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The CompTox Chemistry Dashboard - A Community Data Resource for Environmental Chemistry
Citation:
Williams, A., Chris Grulke, J. Edwards, A. McEachran, K. Mansouri, N. Baker, G. Patlewicz, I. Shah, J. Wambaugh, R. Judson, AND A. Richard. The CompTox Chemistry Dashboard - A Community Data Resource for Environmental Chemistry. Journal of Cheminformatics. Springer, New York, NY, 9(61):1-27, (2017).
Impact/Purpose:
• Agency Research Drivers - Agency regulatory frameworks characterize chemical risk by integrating multiple data streams. These data include traditional toxicity tests in laboratory animals, as well as new data streams, high throughput screening data, and computational models of exposure and dosimetry. The presentation and transparent evaluation of these various data is essential for communicating Agency risk decisions. • Science Challenge – A significant bottleneck for Agency risk decisions is collecting, curating, and comparing disparate data streams. Integrating relevant data streams for a large number of chemicals is facilitated by an online dashboard enabling assessments to be performed in an automated to semi-curated fashion. • Research Approach – A dashboard incorporating various data (e.g, use-specific data/information, physicochemical data, toxicity data, high throughput assay results) and tools (e.g., read-across models, dosimetry predictions) is being developed. All data and algorithms will be made available in web services so that there is rapid reuse of these resources and continual data curation. In addition, expert users will be able to modify the input to models to allow more expert-driven risk assessments. • Results - This work developed an online dashboard that compiled physicochemical data, toxicity data, exposure estimates, and high throughput assay data for hundreds of thousands of chemicals. Predicted data are delivered with full transparency in regards to algorithmic details, training data and applicability of the models. • Anticipated Impact/Expected use – The delivery of the dashboard both enhances the translation of CSS research into a highly usable form both inside the Agency and to the broader scientific community. Next steps in the research include expansion of the types of available data (e.g. production volume, occurrence of chemicals in specific media) and the delivery of prediction models applied in real-time to chemicals not contained in the online database. The ongoing expansion and curation of data delivered via web services will allow for integration to other Agency databases and applications.
Description:
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 (TSCA) 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.
