BrAPI-an application programming interface for plant breeding applications

Autor: Guilhem Sempere, Patrick König, Bruno Costa, Jan Erik Backlund, Jack Elendil B. Lagare, Viana C. Calaminos, Jeremy D. Edwards, Gordon Stephen, Omar Eduardo Benites-Alfaro, Pierre Carceller, Martin Basterrechea Salido, David LeBauer, Maikel P. H. Verouden, Guillaume Cornut, Nicolas Morales, Philip Glaser, David Marshall, Evangelia Papoutsoglou, Cyril Pommier, Guillaume Bauchet, Valentin Guignon, Kelly R. Robbins, Iain Milne, David A. Lyon, Pascal Neveu, Brian Pearce, Chaitanya Sarma, Qi Sun, Nahuel Soldevilla, Sebastian Raubach, Peter Selby, Clarysabel Tovar, Grzegorz Uszynski, Rafael Abbeloos, Reinhard Simon, Paul Shaw, Marie-Angélique Laporte, Mathieu Rouard, Star Yanxin Gao, Naymesh Mistry, Puthick Hok, Uwe Scholz, Trevor W. Rife, Ricardo H. Ramirez-Gonzalez, Dave Matthews, Mehmood Ghaffar, Pierre Larmande, Matthias Lange, Andrzej Kilian, Clayton Birkett, Ivan Perez-Masias, Angel Manica Raquel, Abhishek Rathore, Lukas A. Mueller, Richard Finkers
Přispěvatelé: Wren, Jonathan, Flanders Institute for Biotechnology, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Boyce Thompson Institute [Ithaca], International Potato Center, USDA-ARS : Agricultural Research Service, International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Instituto de Biologia Experimental e Tecnológica (IBET), Wageningen University and Research Centre (WUR), Cornell University [New York], CGIAR, Diversity Arrays Technology Pty Ltd (DArT P/L), Institut de Recherche pour le Développement (IRD), University of Arizona, The James Hutton Institute, LeafNode Technology, Partenaires INRAE, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Kansas State University, Leafnode Technolog, Biometris, Gates Foundation, Bioversity International, Federal Ministry of Education & Research (BMBF) : FKZ 031A536A, 031B0190A, Boyce Thompson Institute for Plant Research CGIAR Research Program on Roots, Tubers and Bananas, Cornell University Excellence in Breeding Platform, 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), John Innes Centre
Rok vydání: 2018
Předmět:
0106 biological sciences
Germplasm
programme informatique
Computer science
[SDV]Life Sciences [q-bio]
Data management
computer.software_genre
01 natural sciences
Biochemistry
F30 - Génétique et amélioration des plantes
User-Computer Interface
Software
Laboratorium voor Plantenveredeling
[MATH]Mathematics [math]
0303 health sciences
Application programming interface
U10 - Informatique
mathématiques et statistiques
Genomics
Original Papers
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
Web service
sélection végétale
Statistics and Probability
Technology and Engineering
Databases and Ontologies
génomique
03 medical and health sciences
Bioinformatique
application informatique
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Life Science
[INFO]Computer Science [cs]
Plant breeding
Genotyping
Molecular Biology
030304 developmental biology
business.industry
Biology and Life Sciences
Amélioration des plantes
Data science
Plant Breeding
business
computer
010606 plant biology & botany
Zdroj: Bioinformatics
BIOINFORMATICS
Bioinformatics (Oxford, England) 35 (2019) 20
Bioinformatics, 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩
Bioinformatics 20 (35), 4147-4155. (2019)
Bioinformatics (Oxford, England), 35(20), 4147-4155
Bioinformatics, Oxford University Press (OUP), 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩
ISSN: 1367-4811
1367-4803
1460-2059
4147-4155
DOI: 10.1093/bioinformatics/btz190⟩
Popis: 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.
Databáze: OpenAIRE
Externí odkaz: