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

Tello-Ruiz, Marcela K, Cezard, Timothee, Andorf, Carson, Balyan, Sonia, Bassil, Nahla V, Beier, Sebastian, Bushakra, Jill M, Chang, Tao-Ho, Chogule, Kapeel, Cobo-Simón, Irene, Dyer, Sarah, Elsik, Christine G, Gladman, Nicholas, Harrison, Melanie, Humann, Jodi, Kim, Catherine, Kumar, Vivek, Nandety, Raja S, Nelson, Rex, Olson, Andrew, Sen, Taner Z, Sheehan, Moira J, Wei, Sharon, Ware, Doreen (April 2026) Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse. Scientific data, 13 (1). p. 885. ISSN 2052-4463 (Public Dataset)

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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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics
organism description > plant
organism description > plant > sorghum
CSHL Authors:
Communities: CSHL labs > Ware lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 16 April 2026
Date Deposited: 15 Jun 2026 12:26
Last Modified: 15 Jun 2026 12:26
Related URLs:
Dataset ID:
  • https://github.com/warelab/gramene-ensembl/blob/e506aaf4001340e91351f0b620dffb9aea25651d/scripts/load-scripts/
URI: https://repository.cshl.edu/id/eprint/42222

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