A presentation given at the Global Marine Summit at UNC Wilmington on October 9th 2019. The focus of the presentation was an overview of the EPA CompTox Chemicals Dashboard with a specific focus on providing access to data to chemicals such as algal toxins and mycotoxins.

1. US EPA CompTox Chemicals Dashboard
Data Integration Hub to Support
Environmental Science
Antony Williams
Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, RTP, NC
Global Marine Summit 2019
UNCW, Wilmington, NC
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. A little bit about me…
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• NMR spectroscopist by training
• …ultimately focused on CASE Analysis
(Computer-Assisted Structure Elucidation)

3. CASE Analysis – Elucidating VERY
complex chemical structures
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4. A little bit about me…
• We built this free website…
• …that has about 100,000 users a day…
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5. Bringing large databases and
CASE together
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• Application of computer-assisted structure
elucidation using ACD/Structure Elucidator
and data obtained from the ChemSpider
database hosted by the RSC

6. Today I represent US EPA…
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7. 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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8. CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
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875k Chemical Substances

9. Type-ahead Search
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10. Substring Search: Enniatin (10/29)
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11. Chemical Details Page
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12. Experimental & Predicted Properties
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13. Open Source Prediction Models
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14. OPERA Predicted Properties
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OPERA Models: https://github.com/kmansouri/OPERA

15. Plus Real-Time Predictions
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16. Toxicity Estimation Software Tool
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17. Access to Chemical Hazard Data
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18. 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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19. In Vitro Bioassay Screening
ToxCast and Tox21
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20. In Vitro Bioassay Screening
ToxCast and Tox21
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21. Identifiers to Support Searches
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22. Built in “Modules”
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23. Literature Searching
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24. Literature Searching
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25. Literature Searching
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26. Sifting retrieved articles
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27. Direct Link to PubMed
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28. Abstract Sifter for Excel
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29. Mapped
Relationships
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30. Relationships in the Data
All chemicals: Same Formula
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31. Relationships in the Data
All chemicals: Same Formula
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32. Relationships in the Data
Structure search the web
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33. Structure search the web
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34. Similar Compounds
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35. Related Substances – Metabolites
and Transformation Products
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36. “External Links” to >70 sites
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37. External Links: CTD
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38. External Links: MassBank
of North America
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39. Chemical Lists
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40. >200 Lists of Chemicals
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41. Filtered Search on Toxins
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42. Mycotoxins with MS Data
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43. EPA Algal Toxins
https://www.epa.gov/cyanohabs
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44. Algal Toxins
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45. Hazard Data for 25/54 Algal Toxins
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46. And who wants to draw these?
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47. When you can download them…
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48. DO WE REALLY
NEED ANOTHER
DATABASE?
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49. Data Quality is important
• Data quality in free web-based databases!
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50. Will the correct Microcystin LR Stand Up?
ChemSpider Skeleton Search
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51. Comparing ChemSpider Structures
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52. Comparing ChemSpider Structures
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53. Other Searches
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54. Delivering a Better Database
• An ideal database would provide:
– Curated CAS Number-Name mappings with “correct”
chemical structures
• We have full time curators checking data
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55. Names to CASRN Mappings
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56. Subtleties
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E/Z-stereochemistry E-stereochemistry
“4-Decene”

57. Crowdsourced Curation
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58. Batch
Searching
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59. 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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60. Batch searching
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61. Public release had 16/17
mycotoxins. Last one registered
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62. Add Other Data of Interest
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63. Related Substance Relationships
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64. MASS AND
FORMULA
SEARCHING
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65. Advanced Searches
Mass and Formula Based Search
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66. Advanced Searches
Mass and Formula Based Search
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67. Batch Searching Formula/Mass
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68. WORK IN
PROGRESS
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69. Predicted Mass Spectra
http://cfmid.wishartlab.com/
• MS/MS spectra prediction for ESI+, ESI-, and EI
• Predictions generated and stored for >800,000
structures, to be accessible via Dashboard
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70. Search Expt. vs. Predicted Spectra

71. Search Expt. vs. Predicted Spectra

72. Spectral Viewer Comparison
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73. Prototype Development
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74. Prototype Development
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75. Agilent Dataset
• Agilent : “Mycotoxins and Metabolites
Personal Compound Database and Library”
• Registered for next release…
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76. Please help
• Help grow the lists of Mycotoxins and Algal
Toxins – please suggest additions
• Next up – structures of microviridins…
• Email me at williams.antony@epa.gov
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77. Conclusion
• Building an integrated hub for environmental chemistry
• Transparent access to data and models
• Data QUALITY is a key focus - ongoing curation
• Microcystins and algal toxins are two growing “lists”
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78. 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

79. 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