postfach 10 01 31, 33501 Bielefeld, Germany.
²³ The Boyce Thompson Institute, Ithaca, NY 14853, USA.
²⁴ Bingen Technical University of Applied Sciences, Berlinstraße, Bingen am Rhein, 109, 55411, Germany.
²⁵ Diversity Arrays Technology (DArT), University of Canberra Kirinari Street, Bruce, ACT, 2617, Australia.
²⁶ Department of Horticulture, Washington State University, Pullman, WA 99164, USA.
²⁷ Royal Botanic Gardens, Kew, Richmond, London, TW9 3AE, England, UK.
²⁸ International Treaty on Plant Genetic Resources for Food and Agriculture, FAO, Viale delle Terme di Caracalla, 00153 Rome, Italy.
²⁹ MrBot Software Solutions, Cartago, 30501, Costa Rica.
³⁰ Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.
³¹ SEQART AFRICA, Old Naivasha road, 00100, Nairobi, Kenya.
³² Breeding Insight, Cornell University, Ithaca, NY 14853, USA.
³³ CIRAD, UMR INTERTRYP, Montpellier, France INTERTRYP, Univ Montpellier, CIRAD, IRD, French Institute of Bioinformatics (IFB), Montpellier, 34980, France.
³⁴ South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34980 Montpellier, France.
³⁵ College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27695, USA.
³⁶ The BrAPI Consortium, Cornell University, Ithaca, NY 14853, USA.

PMID: 40996713
PMCID: PMC12462623
DOI: 10.1093/database/baaf048

BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community

Peter Selby et al. Database (Oxford). 2025.

. 2025 Jan 18:2025:baaf048.

doi: 10.1093/database/baaf048.

Authors

Affiliations

¹ Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
² VIB Agro-incubator, Vlaams Instituut voor Biotechnologie (VIB), 9850 Nevele, Belgium.
³ IFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA, 91057 Evry, France.
⁴ Université Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.
⁵ MISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.
⁶ International Center for Agricultural Research in the Dry Areas (ICARDA), Dalia Bldg, Bashir El Kassar Street, VFPM+GJW, Bayrut, Lebanon.
⁷ International Center for Tropical Agriculture (CIAT), Cali, Valle del Cauca, Colombia.
⁸ Integrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
⁹ Leafnode LLC, 56237 El Batán, Texcoco, México, México.
¹⁰ Institute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, Forschungszentrum Jülich GmbH, Wilhelm Johnen Straße, 52428 Jülich, Germany.
¹¹ Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.
¹² CIRAD, UMR AGAP Institut, 34980, Montpellier, France.
¹³ AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, 34980, France.
¹⁴ Wageningen University and Research, Droevendaalsesteeg, Wageningen, 2, 6708 PB, Netherlands.
¹⁵ Buckler Lab and Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.
¹⁶ USDA-ARS Genomics and Bioinformatics Research Unit, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA.
¹⁷ Department of Plant and Environmental Sciences, Clemson University, 16 N Clemson Ave, Clemson, SC 29631, USA.
¹⁸ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.
¹⁹ Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.
²⁰ College of Agriculture, Louisiana State University (LSU), 106 Martin D. Woodin Hall Baton Rouge, LA 70803, USA.
²¹ VIB Data Core, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.
²² Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Postfach 10 01 31, 33501 Bielefeld, Germany.
²³ The Boyce Thompson Institute, Ithaca, NY 14853, USA.
²⁴ Bingen Technical University of Applied Sciences, Berlinstraße, Bingen am Rhein, 109, 55411, Germany.
²⁵ Diversity Arrays Technology (DArT), University of Canberra Kirinari Street, Bruce, ACT, 2617, Australia.
²⁶ Department of Horticulture, Washington State University, Pullman, WA 99164, USA.
²⁷ Royal Botanic Gardens, Kew, Richmond, London, TW9 3AE, England, UK.
²⁸ International Treaty on Plant Genetic Resources for Food and Agriculture, FAO, Viale delle Terme di Caracalla, 00153 Rome, Italy.
²⁹ MrBot Software Solutions, Cartago, 30501, Costa Rica.
³⁰ Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.
³¹ SEQART AFRICA, Old Naivasha road, 00100, Nairobi, Kenya.
³² Breeding Insight, Cornell University, Ithaca, NY 14853, USA.
³³ CIRAD, UMR INTERTRYP, Montpellier, France INTERTRYP, Univ Montpellier, CIRAD, IRD, French Institute of Bioinformatics (IFB), Montpellier, 34980, France.
³⁴ South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34980 Montpellier, France.
³⁵ College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27695, USA.
³⁶ The BrAPI Consortium, Cornell University, Ithaca, NY 14853, USA.

PMID: 40996713
PMCID: PMC12462623
DOI: 10.1093/database/baaf048

Abstract

Population growth and the impacts of climate change are placing increasing pressure on global agriculture and breeding programmes. Recent advancements in phenotyping techniques, genotyping technologies, and predictive modelling are accelerating genetic gains in breeding programmes, helping researchers and breeders develop improved crops more efficiently. However, these advancements have also led to an overwhelming torrent of fragmented data, creating significant challenges in data integration and management. To address this issue, the Breeding Application Programming Interface (BrAPI) project was established as a standardized data model for breeding data. BrAPI is an international, community-driven effort that facilitates interoperability among databases and tools, improving the sharing and interpretation of breeding-related data. This open-source standard is software-agnostic and can be used by anyone interested in breeding, phenotyping, germplasm, genotyping, and agronomy data management. This manuscript provides an overview of the BrAPI project, highlighting the significant progress made in the development of the data standard and the expansion of its community. It also presents a showcase of the wide variety of BrAPI-compatible tools that have been built to enhance breeding and research activities, demonstrating how the project is advancing agricultural innovation and data management practices.

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Conflict of interest statement

None declared.

Figures

**Figure 1.**
A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org.

**Figure 2.**
A summary of all the tools described below and the general areas each tool is designed to handle. The ‘Generation/Collection’ column indicates that an application is used to input or create new data. The ‘Storage’ column indicates the tool stores that type of data. The ‘Visualization’ column indicates that the application has a way of presenting data to a human user. The ‘Analysis’ column indicates the tool performs calculations to provide new insight.

See this image and copyright information in PMC

References

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1. Selby P, Abbeloos R, Backlund JE et al. BrAPI—an application programming interface for plant breeding applications. Bioinformatics. 2019;35:4147–55. 10.1093/bioinformatics/btz190 - DOI - PMC - PubMed
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1. GA4GH SchemaBlocks . https://github.com/ga4gh-metadata/SchemaBlocks (19 August 2025, date last accessed).
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BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community

Affiliations

BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community

Authors

Affiliations

Abstract

Conflict of interest statement

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References

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