A Metadata Checklist and Data Formatting Guidelines to Make <scp>eDNA FAIR</scp> (Findable, Accessible, Interoperable, and Reusable)

ABSTRACT The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding‐based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data‐driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA‐specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready‐to‐use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user‐driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long‐term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.

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Publication Details

Journal
Environmental DNA
Published
2025-05-01
DOI
https://doi.org/10.1002/edn3.70100
Citations
18
Primary Topic
Environmental DNA in Biodiversity Studies
Type
article
Field-Weighted Citation Impact
30.89

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A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable)

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A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable)

Erin E. Hahn, Nicholas Dunn, Chris Hunter, Sean P. Jungbluth, Luke Thompson, Neha Acharya‐Patel, Cecilia Villacorta‐Rath, Thomas Stjernegaard Jeppesen, Christopher L. Jerde, Mark Louie D. Lopez, Suk Yee Yong, Peggy Newman, Oliver Berry, Miwa Takahashi, Stephen K. Formel, Bettina Thalinger, Joana Paupério, Lynsey R. Harper, Tobias Guldberg Frøslev, Sachit Rajbhandari, Peter Woollard, Shaun Wilkinson, Guy Cochrane, Katy E. Klymus, Bruce E. Deagle, Martin Laporte, Katrina M. West, Katherine Silliman, Andrew Bissett, Caren C. Helbing, Gareth Jenkins, Lynn M. Schriml, Rachel Haderlé
article en
18 citations

Abstract

ABSTRACT The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding‐based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data‐driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA‐specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready‐to‐use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user‐driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long‐term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.

Environmental DNAVol. 7(3)
Global Biodiversity Information Facility (DK), University of Maryland, Baltimore (US), United States Geological Survey (US), Commonwealth Scientific and Industrial Research Organisation (AU), European Bioinformatics Institute (GB), National Oceanic and Atmospheric Administration (US), Natural England (GB), University of California, Santa Barbara (US), Universität Innsbruck (AT), Curtin University (AU), University of Victoria (CA), NOAA Atlantic Oceanographic and Meteorological Laboratories (US), Northern Gulf Institute (US), Institut de Systématique, Évolution, Biodiversité (FR), John Wiley & Sons (United Kingdom) (GB), Australian National Fish Collection (AU), Australian National Wildlife Collection (AU), Université Laval (CA), ACT Government (AU), Columbia Environmental Research Center, Science Analytics and Synthesis, San Francisco State University (US), James Cook University (AU), Mississippi State University (US)
European Commission, Commonwealth Scientific and Industrial Research Organisation, National Oceanic and Atmospheric Administration
Openalex Percentile: Top 0%
Environmental DNA in Biodiversity Studies
30.89
DOIOpen Access PDFOpenAlex
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