The US EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a web-based application providing access to ~875,000 chemical substances and diverse data types including physicochemical property, toxicity and EPA’s ToxCast data. This presentation provided a live demo of the application and its benefits to members of ACS AGRO.

1. EPA CompTox Chemicals Dashboard as a
Data Integration Hub for Environmental
Chemistry Data
Antony Williams
Center for Computational Toxicology and Exposure,
U.S. Environmental Protection Agency, RTP, NC
November 13th 2019
ACS AGRO Webinar
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 Chemicals Dashboard
https://comptox.epa.gov/dashboard
• Freely accessible website and integration hub
– Chemical substances – the majority with structures
– Searchable by chemical, product use and gene
– Experimental and predicted physicochemical property data
– Experimental and predicted fate and transport data
– Bioactivity data for the ToxCast/Tox21 project
– Literature searches for chemicals using public resources
– Links to other agency websites and public data resources
– Batch searching for thousands of chemicals
– Chemical lists of interest – pesticides, leachables, PFAS
– DOWNLOADABLE Open Data for reuse and repurposing
1

3. A single application integrating…
2
SEARCH
TOX DATA
BIOACTIVITY
SIMILARITY
READ-ACROSS
PUBMED
BATCH SEARCH

4. A data integration hub
LOTS of data!
• >875,000 chemicals curated over 20 years
• >700,000 toxicity data points from >30 sources
• Millions of synonyms and identifiers
• Tens of thousands of experimental data points
• Millions of QSAR prediction reports
• Millions of bioactivity data points for >4000
chemicals and hundreds of assay end points
• Searching of Pubmed’s 29 million abstracts
3

5. CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
4
875k Chemical Substances

6. Type-ahead Search
5

7. Substring Search: Enniatin (10/29)
6

8. Chemical Details Page
7

9. Experimental & Predicted Properties
8

10. Open Source Prediction Models
9

11. OPERA Predicted Properties
10
OPERA Models: https://github.com/kmansouri/OPERA

12. Plus Real-Time Predictions
11

13. Toxicity Estimation Software Tool
12

14. Access to Chemical Hazard Data
13

15. 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
14

16. In Vitro Bioassay Screening
ToxCast and Tox21
15

17. In Vitro Bioassay Screening
ToxCast and Tox21
16

18. Identifiers to Support Searches
17

19. Built in “Modules”
18

20. Literature Searching
19

21. Literature Searching
20

22. Literature Searching
21

23. Sifting retrieved articles
22

24. Direct Link to PubMed
23

25. Abstract Sifter for Excel
24

26. Mapped
Relationships
25

27. Relationships in the Data
All chemicals: Same Formula
26

28. Relationships in the Data
All chemicals: Same Formula
27

29. Relationships in the Data
Structure search the web
28

30. Structure search the web
29

31. Similar Compounds
30

32. Related Substances – Metabolites
and Transformation Products
31

33. “External Links” to >70 sites
32

34. External Links: CTD
33

35. External Links: MassBank
of North America
34

36. Chemical Lists
35

37. >200 Lists of Chemicals
36

38. Filtered Search on Toxins
37

39. Mycotoxins with MS Data
38

40. EPA Algal Toxins
https://www.epa.gov/cyanohabs
39

41. Algal Toxins
40

42. Hazard Data for 25/54 Algal Toxins
41

43. And who wants to draw these?
42

44. When you can download them…
43

45. Batch
Searching
44

46. 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?
45

47. Batch searching
46

48. Add Other Data of Interest
47

49. Related Substance Relationships
48

50. MASS AND
FORMULA
SEARCHING
49

51. Advanced Searches
Mass and Formula Based Search
50

52. Advanced Searches
Mass and Formula Based Search
51

53. Batch Searching Formula/Mass
52

54. Crowdsourced Curation
53

55. WORK IN
PROGRESS
54

56. 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
55

57. Search Expt. vs. Predicted Spectra

58. Search Expt. vs. Predicted Spectra

59. Spectral Viewer Comparison
58

60. Prototype Development
59

61. Prototype Development
60

62. Conclusion
• Building an integrated hub for environmental chemistry
• Transparent access to data and models
• Data QUALITY is a key focus - ongoing curation
61

63. Acknowledgements
EPA-RTP
• An enormous team of contributors
from CCTE, 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

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