Data reuse in agricultural genomics research: challenges and recommendations

Alenka Hafner; Victoria DeLeo; Cecilia H Deng; Christine G Elsik; Damarius S Fleming; Peter W Harrison; Theodore S Kalbfleisch; Bruna Petry; Boas Pucker; Elsa H Quezada-Rodríguez; Christopher K Tuggle; James E Koltes

doi:10.1093/gigascience/giae106

Data reuse in agricultural genomics research: challenges and recommendations

Gigascience. 2025 Jan 6:14:giae106. doi: 10.1093/gigascience/giae106.

Authors

Alenka Hafner^{1

2}, Victoria DeLeo³, Cecilia H Deng⁴, Christine G Elsik^{5

6}, Damarius S Fleming⁷, Peter W Harrison⁸, Theodore S Kalbfleisch⁹, Bruna Petry¹⁰, Boas Pucker¹¹, Elsa H Quezada-Rodríguez^{12

13}, Christopher K Tuggle¹⁰, James E Koltes¹⁰

Affiliations

¹ Department of Biology, Frear North, Pennsylvania State University, University Park, PA, 16802, US.
² Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, 16802, US.
³ Bowery Farming, Kearny, NJ, US.
⁴ New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, Auckland, 1025, New Zealand.
⁵ Division of Animal Sciences and Division of Plant Science & Technology, University of Missouri, MO, 65211, US.
⁶ Institute for Data Science & Informatics, University of Missouri, MO, 65211, US.
⁷ Animal Parasitic Diseases Laboratory, United States Department of Agriculture Agricultural Research Service, Beltsville, MD, 20705, US.
⁸ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SD, UK.
⁹ Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40202, US.
¹⁰ Department of Animal Science, Iowa State University, Ames, IA, 50011, US.
¹¹ Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, 38106, Germany.
¹² Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, 04510, México.
¹³ Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México.

Abstract

The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Here, we identify the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research. We propose possible solutions stakeholders could implement to mitigate and overcome these challenges and provide an optimistic perspective on the future of genomics and transcriptomics data reuse.

Keywords: FAIR; agriculture; big data; data reuse; data standards; genomics; metadata; transcriptomics.

Publication types

Review

MeSH terms

Agriculture*
Databases, Genetic
Genomics* / methods
Genomics* / standards
Metadata

Abstract

Publication types

MeSH terms

Grants and funding