US-EPA CompTox Chemicals Dashboard: Bioactivity Data for Endocrine Assays

US-EPA CompTox Chemicals Dashboard: Bioactivity Data for Endocrine Assays

1. 1. Innovative Research for a Sustainable Futurewww.epa.gov/research ORCID: 0000-0002-2668-4821 Antony Williams l williams.antony@epa.gov l 919-541-1033 US-EPA CompTox Chemicals Dashboard: Bioactivity Data for Endocrine Assays Antony J. Williams* and Katie Paul-Friedman U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology (NCCT), Research Triangle Park, NC The CompTox Chemicals Dashboard Navigating the EDSP Universe of Chemicals and Assays Acknowledgements EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases within the DSSTox project and for providing accurate linkages of data to chemical structures, exposure, and hazard data. The data are made available via the EPA’s CompTox Chemicals Dashboard1 (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for ~875,000 chemical substances, the majority of these represented with chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data, and linkages to a growing list of literature, toxicology, and analytical chemistry websites. The dashboard version 3:March 2019 release includes support for the invitroDBv3.1 data release2 and includes new functionality to interact with all ToxCast and Tox21 data with the intention of replacing the previously available EDSP21 and ToxCast dashboards. The previous dashboards will be retired in summer 2019. The screenshots below illustrate navigation of bioactivity data associated with a single chemical, Bisphenol A. Version 3 of the dashboard includes all data associated with the invitroDBv3.1 data release. The CompTox Chemicals Dashboard provides access to data associated with 875k chemical substances. Integrating data from a series of databases into a simple to use web- based interface, the dashboard provides access to experimental and predicted physicochemical properties and fate and transport data, in vivo hazard and exposure data. The dashboard provides real-time prediction for both property and toxicity endpoints, batch searching for thousands of chemicals and new approaches to navigate through bioactivity data. This includes a segregated list of the EDSP universe of chemicals and assays associated with the invitroDBv3.1 release of data. References 1. Williams et al., The CompTox Chemicals Dashboard, Journal of Cheminformatics, 2017, 9:61, https://doi.org/10.1186/s13321-017-0247-6 2. Downloadable invitrodbv3.1 data: https://www.epa.gov/chemical- research/exploring-toxcast-data-downloadable-data 3. tcpl version 2.0.1 available on CRAN https://cran.r-project.org/web/packages/tcpl/ We thank the NCCT software development team led by Jeff Edwards and Jeremy Dunne for their development of the Dashboard and underlying infrastructure. We acknowledge Keith Houck and Richard Judson for their ongoing guidance in the Toxcast and EDSP21 projects. The following ORISE postdoctoral and student service contractors provided enormous contributions to the delivery of the invitroDBv3.1 release: Jason Brown, Nathaniel Rush, Anita Simha and Mahmoud Shobair. This poster does not necessarily reflect EPA policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. Navigating Lists of Chemicals and AssaysAbstract A simplified navigation of lists of chemicals and assays has been introduced into the latest release of the dashboard. The data associated with an assay endpoint allows for navigation of the associated set of chemicals with intuitive filtering. Data can be downloaded to the desktop for further analysis (e.g. as Excel files) or passed to the integrated batch search to intersect with additional data of interest for the selected chemicals. Problem Definition and Goals Problem: The support of multiple dashboards is inefficient and has required significant overhead. Improved efficiencies and functionality enhancements have resulted from migrating functionality in the EDSP21 and ToxCast dashboards to the CompTox Chemicals Dashboard. This migration was synchronized to the release of the invitroDBv3.1 data expanding coverage of both the number of chemicals and assays available. SUMMARY VIEW: A summary view of bioactivity data for Bisphenol A. Clicking on each individual data point displays the assay description and associated meta data in a summary form. More expansive details for each assay are available including citations, reagents and ToxCast Pipeline (tcpl) processing3 analysis. ASSAY HIT-CALL TABLE: A table of the hit calls for a chemical with details including the AC50 values, a subset of associated fit parameters and mappings to the AOP-Wiki. All data can be downloaded in Excel format for review and analysis. BIOACTIVITY CURVES: The ability to view only EDSP-related assays, or the entire suite of assays associated with Toxcast and Tox21, as shown, brings the previous dashboards together into a single application. Related data and utilities ToxCast data, including single concentration screening data and other supporting information, are available freely in invitrodb_v3.1, which is managed using tcpl v.2.0.1. Download invitrodb_v3.1: https://www.epa.gov/chemical-research/exploring-toxcast-data- downloadable-data Download the R package for the ToxCast Pipeline (tcpl v2.0.1) and peruse the tcpl v2.0.1 vignettes that explain the package and invitrodb structure: https://cran.r-project.org/web/packages/tcpl/index.html (also available on Git and EPA FTP)