Evidence map›Paper›PMID 40996713›Full record

ArticleDatabase : the journal of biological databases and curation2025

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

Peter Selby, Rafael Abbeloos, Anne-Francoise Adam-Blondon, Francisco J Agosto-Pérez, Michael Alaux, Isabelle Alic, Khaled Al-Shamaa, Johan Steven Aparicio, Jan Erik Backlund, Aldrin Batac and 67 more

Abstract read
In one paragraph

Article in Database : the journal of biological databases and curation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

77 authors.

Peter SelbyPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-7151-4445
Rafael AbbeloosVIB Agro-incubator, Vlaams Instituut voor Biotechnologie (VIB), 9850 Nevele, Belgium.ORCID 0000-0002-0177-3887
Anne-Francoise Adam-BlondonIFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA, 91057 Evry, France.ORCID 0000-0002-3412-9086
Francisco J Agosto-PérezPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0002-5059-253X
Michael AlauxUniversité Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.ORCID 0000-0001-9356-4072
Isabelle AlicMISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.ORCID 0000-0002-8961-6068
Khaled Al-ShamaaInternational Center for Agricultural Research in the Dry Areas (ICARDA), Dalia Bldg, Bashir El Kassar Street, VFPM+GJW, Bayrut, Lebanon.ORCID 0000-0002-7668-3798
Johan Steven AparicioInternational Center for Tropical Agriculture (CIAT), Cali, Valle del Cauca, Colombia.
Jan Erik BacklundIntegrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
Aldrin BatacIntegrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
Sebastian BeierInstitute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, Forschungszentrum Jülich GmbH, Wilhelm Johnen Straße, 52428 Jülich, Germany.ORCID 0000-0002-2177-8781
Gabriel BesombesMISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.ORCID 0009-0004-1359-2145
Alice BoizetCIRAD, UMR AGAP Institut, 34980, Montpellier, France.ORCID 0000-0003-4096-6689
Matthijs BrouwerWageningen University and Research, Droevendaalsesteeg, Wageningen, 2, 6708 PB, Netherlands.ORCID 0000-0001-8183-0484
Terry CasstevensBuckler Lab and Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-7602-0487
Arnaud CharleroyMISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.ORCID 0009-0009-7575-3617
Keo CorakUSDA-ARS Genomics and Bioinformatics Research Unit, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA.ORCID 0000-0002-4129-3319
Chaney CourtneyDepartment of Plant and Environmental Sciences, Clemson University, 16 N Clemson Ave, Clemson, SC 29631, USA.
Mariano CrimiIntegrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
Gouripriya DavuluriLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.ORCID 0009-0005-2308-0773
Kauê de SousaBioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.ORCID 0000-0002-7571-7845
Jeremy DestinUniversité Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.
Stijn DhondtVIB Agro-incubator, Vlaams Instituut voor Biotechnologie (VIB), 9850 Nevele, Belgium.ORCID 0000-0003-4402-2191
Ajay DhunganaCollege of Agriculture, Louisiana State University (LSU), 106 Martin D. Woodin Hall Baton Rouge, LA 70803, USA.ORCID 0009-0007-2639-6604
Bert DroesbekeVIB Data Core, Vlaams Instituut voor Biotechnologie (VIB), 9052 Ghent, Belgium.ORCID 0000-0003-0522-5674
Manuel FeserLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.ORCID 0000-0001-6546-1818
Mirella Flores-GonzalezThe Boyce Thompson Institute, Ithaca, NY 14853, USA.ORCID 0000-0002-7759-1617
Valentin GuignonBioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.ORCID 0000-0003-0903-6811
Corina HabitoIntegrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
Asis HallabInstitute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, Forschungszentrum Jülich GmbH, Wilhelm Johnen Straße, 52428 Jülich, Germany.ORCID 0000-0002-2421-5431
Jenna HershbergerDepartment of Plant and Environmental Sciences, Clemson University, 16 N Clemson Ave, Clemson, SC 29631, USA.ORCID 0000-0002-3147-6867
Puthick HokDiversity Arrays Technology (DArT), University of Canberra Kirinari Street, Bruce, ACT, 2617, Australia.
Amanda M Hulse-KempUSDA-ARS Genomics and Bioinformatics Research Unit, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA.ORCID 0000-0001-9670-9433
Lynn Carol JohnsonBuckler Lab and Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-8103-2722
Sook JungDepartment of Horticulture, Washington State University, Pullman, WA 99164, USA.ORCID 0000-0003-3968-2769
Paul KerseyRoyal Botanic Gardens, Kew, Richmond, London, TW9 3AE, England, UK.
Andrzej KilianDiversity Arrays Technology (DArT), University of Canberra Kirinari Street, Bruce, ACT, 2617, Australia.
Patrick KönigLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.ORCID 0000-0002-8948-6793
Suman KumarLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.ORCID 0009-0005-5832-7190
Josh Lamos-SweeneyPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
Laszlo LangBingen Technical University of Applied Sciences, Berlinstraße, Bingen am Rhein, 109, 55411, Germany.ORCID 0009-0009-8936-4532
Matthias LangeLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.ORCID 0000-0002-4316-078X
Marie-Angélique LaporteBioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.ORCID 0000-0002-8461-9745
Taein LeeDepartment of Horticulture, Washington State University, Pullman, WA 99164, USA.ORCID 0000-0002-2000-2586
Erwan Le FlochUniversité Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.ORCID 0000-0002-1010-6859
Francisco LópezInternational Treaty on Plant Genetic Resources for Food and Agriculture, FAO, Viale delle Terme di Caracalla, 00153 Rome, Italy.
Brandon MadrizMrBot Software Solutions, Cartago, 30501, Costa Rica.
Dorrie MainDepartment of Horticulture, Washington State University, Pullman, WA 99164, USA.ORCID 0000-0002-1162-2724
Marco MarsellaInternational Treaty on Plant Genetic Resources for Food and Agriculture, FAO, Viale delle Terme di Caracalla, 00153 Rome, Italy.ORCID 0000-0003-0334-8785
Maud MartyUniversité Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.ORCID 0009-0001-8764-6466
Célia MichoteyUniversité Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.ORCID 0000-0003-1877-1703
Zachary MillerBuckler Lab and Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0002-5454-4527
Iain MilneDepartment of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.ORCID 0000-0002-4126-0859
Lukas A MuellerThe Boyce Thompson Institute, Ithaca, NY 14853, USA.ORCID 0000-0001-8640-1750
Moses NderituSEQART AFRICA, Old Naivasha road, 00100, Nairobi, Kenya.
Pascal NeveuMISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.ORCID 0000-0003-4189-7793
Nick PalladinoBreeding Insight, Cornell University, Ithaca, NY 14853, USA.ORCID 0009-0009-1645-297X
Tim ParsonsBreeding Insight, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-6209-2455
Cyril PommierUniversité Paris-Saclay, INRAE, BioinfOmics, URGI, 78026, Versailles, France.ORCID 0000-0002-9040-8733
Jean-François RamiCIRAD, UMR AGAP Institut, 34980, Montpellier, France.ORCID 0000-0002-5679-3877
Sebastian RaubachDepartment of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.ORCID 0000-0001-5659-247X
Trevor RifeDepartment of Plant and Environmental Sciences, Clemson University, 16 N Clemson Ave, Clemson, SC 29631, USA.ORCID 0000-0002-5974-6523
Kelly RobbinsPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0001-9522-9585
Mathieu RouardBioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France.ORCID 0000-0003-0284-1885
Joseph RuffRoyal Botanic Gardens, Kew, Richmond, London, TW9 3AE, England, UK.
Guilhem SempéréCIRAD, UMR INTERTRYP, Montpellier, France INTERTRYP, Univ Montpellier, CIRAD, IRD, French Institute of Bioinformatics (IFB), Montpellier, 34980, France.ORCID 0000-0001-7429-2091
Romil Mayank ShahCollege of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27695, USA.
Paul ShawDepartment of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.ORCID 0000-0002-0202-1150
Becky SmithDepartment of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.ORCID 0000-0002-8968-3383
Nahuel SoldevillaIntegrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
Anne TireauMISTEA, University of Montpellier, INRAE, Institut Agro, 34000 Montpellier, France.ORCID 0000-0001-8501-6922
Clarysabel TovarIntegrated Breeding Platform, 56237 El Batán, Texcoco, México, México.
Grzegorz UszynskiDiversity Arrays Technology (DArT), University of Canberra Kirinari Street, Bruce, ACT, 2617, Australia.
Vivian Bass VegaBingen Technical University of Applied Sciences, Berlinstraße, Bingen am Rhein, 109, 55411, Germany.ORCID 0009-0002-2476-9888
Stephan WeiseLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.ORCID 0000-0003-4031-9131
Shawn C YarnesBreeding Insight, Cornell University, Ithaca, NY 14853, USA.ORCID 0000-0002-1090-0403
The BrAPI ConsortiumThe BrAPI Consortium, Cornell University, Ithaca, NY 14853, USA.

Funding

Agence Nationale de la Recherche ANR-11-INBS-0012Bill and Melinda Gates FoundationFoundation for Food and Agriculture Research CA20-SS-0000000103German Ministry of Research and Education FKZ 031B1302AGerman Research Foundation 442032008Horizon 2020 - Research and Innovation Framework Programme 862613National Institute of Food and Agriculture 2022-51181-38449National Institute of Food and Agriculture 2022-67021-37024The Innovation Lab for Crop Improvement Cornell 7200AA19LE00005U.S. Department of Agriculture 8062-21000-043-004-AU.S. Department of Agriculture 8062-21000-052-002-AU.S. Department of Agriculture 8062-21000-052-003-A
6 · The paper itself

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.

Indexed as

Databases, GeneticPlant BreedingSoftwareCrops, Agricultural

Identifiers

PMID40996713
PMCPMC12462623

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.