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

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

Research output: Contribution to journal › Review article › peer-review

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.

Original language	English
Article number	giae106
Journal	GigaScience
Volume	14
DOIs	https://doi.org/10.1093/gigascience/giae106
State	Published - 2025

Bibliographical note

Publisher Copyright:
© 2025 The Author(s).

Keywords

FAIR
agriculture
big data
data reuse
data standards
genomics
metadata
transcriptomics

ASJC Scopus subject areas

General Medicine

Access to Document

10.1093/gigascience/giae106

Cite this

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title = "Data reuse in agricultural genomics research: Challenges and recommendations",

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",

author = "Alenka Hafner and Victoria Deleo and Deng, {Cecilia H.} and Elsik, {Christine G.} and {S Fleming}, Damarius and Harrison, {Peter W.} and Kalbfleisch, {Theodore S.} and Bruna Petry and Boas Pucker and Quezada-Rodr{\'i}guez, {Elsa H.} and Tuggle, {Christopher K.} and Koltes, {James E.}",

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year = "2025",

doi = "10.1093/gigascience/giae106",

language = "English",

volume = "14",

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T2 - Challenges and recommendations

AU - Hafner, Alenka

AU - Deleo, Victoria

AU - Deng, Cecilia H.

AU - Elsik, Christine G.

AU - S Fleming, Damarius

AU - Harrison, Peter W.

AU - Kalbfleisch, Theodore S.

AU - Petry, Bruna

AU - Pucker, Boas

AU - Quezada-Rodríguez, Elsa H.

AU - Tuggle, Christopher K.

AU - Koltes, James E.

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

KW - FAIR

KW - agriculture

KW - big data

KW - data reuse

KW - data standards

KW - genomics

KW - metadata

KW - transcriptomics

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DO - 10.1093/gigascience/giae106

M3 - Review article

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JO - GigaScience

JF - GigaScience

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ER -

Data reuse in agricultural genomics research: Challenges and recommendations

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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