Title
BrAPI - An application programming interface for plant breeding applications
Date Issued
15 October 2019
Access level
open access
Resource Type
research article
Author(s)
Selby P.
Abbeloos R.
Backlund J.E.
Basterrechea Salido M.
Bauchet G.
Benites-Alfaro O.E.
Birkett C.
Calaminos V.C.
Carceller P.
Cornut G.
Vasques Costa B.
Edwards J.D.
Finkers R.
Yanxin Gao S.
Ghaffar M.
Glaser P.
Guignon V.
Hok P.
Kilian A.
König P.
Lagare J.E.B.
Lange M.
Laporte M.A.
Larmande P.
Lebauer D.S.
Lyon D.A.
Marshall D.S.
Matthews D.
Milne I.
Mistry N.
Morales N.
Mueller L.A.
Neveu P.
Papoutsoglou E.
Pearce B.
Perez-Masias I.
Pommier C.
Ramírez-González R.H.
Rathore A.
Raquel A.M.
Raubach S.
Rife T.
Robbins K.
Rouard M.
Sarma C.
Scholz U.
Sempéré G.
Shaw P.D.
Soldevilla N.
Stephen G.
Sun Q.
Tovar C.
Uszynski G.
Verouden M.
Wren J.
Patranca E.I.R.L.
Abstract
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.
Start page
4147
End page
4155
Volume
35
Issue
20
Language
English
OCDE Knowledge area
Ciencias de la computación
Subjects
Scopus EID
2-s2.0-85067510305
PubMed ID
Source
Bioinformatics
ISSN of the container
13674803
Sponsor(s)
The BrAPI consortium gratefully acknowledges The Bill and Melinda Gates Foundation for providing funds and support for an organizational meeting in Seattle and three hackathons. We would also like to thank the following organizations for hosting BrAPI Hackathons: GOBii, The Boyce Thompson Institute, INRA, CGIAR Bioversity International, and CGIAR Research Program on Roots, Tubers, and Bananas. We acknowledge Elixir (European Infrastructure for bio-informatic, supported by the ELIXIR-EXCELERATE project funded by the European Commission within the Research Infrastructures program of Horizon 2020, grant agreement numbers 676559 ) and Phenome EMPHASIS.fr (French Phenotyping Infrastructure funded by the Infrastructure Biologie SantÕ ’Phenome-FPPN’ supported by the French National Research Agency, ANR-11-INBS-0012) for the adoption and support of the BrAPI. We also acknowledge the Excellence in Breeding Platform (EiB) for their ongoing support of the BrAPI effort.
This work was supported by the Bill and Melinda Gates Foundation, Bioversity International, German BMBF (FKZ 031A536A and 031B0190A), the Boyce Thompson Institute for Plant Research, the CGIAR Research Program on Roots, Tubers and Bananas, Cornell University, and the Excellence in Breeding Platform.
Cornell University, https://cornell.edu BTI, https://btiscience.org Description: large scale and efficient genotyping storage system including data analysis workflows https://triticeaetoolbox.org USDA, https://usda.gov Description: comprehensive breeding management system designed for wheat https://www.crop-diversity.org/mgis Bioversity International, https://bioversityinternational.org, (Ruas et al., 2017) Description: information system on banana germplasm http://gigwa.southgreen.fr CIRAD, IRD (South Green) Description: Gigwa (Sempéré et al., 2016) is a web-application that aims at storing and exposing genotypic datasets and provides a web interface for filtering them in real time. It is able to interoperate with genome browsers and export results into several formats. https://www.eu-sol.wur.nl Wageningen University & Research, https://wur.nl Description: this site contains information about a collection composed of ~7000 domesticated (S. lycopersi-cum) lines, along with representative wild species, collected with the scope of the european project EU-SOL. This germplasm was generously provided by different international genebanks and by donations from private collections. This Integrated Project is supported by the European Commission through the 6th framework program. Contract number: FOOD-CT-2006-016214 https://urgi.versailles.inra.fr/gnpis INRA, https://www.inra.fr Description: French national archive for plant phenotyping data. It provides any type of PGR and Phenotyping data. Used for instance by Perpheclim for climate change adaptation studies and as a data re-pository in the Elixir federation which is under construction. It contains almost a thousand Phenotyping tri-als over thousands of woody and annual plant varieties. https://kddart.diversityarrays.com/brapi/v1/ DArT, http://www.kddart.org Description: genotype and phenotype database, linked to genotyping service http://www.cropontology.org/ Bioversity, https://bioversityinternational.org Description: database of available trait ontologies for diverse crops in the CGIAR system https://pippa.psb.ugent.be VIB https://www.psb.ugent.be/ Description: PSB Interface for Plant Phenotype Analysis http://www.phis.inra.fr INRA, https://www.inra.fr Description: ontology-driven Information System designed for Plant Phenomics. PHIS is designed to store, or-ganize and manage highly heterogeneous and multi-spatial and temporal data from multiple sources (field, greenhouse). https://fair-ipk.ipk-gatersleben.de/public/breedin IPK-Gatersleben, https://www.ipk-gatersleben.de gapi.html Description: among other, FAIR-IPK offers access to IPK genbank information system GBIS. This comprise passport data (information on the identity, history, geographical origin and botanical classification of the material) of the 150, 780 accessions in Gatersleben (as of 30 June 2016), including the Satellite Collections North in Gross Lüsewitz (potatoes) and Malchow/Poel (oil and fodder crops). https://terraref.ncsa.illinois.edu/bety https://terraref.org Description: an open access reference database for high throughput phenomics. Crops include sorghum and wheat.
Sources of information:
Directorio de Producción Científica
Scopus