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A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data

BACKGROUND: Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Ac...

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Autores principales: Nault, Rance, Cave, Matthew C., Ludewig, Gabriele, Moseley, Hunter N.B., Pennell, Kelly G., Zacharewski, Tim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Environmental Health Perspectives 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10289218/
https://www.ncbi.nlm.nih.gov/pubmed/37352010
http://dx.doi.org/10.1289/EHP11484
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author Nault, Rance
Cave, Matthew C.
Ludewig, Gabriele
Moseley, Hunter N.B.
Pennell, Kelly G.
Zacharewski, Tim
author_facet Nault, Rance
Cave, Matthew C.
Ludewig, Gabriele
Moseley, Hunter N.B.
Pennell, Kelly G.
Zacharewski, Tim
author_sort Nault, Rance
collection PubMed
description BACKGROUND: Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise. OBJECTIVE: In this commentary, we examine the current state of managing data and metadata—referred to collectively as (meta)data—in the experimental environmental health sciences. We introduce new tools and resources based on in vivo experiments to serve as examples for the broader field. METHODS: We discuss previous and ongoing efforts to improve (meta)data collection and curation. These include global efforts by the Functional Genomics Data Society to develop metadata collection tools such as the Investigation, Study, Assay (ISA) framework, and the Center for Expanded Data Annotation and Retrieval. We also conduct a case study of in vivo data deposited in the Gene Expression Omnibus that demonstrates the current state of in vivo environmental health data and highlights the value of using the tools we propose to support data deposition. DISCUSSION: The environmental health science community has played a key role in efforts to achieve the goals of the FAIR guiding principles and is well positioned to advance them further. We present a proposed framework to further promote these objectives and minimize the obstacles between data producers and data scientists to maximize the return on research investments. https://doi.org/10.1289/EHP11484
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spelling pubmed-102892182023-06-24 A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data Nault, Rance Cave, Matthew C. Ludewig, Gabriele Moseley, Hunter N.B. Pennell, Kelly G. Zacharewski, Tim Environ Health Perspect Commentary BACKGROUND: Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise. OBJECTIVE: In this commentary, we examine the current state of managing data and metadata—referred to collectively as (meta)data—in the experimental environmental health sciences. We introduce new tools and resources based on in vivo experiments to serve as examples for the broader field. METHODS: We discuss previous and ongoing efforts to improve (meta)data collection and curation. These include global efforts by the Functional Genomics Data Society to develop metadata collection tools such as the Investigation, Study, Assay (ISA) framework, and the Center for Expanded Data Annotation and Retrieval. We also conduct a case study of in vivo data deposited in the Gene Expression Omnibus that demonstrates the current state of in vivo environmental health data and highlights the value of using the tools we propose to support data deposition. DISCUSSION: The environmental health science community has played a key role in efforts to achieve the goals of the FAIR guiding principles and is well positioned to advance them further. We present a proposed framework to further promote these objectives and minimize the obstacles between data producers and data scientists to maximize the return on research investments. https://doi.org/10.1289/EHP11484 Environmental Health Perspectives 2023-06-23 /pmc/articles/PMC10289218/ /pubmed/37352010 http://dx.doi.org/10.1289/EHP11484 Text en https://ehp.niehs.nih.gov/about-ehp/licenseEHP is an open-access journal published with support from the National Institute of Environmental Health Sciences, National Institutes of Health. All content is public domain unless otherwise noted.
spellingShingle Commentary
Nault, Rance
Cave, Matthew C.
Ludewig, Gabriele
Moseley, Hunter N.B.
Pennell, Kelly G.
Zacharewski, Tim
A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
title A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
title_full A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
title_fullStr A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
title_full_unstemmed A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
title_short A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
title_sort case for accelerating standards to achieve the fair principles of environmental health research experimental data
topic Commentary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10289218/
https://www.ncbi.nlm.nih.gov/pubmed/37352010
http://dx.doi.org/10.1289/EHP11484
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