The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and 2000 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the latest release of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

1. US-EPA CompTox Chemicals Dashboard –
integrating chemistry and biology data to
serve computational toxicology and
environmental science
Antony Williams, Chris Grulke, Ann Richard, Richard Judson, Imran Shah
Grace Patlewicz, John Wambaugh, Katie Paul-Friedman,
Jeremy Dunne and Jeff Edwards
National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC
August 2019
ACS Fall Meeting, San Diego
http://www.orcid.org/0000-0002-2668-4821
The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA

2. CompTox Portal
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3. CompTox Chemicals Dashboard
• A publicly accessible website delivering access:
– ~875,000 chemicals with related property data
– Searchable by chemical, product use, gene and assay (ToxCast)
– Experimental and predicted physicochemical property data
– “Bioactivity data” for the ToxCast/Tox21 project
– Links to other agency websites and public data resources
– “Literature” searches for chemicals using public resources
– “Batch searching” for thousands of chemicals
– DOWNLOADABLE Open Data for reuse and repurposing
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4. CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
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875k Chemical Substances

5. BASIC Search
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6. Detailed Chemical Pages
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7. Experimental and Predicted Data
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8. Transparency for prediction models
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9. OPERA Predicted Properties
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OPERA Models: https://github.com/kmansouri/OPERA

10. Access to Chemical Hazard Data
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11. Hazard Data from “ToxVal_DB”
• ToxVal Database contains following data:
–~800,000 toxicity values
–~30 sources of data
–~22,000 sub-sources
–~5000 journals cited
–~70,000 literature citations
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12. In Vitro Bioassay Screening
ToxCast and Tox21
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13. In Vitro Bioassay Screening
ToxCast and Tox21
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14. Bioactivity: Downloadable Data
https://www.epa.gov/chemical-research/exploring-toxcast-data-
downloadable-data
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15. Sources of Exposure to Chemicals
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16. Sources of Exposure to Chemicals
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17. An “Executive Summary”
Quick Look Tox Info
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18. Identifiers to Support Searches
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19. Built in “Modules”
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20. Abstract Sifter for Excel
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21. Literature Searching
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22. Literature Searching
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23. Literature Searching
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24. Generalized Read-Across (GenRA)
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25. Related Publications
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26. Mapped
Relationships
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27. Relationships in the Data
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28. 27

29. Bisphenol A
27 Total MS-Ready Mappings
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30. Related Substances – Transformation
Products, “Monomer-Polymer”
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What No
Structures???

31. Quality Control
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32. Quality Control of the Database
• We have full time curators checking data
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33. Names to CASRN Mappings
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34. Subtleties
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E/Z-stereochemistry E-stereochemistry
“4-Decene”

35. CAS Registry Numbers
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36. Crowdsourced Curation
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37. Chemical Lists
and
Categories
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38. Category example – PAHs
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39. EPAHFR: Hydraulic Fracturing
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40. List of Assays

41. From Assay to Chemicals…
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42. Other Searches
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43. Product/Use Categories
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44. Lubricant
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45. Lots of UVCBS in Commerce….
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46. Other Searches
Chemical-Biology
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47. Assay/Gene Search
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48. Assay/Gene Search
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49. Batch
Searching
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50. Batch Searching
• Singleton searches are useful but people
generally want data on LOTS of chemicals!
• Typical questions
– What is the list of chemicals for the formula CxHyOz
– What is the list of chemicals for a mass +/- error
– Can I get chemical lists in Excel files? In SDF files?
– Can I include properties in the download file?
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51. Batch Search Names
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Excel
Download

52. Add Other Data of Interest
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53. Built in Checks…
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54. Related Substance Relationships

55. Real-Time
Predictions
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56. Real-Time Predictions
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57. Real-Time Predictions
with detailed calculation reports
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58. Real-Time Predictions
with detailed calculation reports
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59. Open Data
Download Files
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60. Downloadable Data
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61. Conclusion
• Building an integrated hub for environmental chemistry
data to serve computational toxicology
• Transparent access to data and models – file
downloads, SQL data dumps and web services
• Expansion of functionality to serve all data streams
generated by NCCT across the agency & community
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• Data QUALITY is a key
focus - ongoing curation
• We are committed to open
API development with time..

62. Acknowledgements
EPA-RTP
• An enormous team of contributors
from NCCT, especially the IT
software development team
• Our curation team for their care
and focus on data quality
• Multiple centers and laboratories
across the EPA
• Many public domain databases
and open data contributors

63. Contact
Antony Williams
NCCT, US EPA Office of Research and Development,
Williams.Antony@epa.gov
ORCID: https://orcid.org/0000-0002-2668-4821
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https://doi.org/10.1186/s13321-017-0247-6