Filters








65 Hits in 3.1 sec

BrAPI - an Application Programming Interface for Plant Breeding Applications

Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar Benites-Alfaro, Clay Birkett, Viana C Calaminos, Pierre Carceller, Guillaume Cornut, Bruno Vasques Costa, Jeremy D Edwards, Richard Finkers (+44 others)
2019 Bioinformatics  
Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration.  ...  We also acknowledge the Excellence in Breeding Platform (EiB) for their ongoing support of the BrAPI effort.  ...  Acknowledgements 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.  ... 
doi:10.1093/bioinformatics/btz190 pmid:30903186 pmcid:PMC6792114 fatcat:fudu7xsp6ffqlkinynmvrjsyye

ELIXIR-EXCELERATE D7.3: Implementation of BRAPI (Plant Breeding API) at all participating nodes

Célia Miguel, Cyril Pommier, Richard Finkers, Frederik Coppens, Dan Bolser, Manuel Ruiz, Anne-Françoise Adam-Blondon, Kristina Gruden, Živa Ramšak, Evangelia Papoutsoglou, Daniel Faria, Bruno Costa (+1 others)
2019 Zenodo  
This service uses the Breeding API (BrAPI1), an API for accessing data relevant for plant breeding developed by the international plant community (Deliverable 7.2).  ...  This work represents a major step towards plant FAIR data and a significant tool for the international plant community focused on plant breeding, [...]  ...  BrAPI endpoints implemented by the participants.  ... 
doi:10.5281/zenodo.3354265 fatcat:4zajlvihszaq3kulzxle7dekaq

D7.2 Phenotypic Data Exposed Through Integrating Api By All Participants

Célia Miguel, Cyril Pommier, Richard Finkers, Frederik Coppens, Dan Bolser
2018 Zenodo  
This architecture uses the Breeding API (BrAPI, www.brapi.org ), an API for accessing data relevant for plant breeding developed by the international plant community.  ...  High-throughput "omics" technologies are widely used and increasingly important to support plant biology research and breeding of diverse plant species for production of food, feed, fibre and other biomaterials  ...  plant Breeding Application Programming Interface, BrAPI , supporting access and exposing datasets annotated according to the developed standards, from all participating nodes.  ... 
doi:10.5281/zenodo.1452451 fatcat:oycqplrtlrborjkoaiakrvw544

Programmatic Access to FAIRified Digital Plant Genetic Resources

Mehmood Ghaffar, Danuta Schüler, Patrick König, Daniel Arend, Astrid Junker, Uwe Scholz, Matthias Lange
2019 Journal of Integrative Bioinformatics  
As one of the worlds leading plant research institutes it is of vital interest for the IPK-Gatersleben to transform legacy data infrastructures into a bio-digital resource center for plant genetics resources  ...  Genetic variance within the genotype of population and its mapping to phenotype variance in a systematic and high throughput manner is of interest for biodiversity and breeding research.  ...  Furthermore, thanks to Jens Bauernfeind and Thomas Muench for great technical support and for hosting the RESTFull services. We like to thank Heiko Miehe for providing great IT service coordination.  ... 
doi:10.1515/jib-2019-0060 pmid:31913851 pmcid:PMC7074143 fatcat:ws4g2hgp4jh3fpe76dsqepmh64

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski (+8 others)
2021 Briefings in Bioinformatics  
least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data.  ...  Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets.  ...  USDA is an equal opportunity provider and Employer.  ... 
doi:10.1093/bib/bbab238 pmid:34251419 pmcid:PMC8574961 fatcat:khqsm7dedrgupeu7h5iyaoi7wi

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation [article]

Peter Bradbury, Terry Casstevens, Sarah E Jensen, Lynn C Johnson, Zachary R Miller, Brandon Monier, Maria Cinta Romay, Baoxing Song, Edward S Buckler
2021 bioRxiv   pre-print
Results: The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service.  ...  The PHG is a platform and environment for the understanding and application of genomic diversity. Availability: All resources listed here are freely available.  ...  Ktor is a framework for creating web applications using the Kotlin programming language. BrAPI is a specification for a RESTful web service for sharing plant breeding data.  ... 
doi:10.1101/2021.08.27.457652 fatcat:2dea6tyunfcmjogkuaaq5rpxse

Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Evangelia A. Papoutsoglou, Daniel Faria, Daniel Arend, Elizabeth Arnaud, Ioannis N. Athanasiadis, Inês Chaves, Frederik Coppens, Guillaume Cornut, Bruno V. Costa, Hanna Ćwiek‐Kupczyńska, Bert Droesbeke, Richard Finkers (+25 others)
2020 New Phytologist  
We have produced the MIAPPE 1.1 release which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions  ...  This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity.  ...  We are grateful for all  ... 
doi:10.1111/nph.16544 pmid:32171029 fatcat:a2a5chl6xzcazllkhhtcoqjpku

Intercross: An Android app for plant breeding and genetics cross management

Trevor W. Rife, Chaney Courtney, Guillaume Bauchet, Mitchell Neilsen, Jesse A. Poland
2022 Crop science  
basis of a plant breeding program.  ...  tool to digitize crossing data for breeding programs.  ...  IMPLEMENTATION We have designed and developed Intercross, an Android application, which aims to be a simple addition to plant breeding workflows.  ... 
doi:10.1002/csc2.20702 fatcat:tzs4fj34wvcdxhpsqsre6vb5mi

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation

P J Bradbury, T Casstevens, S E Jensen, L C Johnson, Z R Miller, B Monier, M C Romay, B Song, E S Buckler, Christina Kendziorski
2022 Bioinformatics  
Results The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service.  ...  The PHG is a platform and environment for the understanding and application of genomic diversity. Availability All resources listed here are freely available.  ...  Ktor is a framework for creating web applications using the Kotlin programming language. BrAPI is a specification for a RESTful web service for sharing plant breeding data.  ... 
doi:10.1093/bioinformatics/btac410 pmid:35748708 pmcid:PMC9344836 fatcat:powapohi5ze6li7ip5li5hhw6q

Intercross: An Android app for plant breeding and genetics cross management [article]

Trevor W. Rife, Chaney Courtney, Guillaume Bauchet, Mitchell Neilsen, Jesse A. Poland
2021 arXiv   pre-print
basis of a plant breeding program.  ...  tool to digitize crossing data for breeding programs.  ...  IMPLEMENTATION We have designed and developed Intercross, an Android application, that aims to be a simple addition to plant breeding workflows.  ... 
arXiv:2107.05844v1 fatcat:yk42e7tow5hunixwjyfboa76cy

Strategies for Effective Use of Genomic Information in Crop Breeding Programs Serving Africa and South Asia

Nicholas Santantonio, Sikiru Adeniyi Atanda, Yoseph Beyene, Rajeev K. Varshney, Michael Olsen, Elizabeth Jones, Manish Roorkiwal, Manje Gowda, Chellapilla Bharadwaj, Pooran M. Gaur, Xuecai Zhang, Kate Dreher (+7 others)
2020 Frontiers in Plant Science  
Progress on GOBii, EiB, and implementation of GS in CIMMYT and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) breeding programs are discussed, as well as strategies for routine  ...  implementation of GS in breeding programs serving Africa and South Asia.  ...  Common standards for Application Program Interfaces (API), such as BrAPI, will enable customization for a variety of breeding processes.  ... 
doi:10.3389/fpls.2020.00353 pmid:32292411 pmcid:PMC7119190 fatcat:lrdk76gezbcujdjowcdi55moma

Making waves in Breedbase: An integrated spectral data storage and analysis pipeline for plant breeding programs

Jenna Hershberger, Nicolas Morales, Christiano C. Simoes, Bryan Ellerbrock, Guillaume Bauchet, Lukas A. Mueller, Michael A. Gore
2021 tppj  
Visible and near-infrared spectroscopy (Vis-NIRS) is a promising tool for increasing phenotyping throughput in plant-breeding programs, but existing analysis software packages are not optimized for a breeding  ...  Additionally, commercial software options are often outside of budget constraints for some breeding and research programs.  ...  This is especially useful in the context of plant breeding programs, which often rely on expensive and time-consuming quality trait information for the development and release of improved plant varieties  ... 
doi:10.1002/ppj2.20012 fatcat:5tdrd2nfana3tf5qzbk2vzv6dm

Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS

C. Pommier, C. Michotey, G. Cornut, P. Roumet, E. Duchêne, R. Flores, A. Lebreton, M. Alaux, S. Durand, E. Kimmel, T. Letellier, G. Merceron (+8 others)
2019 Plant Phenomics  
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures.  ...  GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures  ...  Gauffreteau, who entrusted GnpIS for the publication of their data that made the first important public  ... 
doi:10.34133/2019/1671403 pmid:33313522 pmcid:PMC7718628 fatcat:rbvmsk4pa5ffbf2igc5b6x6gxu

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

Annemarie H. Eckes, Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer, Wiktor Jurkowski
2017 F1000Research  
Qiu D, et al.: Integrated marker system for oilseed rape breeding. 2006. 18.  ...  A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users.  ...  Minimum Information About a Plant Phenotyping Experiment (MIAPPE); and to Manuel Corpas for introducing us to the ELIXIR programme, immensely important for future phases of BIP development.  ... 
doi:10.12688/f1000research.11301.2 pmid:28529710 pmcid:PMC5428495 fatcat:zgrhawfj65de5gqngd755tcawi

From bits to bites: advancement of the germinate platform to support genetic resources collections and pre‐breeding informatics for crop wild relatives

Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo M. Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, Alan Humphries, David Jordan (+23 others)
2020 Crop science  
Management and distribution of experimental data from prebreeding projects is important to ensure uptake of germplasm into breeding and research programs.  ...  dasyphyllum Plant breeding application programming interface.  ...  sunflower breeding programs.  ... 
doi:10.1002/csc2.20248 fatcat:ptp7d2ekjjg4bkxdnw2a6tru54
« Previous Showing results 1 — 15 out of 65 results