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

By Antony J. Williams, Christopher M. Grulke, J. Edwards, Andrew Mceachran, Kamel Mansouri, Nancy C. Baker, Grace Patlewicz, I. Shah, J. Wambaugh, Richard S. Judson and 1 more. Journal of Cheminformatics, 2017

951 citations recorded by the source corpus.

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.

Subfields: Biomedical Engineering, Molecular Biology, Pollution

View Paper: https://www.semanticscholar.org/paper/ad0782eda8db0b276e772744d78e4c1d8567adb7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biomedical Engineering

1. Oliver Fiehn
2. Antony J. Williams

In Molecular Biology

1. Tobias Kind
2. Oliver Fiehn
3. I. Blaženović
4. Jian Ji
5. Xianhuan Shen
6. Langhui Li
7. M. Tan
8. Zunnan Huang

Citations in the corpus

• Computational Approaches in Preclinical Studies on Drug Discovery and Development (2020, background): “The EPA Distributed Structure-Searchable Toxicity (DSSTox) database, which provides a series of documented, standardized and complete structure annotated toxicity information files, Except for the databases introduced above, some newly constructed ADMET-related databases should also be of concern, fo”
• The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency. (2019, background): “gov/dashboard/; Accessed February 14, 2019) provides a portal for EPA researchers, the public, and the scientific community to access DSSTox chemistry data (Williams et al., 2017).”
• OPERA models for predicting physicochemical properties and environmental fate endpoints (2018, methodology): “1 and 6 were generated for the full set of models and are provided in the Additional file 1: S1 as well as the calculation reports on the CompTox Chemistry Dashboard [83, 84].”
• Per- and Polyfluoroalkyl Substance Toxicity and Human Health Review: Current State of Knowledge and Strategies for Informing Future Research (2020, background): “…(–CnF2n–) moiety (Organisation for Economic Co‐operation Development 2018), and the US Environmental Protection Agency (USEPA) has a curated list of over 8000 PFAS included, based on structure (US Environmental Protection Agency 2018) from the CompTox Chemicals Dashboard (Williams et al. 2017).”
• Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, methodology): “For exposome related research, environmental database resources can be utilized [43,44].”