Evidence map›Paper›PMID 41385557›Full record

ArticlePloS one2025

DeltaBreed: A BrAPI-centric breeding data information system.

Shawn C Yarnes, Nick Palladino, Dave J Meidlinger, David R Philips, Heather M Sweeney, Shahana A Mustafa, Matthew L Mandych, Sam Bouabane, Tim E Parsons, Tyler J Slonecki and 14 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

24 authors.

Shawn C YarnesBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Nick PalladinoBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.ORCID https://orcid.org/0009-0009-1645-297X
Dave J MeidlingerBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
David R PhilipsBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Heather M SweeneyBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Shahana A MustafaBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Matthew L MandychBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Sam BouabaneBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Tim E ParsonsBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.ORCID https://orcid.org/0000-0001-6209-2455
Tyler J SloneckiBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.
Dongyan ZhaoBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.ORCID https://orcid.org/0000-0002-2080-8416
Trevor W RifePlant and Environmental Sciences Department, Clemson University, Florence, South Carolina, United States of America.
Bryan J EllerbrockPlant and Environmental Sciences Department, Clemson University, Florence, South Carolina, United States of America.
Chaney CourtneyPlant and Environmental Sciences Department, Clemson University, Florence, South Carolina, United States of America.
Peter SelbySchool of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America.
Lukas A MuellerBoyce Thompson Institute, Cornell University, Ithaca, New York, United States of America.
Mirella Flores-GonzalezBoyce Thompson Institute, Cornell University, Ithaca, New York, United States of America.
Johan S AparicioDepartment of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.ORCID https://orcid.org/0000-0003-3580-5354
Khaled Al-Sham'aaGenetic Innovation Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt.
Sebastian RaubachInformation & Computational Sciences Department, The James Hutton Institute, Dundee, Scotland, United Kingdom.
Jean-Luc JanninkPlant, Soil and Nutrition Laboratory, Robert W. Holley Center for Agriculture & Health, United States of America Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America.
Edward S BucklerPlant, Soil and Nutrition Laboratory, Robert W. Holley Center for Agriculture & Health, United States of America Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America.
Craig T BeilBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.ORCID https://orcid.org/0000-0002-1756-9987
Moira J SheehanBreeding Insight, Cornell Institute for Biotechnology, Cornell University, Ithaca, New York, United States of America.ORCID https://orcid.org/0000-0002-3400-2165

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

DeltaBreed is a unified breeding data management system designed by Breeding Insight (BI, Cornell University) to serve the wide diversity of USDA-ARS specialty crop and livestock breeding programs. DeltaBreed has a RESTful microservice architecture that utilizes the BrAPI v2.1 Java Test Server as its primary database. The system is interoperable with many BrAPI-compliant applications (BrApps), including Field Book v6.1.0, and is continually aligned with the most recent BrAPI specifications (BrAPI v2.1). Here we describe the features of DeltaBreed v1.0, a minimum viable product, and how we aligned data capture and validation with community standards. We highlight the modules for management of germplasm, observation variables, experiments and observations, genotypic sample submission, and a prototype genomic database that supports polyploid and multiallelic genomic data, as well as SNP data. Several test cases are illustrated to demonstrate the successes and challenges of interoperability with other open-source BrAPI-enabled software packages. We also discuss expansion and enhancement plans for future DeltaBreed versions, as well as outline possible solutions to known limitations. To our knowledge, DeltaBreed is the first species-agnostic, fully BrAPI-compliant breeding data management system built for transactional use.

Indexed as

BreedingDatabases, GeneticPlant BreedingSoftwareAnimalsCrops, AgriculturalGenomicsGenotypePolymorphism, Single Nucleotide

Identifiers

PMID41385557
PMCPMC12700463

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.