Evidence map›Paper›PMID 41991945›Full record

ArticleScientific data2026

Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.

Marcela K Tello-Ruiz, Timothee Cezard, Carson Andorf, Sonia Balyan, Nahla V Bassil, Sebastian Beier, Jill M Bushakra, Tao-Ho Chang, Kapeel Chogule, Irene Cobo-Simón and 14 more

Abstract readDataset
In one paragraph

Article in Scientific data, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. The future is FAIR: a community framework for enhanced data management and data sharing.Database : the journal of biological databases and curation · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

24 authors.

Marcela K Tello-RuizCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA. marcela@phxbio.org.ORCID 0000-0002-7499-5368
Timothee CezardEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Carson AndorfDepartment of Computer Science, Iowa State University, Ames, IA, 50011, USA.
Sonia BalyanIndian Biological Data Centre, Regional Centre for Biotechnology, Faridabad, Haryana, 121001, India.
Nahla V BassilUSDA ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA.
Sebastian BeierInstitute of Bio- and Geosciences (IBG-4 Bioinformatics), CEPLAS, BIOSC, Forschungszentrum Jülich GmbH, Wilhelm Johnen Straße, Jülich, Germany.ORCID 0000-0002-2177-8781
Jill M BushakraUSDA ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA.
Tao-Ho ChangProgram in Plant Health Care, Academy of Circular Economy, National Chung Hsing University, Taichung, Taiwan.
Kapeel ChoguleCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Irene Cobo-SimónInstitute of Forest Science, National Center National Institute for Agricultural and Food Research and Technology, Spanish National Research Council (ICIFOR-INIA-CSIC), Madrid, Spain.
Sarah DyerEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Christine G ElsikDivision of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Nicholas GladmanCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Melanie HarrisonUSDA ARS, Plant Genetic Resources Conservation Unit, Griffin, GA, 30223, USA.
Jodi HumannDepartment of Horticulture, Washington State University, Pullman, WA, 99164, USA.
Catherine KimCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Vivek KumarCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Raja S NandetyUSDA ARS PA, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA.ORCID 0000-0002-1129-0790
Rex NelsonUnited States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA.
Andrew OlsonCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Taner Z SenUSDA ARS, Crop Improvement and Genetics Research, Albany, CA, 94710, USA.
Moira J SheehanDepartment of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA.
Sharon WeiCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
Doreen WareCold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA. ware@cshl.edu.ORCID 0000-0002-8125-3821

Funding

National Science Foundation (NSF) 2126334NIH HHS S10 OD0286321-01United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 2030-21000-056-00DUnited States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 5030-21000-072-000DUnited States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 8062-21000-051-000DWellcome Trust (Wellcome) 228142/Z/23/Z
6 · The paper itself

Abstract

Agricultural research has long faced challenges with data sharing, often relying on informal networks and requiring significant effort to clean and harmonize data. This hampers collaboration and limits data reuse. While FAIR (Findable, Accessible, Interoperable, and Reusable) principles are widely adopted in biomedical research, their uptake in agricultural genomics has lagged. The AgBioData Standards for Genetic Variation Working Group aims to close this gap by promoting FAIR data practices. We surveyed current standards for managing agricultural genetic variation and recommend adopting reference SNP identifiers (rsIDs) as a key step. We present examples from crop research communities with varying data maturity, including those without reference assemblies. Milestones include introducing nearly 220 million rsIDs to Gramene and pangenome databases, projecting rsIDs from reference to pangenome varieties in sorghum and maize, and developing an agricultural FAIR guide for rsID adoption. Better coordination among data producers, repositories, and breeding platforms is essential to improve interoperability, consistency, and accelerate genetic variant discovery for crop trait improvement.

Indexed as

Crops, AgriculturalGenomicsPolymorphism, Single NucleotideAgricultureDatabases, GeneticInformation DisseminationSorghumZea mays

Identifiers

PMID41991945
PMCPMC13260324

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.