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. 2019 Oct 15;35(20):4147-4155.
doi: 10.1093/bioinformatics/btz190.

BrAPI-an application programming interface for plant breeding applications

Peter Selby  1 , Rafael Abbeloos  2 , Jan Erik Backlund  3 , Martin Basterrechea Salido  4 , Guillaume Bauchet  5 , Omar E Benites-Alfaro  6   7 , Clay Birkett  8 , Viana C Calaminos  9 , Pierre Carceller  10 , Guillaume Cornut  11 , Bruno Vasques Costa  12 , Jeremy D Edwards  13 , Richard Finkers  14 , Star Yanxin Gao  15 , Mehmood Ghaffar  4 , Philip Glaser  15 , Valentin Guignon  16 , Puthick Hok  17 , Andrzej Kilian  17 , Patrick König  4 , Jack Elendil B Lagare  9 , Matthias Lange  4 , Marie-Angélique Laporte  16 , Pierre Larmande  18 , David S LeBauer  19 , David A Lyon  5 , David S Marshall  20   21 , Dave Matthews  8 , Iain Milne  20 , Naymesh Mistry  22 , Nicolas Morales  5 , Lukas A Mueller  5 , Pascal Neveu  23 , Evangelia Papoutsoglou  14 , Brian Pearce  17 , Ivan Perez-Masias  6 , Cyril Pommier  11 , Ricardo H Ramírez-González  24 , Abhishek Rathore  25 , Angel Manica Raquel  9 , Sebastian Raubach  20 , Trevor Rife  26 , Kelly Robbins  1 , Mathieu Rouard  16 , Chaitanya Sarma  25 , Uwe Scholz  4 , Guilhem Sempéré  10   27 , Paul D Shaw  20 , Reinhard Simon  28 , Nahuel Soldevilla  3   29 , Gordon Stephen  20 , Qi Sun  15 , Clarysabel Tovar  3   29 , Grzegorz Uszynski  17 , Maikel Verouden  30 ; BrAPI consortium
Affiliations

BrAPI-an application programming interface for plant breeding applications

Peter Selby et al. Bioinformatics. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
An example BrAPI response object. This object shows a generic response with ‘metadata’, a ‘master’ result record and a set of ‘data’ records
Fig. 2.
Fig. 2.
A screenshot of an example web application that retrieves information through BrAPI. Such applications are often referred to as ‘BrAPPs’. This application, called ‘Graphical Filtering’, allows to filter accessions by phenotypic data, by interactively selecting ranges of trait values for different traits in the dataset. Data from Cassavabase (https://cassavabase.org/) are shown, but BrAPPs seamlessly integrate with any BrAPI-enabled database
Fig. 3.
Fig. 3.
BRAVA portal. (A) List of publicly available endpoints and their compliance status according to BRAVA. An expanded report panel shows the individual test results for the selected resource. (B) ‘Test your own’ panel where the user can test a custom URL or (C) subscribe to get periodic reports
See this image and copyright information in PMC

References

    1. Cooper L. et al. (2018) The planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Res., 46, D1168–D1180. - PMC - PubMed
    1. Ćwiek-Kupczyńska H.T. et al. (2016) Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods, 12, 44. - PMC - PubMed
    1. Doan A. et al. (2004) Introduction to the special issue on semantic integration. ACM SIGMOD Record, 33, 11.
    1. Dowell R.D. et al. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7. - PMC - PubMed
    1. Fielding R.T., Taylor R.N. (2002) Principled design of the modern web architecture. ACM Trans. Internet Technol., 2, 115–150.

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