BrAPI—an application programming interface for plant breeding applications

Selby Peter, Abbeloos Rafael, Backlund Jan Erik, Basterrechea Salido Martin, Bauchet Guillaume, Benites-Alfaro Omar E., Birkett Clay, Calaminos Viana C., Carceller Pierre, Cornut Guillaume, Vasques Costa Bruno, Edwards Jeremy D., Finkers Richard, Yanxin Gao Star, 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 S., Lyon David A., Marshall David S., Matthews Dave, Milne Iain, Mistry Naymesh, Morales Nicolas, Mueller Lukas, Neveu Pascal, Papoutsoglou Evangelia, Pearce Brian, Perez-Masias Ivan, Pommier Cyril, Ramírez-González Ricardo H., Rathore Abhishek, Raquel Angel Manica, Raubach Sebastian, Rife Trevor, Robbins Kelly, Rouard Mathieu, Sarma Chaitanya, Scholz Uwe, Sempere Guilhem, et al.. 2019. BrAPI—an application programming interface for plant breeding applications. Bioinformatics, 35 (20) : 4147-4155.

Quartile : Outlier, Sujet : MATHEMATICAL & COMPUTATIONAL BIOLOGY / Quartile : Q1, Sujet : BIOCHEMICAL RESEARCH METHODS / Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Résumé : 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.

Mots-clés Agrovoc : amélioration des plantes, bioinformatique, génomique

Mots-clés libres : API, REST, Plant Breeding, Consortium

Classification Agris : F30 - Génétique et amélioration des plantes
U10 - Informatique, mathématiques et statistiques

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

• Selby Peter, Cornell University (USA)
• Abbeloos Rafael, VIB (BEL)
• Backlund Jan Erik, CIMMYT (MEX)
• Basterrechea Salido Martin, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Bauchet Guillaume, Boyce Thompson Institute for Plant Research (USA)
• Benites-Alfaro Omar E., CIP (PER)
• Birkett Clay, USDA (USA)
• Calaminos Viana C., IRRI [International Rice Research Institute] (PHL)
• Carceller Pierre, Université de Montpellier (FRA)
• Cornut Guillaume, INRA (FRA)
• Vasques Costa Bruno, IBET (PRT)
• Edwards Jeremy D., USDA (USA)
• Finkers Richard, Wageningen University and Research Centre (NLD)
• Yanxin Gao Star, Cornell University (USA)
• Ghaffar Mehmood, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Glaser Philip, Cornell University (USA)
• Guignon Valentin, Bioversity International (FRA)
• Hok Puthick, Diversity Arrays Technology (AUS)
• Kilian Andrzej, Diversity Arrays Technology (AUS)
• König Patrick, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Lagare Jack Elendil B., IRRI [International Rice Research Institute] (PHL)
• Lange Matthias, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Laporte Marie-Angélique, Bioversity International (FRA)
• Larmande Pierre, IRD (FRA)
• LeBauer David S., Arizona State University (USA)
• Lyon David A., Boyce Thompson Institute for Plant Research (USA)
• Marshall David S., The James Hutton Institute (GBR)
• Matthews Dave, USDA (USA)
• Milne Iain, The James Hutton Institute (GBR)
• Mistry Naymesh, LeafNode Technology (NZL)
• Morales Nicolas, Boyce Thompson Institute for Plant Research (USA)
• Mueller Lukas, Boyce Thompson Institute for Plant Research (USA) - auteur correspondant
• Neveu Pascal, INRA (FRA)
• Papoutsoglou Evangelia, Wageningen University (NLD)
• Pearce Brian, Diversity Arrays Technology (AUS)
• Perez-Masias Ivan, CIP (PER)
• Pommier Cyril, INRA (FRA)
• Ramírez-González Ricardo H., John Innes Centre (NOR)
• Rathore Abhishek, ICRISAT (IND)
• Raquel Angel Manica, IRRI [International Rice Research Institute] (PHL)
• Raubach Sebastian, ICRISAT (IND)
• Rife Trevor, Kansas State University (USA)
• Robbins Kelly, Cornell University (USA)
• Rouard Mathieu, Bioversity International (FRA)
• Sarma Chaitanya, ICRISAT (IND)
• Scholz Uwe, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA) ORCID: 0000-0001-7429-2091
• et al.

Source : Cirad-Agritrop (https://agritrop.cirad.fr/592426/)

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