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

Abstract

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.

Figure 1.

Comparison of metadata terms listed in the TERM, TBC, and MIATE/invivo reporting standards. Each standard was manually examined. Only metadata requirements relevant to in vivo experiments for each reporting standard were included for comparison. Because of the use of different vocabularies, each reporting standard metadata term was manually mapped to an equivalent term in the other reporting standards if one were present. Mapping summary can be found in Excel Table S1. The Venn diagram shows the number of common and unique terms for each reporting standard. Note: MIATE/invivo, Minimum Information about Animal Toxicology Experiments in Vivo; TBC, Tox Bio Checklist; TERM, Toxicology Experiment Reporting Module.

Figure 2.

Evaluation of GEO deposited metadata conformance to the in vivo experimental environmental health science reporting standards TERM, TBC, and MIATE/invivo. GEO was queried for mouse and rat data sets using the keywords “dose-response,” “toxicology,” or “dose,” followed by computational extraction of metadata. Following semiautomated metadata assessment to remove studies involving biological (e.g., infections), physical (e.g., cold temperature), or psychological stressors, a total of 1,233 GEO data sets were examined (Excel Table S2). Expected terms were compared to requested metadata in TERM, TBC, and MIATE/invivo reporting standards (Excel Table S3). (A) Percentage of data sets providing each reporting standard term is shown. (B) Top 15 data sets providing the most terms present in any reporting standards shown as a heat map indicating which term was reported. Bolded GEO accession identifiers represent data sets using a draft version of MIATE/invivo. Documentation and code for reproducibility are provided as a supplemental document (MIATE-3.0.1.zip) and available as part of MIATE/invivo resources (doi.org/10.5281/zenodo.7667576). Data used for plotting are provided in supplementary tables (Excel Table S4–S5). Note: GEO, Gene Expression Omnibus; MIATE/invivo, Minimum Information about Animal Toxicology Experiments in Vivo; TBC, Tox Bio Checklist; TERM, Toxicology Experiment Reporting Module.