| Title: |
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community |
| Authors: |
Selby, Peter; Abbeloos, Rafael; Adam-Blondon, Anne-Francoise; Agosto-Pérez, Francisco, J.; Alaux, Michael; Alic, Isabelle; Al-Shamaa, Khaled; Aparicio, Johan, Steven; Backlund, Jan, Erik; Batac, Aldrin; Beier, Sebastian; Besombes, Gabriel; Boizet, Alice; Brouwer, Matthijs; Casstevens, Terry; Charleroy, Arnaud; Corak, Keo; Courtney, Chaney; Crimi, Mariano; Davuluri, Gouripriya; de Sousa, Kauê; Destin, Jeremy; Dhondt, Stijn; Dhungana, Ajay; Droesbeke, Bert; Feser, Manuel; Flores-Gonzalez, Mirella; Guignon, Valentin; Habito, Corina; Hallab, Asis; Hershberger, Jenna; Hok, Puthick; Hulse-Kemp, Amanda, M.; Johnson, Lynn, Carol; Jung, Sook; Kersey, Paul; Kilian, Andrzej; König, Patrick; Kumar, Suman; Lamos-Sweeney, Josh; Lang, Laszlo; Lange, Matthias; Laporte, Marie-Angélique; Lee, Taein; Le Floch, Erwan; López, Francisco; Madriz, Brandon; Main, Dorrie; Marsella, Marco; Marty, Maud; Michotey, Célia; Miller, Zachary; Milne, Iain; Mueller, Lukas, A.; Nderitu, Moses; Neveu, Pascal; Palladino, Nick; Parsons, Tim; Pommier, Cyril; Rami, Jean-François; Raubach, Sebastian; Rife, Trevor; Robbins, Kelly; Rouard, Mathieu; Ruff, Joseph; Sempéré, Guilhem; Shah, Romil, Mayank; Shaw, Paul; Smith, Becky; Soldevilla, Nahuel; Tireau, Anne; Tovar, Clarysabel; Uszynski, Grzegorz; Vega, Vivian, Bass; Weise, Stephan; Yarnes, Shawn, C.; Consortium, The Brapi |
| Contributors: |
School of Integrative Plant Science CALS; College of Agriculture and Life Sciences Cornell University (CALS); Cornell University New York -Cornell University New York; Vlaams Instituut voor Biotechnologie = Flanders Institute for Biotechnology Ghent (VIB); Institut Français de Bioinformatique (IFB-core); Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); IR BioInfOmics; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Ressources génomique-info (URGI); Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro); International Center for Agricultural Research in the Dry Areas (ICARDA); Consultative Group on International Agricultural Research CGIAR (CGIAR); International Center for Tropical Agriculture Colombie (CIAT); Integrated Breeding Platform; Leafnode LLC; Institute of Bio- and Geosciences Jülich (IBG); Forschungszentrum Jülich GmbH; Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association; Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP); Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM); Département Systèmes Biologiques (Cirad-BIOS); Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad); Wageningen University and Research Wageningen (WUR); Cornell University Ithaca (CU); USDA-ARS : Agricultural Research Service; Clemson University; Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK-Gatersleben); The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT) France; Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) Rome (Alliance); Consultative Group on International Agricultural Research CGIAR (CGIAR)-Consultative Group on International Agricultural Research CGIAR (CGIAR); Louisiana State University BatonRouge (LSU); Universität Bielefeld = Bielefeld University; Bingen Technical University of Applied Sciences = Technische Hochschule Bingen (TH Bingen); Diversity Arrays Technology Pty Ltd (DArT P/L); University of Canberra; Washington State University (WSU); Royal Botanic Gardens Kew; International Treaty on Plant Genetic Resources for Food and Agriculture, FAO (ITPGRFA (FAO)); MrBot Software Solutions; The James Hutton Institute; Seqart Africa, Old Naivasha Rd, Kenyatta University, Kenya.; Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP); Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM); South Green Bioinformatics Platform Montpellier; North Carolina State University Raleigh (NC State); University of North Carolina System (UNC); The BrAPI Project is funded by the U.S. Department of Agriculture, National Institute of Food and Agriculture (grant number 2022-67021-37024).This work is also supported by• The U.S. Department of Agriculture, National Institute of Food and Agriculture (grant number 2022-51181-38449).• The U.S. Department of Agriculture, National Institute of Food and Agriculture National Research Support Project 10.• The U.S. Department of Agriculture (grant numbers 8062-21000-043-004-A, 8062-21000-052-002-A, and 8062-21000-052-003-A).• The Innovation Lab for Crop Improvement Cornell (grant number 7200AA19LE00005).• The Foundation for Food & Agriculture Research (grant number CA20-SS-0000000103).• The European Union’s Horizon 2020 Research and Innovation Programme under (grant number 862613).• The ELIXIR initiative, the research infrastructure for life science data.• The German Ministry of Research and Education (grant number FKZ 031B1302A).• The German Research Foundation DFG (grant number 442032008) (NFDI4Biodiversity). NFDI4Biodiversity is part of the National Research Data Infrastructure in Germany (www.nfdi.de).• The Agence Nationale de la Recherche, programme Investissements d’avenir (grant number ANR-11-INBS-0012).• The French Network of Biological Resource Centres for Research in Biology, Agronomy and Environment, doi:10.15454/b4ec-tf49.• The Bill and Malinda Gates Foundation in cooperation with the Excellence in Breeding Platform of the CGIAR.; ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011); European Project: 862613,H2020-SFS-2018-2020,H2020-SFS-2019-2,AGENT(2020) |
| Source: |
ISSN: 1758-0463. |
| Publisher Information: |
CCSD; Oxford University Press |
| Publication Year: |
2025 |
| Subject Terms: |
[INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB]; [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation; [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]; [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding; [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; [SDV.SA.STA]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of agriculture |
| Description: |
International audience ; 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 st andardized dat a model for breeding data. BrAPI is an international, community-driven effort that facilit ates interoperabilit y among dat abases 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 , phenot yping , germplasm, genot yping , 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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/40996713; info:eu-repo/grantAgreement//862613/EU/Activated GEnebank NeTwork/AGENT; PUBMED: 40996713; WOS: 001578541400001 |
| DOI: |
10.1093/database/baaf048 |
| Availability: |
https://hal.inrae.fr/hal-05290990; https://hal.inrae.fr/hal-05290990v1/document; https://hal.inrae.fr/hal-05290990v1/file/baaf048.pdf; https://doi.org/10.1093/database/baaf048 |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.68C73055 |
| Database: |
BASE |