Curation of a list of chemicals in biosolids from EPA National Sewage Sludge Surveys &amp; Biennial Review Reports

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Abstract

Section 405(d) of the Clean Water Act requires the US Environmental Protection Agency to review sewage sludge regulations every two years to identify any additional pollutants that may occur in biosolids and to set regulations for pollutants identified in biosolids if sufficient scientific evidence shows they may harm human health or the environment. To date, EPA has conducted eight biennial reviews to identify chemical and microbial pollutants and three national sewage sludge surveys to identify pollutants and obtain concentration data for chemicals found in biosolids. Prior to 2021, there was inconsistent reporting of chemicals identified and EPA did not cumulatively track chemicals in biosolids. Through the efforts presented here, EPA produced a list of 726 chemicals and structure-based classes found in biosolids based on biennial reviews and national sewage sludge surveys. Summary statistics of concentration data are also reported for the 484 chemicals found in the three national sewage sludge surveys. The creation of the Biosolids List supports EPA in assessing the potential risk of chemical pollutants found in biosolids.

Abstract

Measurement(s)	biosolids • chemicals
Technology Type(s)	digital curation
Sample Characteristic - Location	United States of America

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The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

Antony J. Williams, Christopher Grulke, Jeff Edwards … (2018)

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency’s (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA’s DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a flexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists. Electronic supplementary material The online version of this article (10.1186/s13321-017-0247-6) contains supplementary material, which is available to authorized users.

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InChI, the IUPAC International Chemical Identifier

Stephen R Heller, Alan McNaught, Igor Pletnev … (2015)

This paper documents the design, layout and algorithms of the IUPAC International Chemical Identifier, InChI.

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EPA’s DSSTox database: History of development of a curated chemistry resource supporting computational toxicology research

Christopher Grulke, Antony J. Williams, Inthirany Thillanadarajah … (2019)

The US Environmental Protection Agency’s (EPA) Distributed Structure-Searchable Toxicity (DSSTox) database, launched publicly in 2004, currently exceeds 875 K substances spanning hundreds of lists of interest to EPA and environmental researchers. From its inception, DSSTox has focused curation efforts on resolving chemical identifier errors and conflicts in the public domain towards the goal of assigning accurate chemical structures to data and lists of importance to the environmental research and regulatory community. Accurate structure-data associations, in turn, are necessary inputs to structure-based predictive models supporting hazard and risk assessments. In 2014, the legacy, manually curated DSSTox_V1 content was migrated to a MySQL data model, with modern cheminformatics tools supporting both manual and automated curation processes to increase efficiencies. This was followed by sequential auto-loads of filtered portions of three public datasets: EPA’s Substance Registry Services (SRS), the National Library of Medicine’s ChemID, and PubChem. This process was constrained by a key requirement of uniquely mapped identifiers (i.e., CAS RN, name and structure) for each substance, rejecting content where any two identifiers were conflicted either within or across datasets. This rejected content highlighted the degree of conflicting, inaccurate substance-structure ID mappings in the public domain, ranging from 12% (within EPA SRS) to 49% (across ChemID and PubChem). Substances successfully added to DSSTox from each auto-load were assigned to one of five qc_levels, conveying curator confidence in each dataset. This process enabled a significant expansion of DSSTox content to provide better coverage of the chemical landscape of interest to environmental scientists, while retaining focus on the accuracy of substance-structure-data associations. Currently, DSSTox serves as the core foundation of EPA’s CompTox Chemicals Dashboard [https://comptox.epa.gov/dashboard], which provides public access to DSSTox content in support of a broad range of modeling and research activities within EPA and, increasingly, across the field of computational toxicology.

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Author and article information

Contributors

Antony J. Williams:

ORCID: http://orcid.org/0000-0002-2668-4821

Williams.antony@epa.gov

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2052-4463

Publication date (Electronic): 19 April 2022

Publication date PMC-release: 19 April 2022

Publication date Collection: 2022

Volume: 9

Electronic Location Identifier: 180

Affiliations

[1 ]GRID grid.418698.a, ISNI 0000 0001 2146 2763, Oak Ridge Institute for Science and Education (ORISE) Research Participant hosted by EPA. Office of Water, , U.S. Environmental Protection Agency, ; 1200 Pennsylvania Avenue, N.W., Washington, DC 20460 USA

[2 ]GRID grid.418698.a, ISNI 0000 0001 2146 2763, Office of Water, U.S. Environmental Protection Agency, ; 1200 Pennsylvania Avenue, N.W., Washington, DC 20460 USA

[3 ]GRID grid.418698.a, ISNI 0000 0001 2146 2763, Center for Computational Toxicology and Exposure, Office of Research and Development, , U.S. Environmental Protection Agency, ; 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA

[4 ]GRID grid.417548.b, ISNI 0000 0004 0478 6311, Present Address: Office of Pest Management Policy, U.S. Department of Agriculture, ; 1400 Independence Ave., S.W., Washington, DC 20250 USA

Author information

Antony J. Williams http://orcid.org/0000-0002-2668-4821

Article

Publisher ID: 1267

DOI: 10.1038/s41597-022-01267-9

PMC ID: 9018786

PubMed ID: 35440785

SO-VID: 95b7ff22-dd15-4126-a245-32deec061b28

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 18 January 2022

Date accepted : 7 March 2022

Funding

Funded by: FundRef https://doi.org/10.13039/100000139, U.S. Environmental Protection Agency (US Environmental Protection Agency);

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Keywords: environmental monitoring,environmental chemistry

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Keywords: environmental monitoring, environmental chemistry

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Curation of a list of chemicals in biosolids from EPA National Sewage Sludge Surveys & Biennial Review Reports

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EPA CompTox Chemicals Dashboard

Most cited references 4

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

InChI, the IUPAC International Chemical Identifier

EPA’s DSSTox database: History of development of a curated chemistry resource supporting computational toxicology research

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