As part of its mission the Center for Computational Toxicology and Exposure (CCTE) delivers access to chemicals related data via online Dashboards. The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) provides access to >900,000 chemicals and associated data including experimental and predicted property data, in vivo hazard data, in vitro bioactivity data, exposure data, and various other data types. The application provides a set of flexible searches allowing for search, visualization and downloads of the data to the desktop for further interrogation. This presentation will provide an overview of the Dashboard and other proof-of-concept applications that are now publicly available (https://www.epa.gov/chemical-research/cheminformatics). For example, the Hazard Comparison module (shown in the figure below) allows profiling of chemicals based on toxicity types (https://doi.org/10.1007/s10098-019-01795-w). This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

1. Center for Computational Toxicology and Exposure, US-EPA, RTP, NC
http://www.orcid.org/0000-0002-2668-4821
Accessing Environmental Chemistry
Data via Data Dashboards
The views expressed in this presentation are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA
Antony J. Williams
BfR – German Federal Institute for Risk Assessment – April 7th 2022

2. Many other talks on SlideShare
https://www.slideshare.net/AntonyWilliams/
• Slides will be circulated after the presentation

3. This talk is an overview
• This talk is a high-level overview only. We can provide trainings into
the individual modules and data as required
• LOTS of training materials are available https://www.epa.gov/chemical-
research/new-approach-methods-nams-training

4. 20 Years of Curating Data in Our Team

5. CompTox Chemicals Dashboard
>1.2 million chemicals

6. The Charge for the Dashboard
• Develop a “first-stop-shop” for environmental chemical data
to support EPA and partner decision making:
– Centralized location for relevant chemical data
– Chemistry, exposure, hazard and dosimetry
– Combination of existing data and predictive models
– Publicly accessible, periodically updated, curated
• Easy access to data improves efficiency and ultimately
accelerates chemical risk assessment

7. CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
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SEARCH
TOX DATA
BIOACTIVITY
SIMILARITY
READ-ACROSS
PUBMED
BATCH SEARCH

8. Detailed Chemical Pages
• Chemical page: Wikipedia snippet when available, intrinsic
properties, structural identifiers, linked substances

9. “Executive Summary”
• Overview of toxicity-
related info
• Quantitative values
• Physchem. and Fate &
Transport
• Adverse Outcome
Pathway links
• In vitro bioactivity
summary plot

10. Experimental and Predicted Data
• Physchem and Fate & Transport
experimental and predicted data
• Data can be downloaded as Excel,
TSV and CSV files

11. Chemical Hazard Data
ToxVal Database
• >50k chemicals
• >770k tox. values
• >30 sources of data
• ~5k journals cited
• ~70k citations

12. Safety Data

13. Sources of Exposure to Chemicals

14. Bioactivity Data

15. ToxCast

16. Bioactivity Data
Summary views of >2000 Assay Endpoints

17. Bioactivity Data
Full transparency of data…

18. Bioactivity Data
…including concentration-response

19. How can these data be used?
Combine in vitro and httk
Combine in vitro data
(AC50s in uM) with httk
data to get bioactivity-
exposure ratios and PODs

20. Bioactivity Data
NEW High-Throughput Transcriptomics

21. Use Models Derived from the Data
CERAPP and CoMPARA
available in OPERA

22. Searching Literature
and the Internet

23. Literature Searching
• Real-time retrieval of data from PubMed ~30
million abstracts and growing)
• Choose from set of pre-defined queries
• Adjust and fine tune queries based on interests

24. Literature Searching
• “Sifting” of results using
multiple terms
• Frequency counting terms
• Color highlighting of terms
• Download list to Excel
• Send list to PubMed for
downloading ref. file
• Direct link via PubMed ID

25. What’s the best way to search the
internet for chemical data?
• We know how complex chemicals identifiers are…
• CASRN(s)
• Hundreds of names (maybe)
• SMILES
• InChIs
• EINECS, EC numbers
• What can WE do to help you navigate the internet?

26. External Links – Also use Identifiers
Names, CASRN, PubChem IDs, InChIs…
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27. External Links
• Links to ~90 websites providing access to
additional data on the chemical of interest

28. Chemical Lists and
Categories

29. A List of Lists of Chemicals
https://comptox.epa.gov/dashboard/chemical_lists

30. The OECD List of PFAS
http://www.oecd.org/chemicalsafety/portal-perfluorinated-chemicals/
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31. PFAS List Paper
https://doi.org/10.3389/fenvs.2022.850019
• What makes our efforts
different?
• MANUAL curation work
• Building lists, cross-
referencing, mapping
relationships, sourcing
and curating data

32. What about PFAS?

33. Are there Similar Compounds?

34. Relationships in the data

35. Markush Chemicals
• PFOS is a member of linear perfluoroalkyl sulfonates
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36. …and their Markush Children…
• Linear perfluoroalkyl sulfonates has children…

37. EFSA List

38. MTOX biomarkers

39. Batch Searching

40. Batch Searching
• Singleton searches are great but…
• …we generally want data on LOTS of chemicals!
• Typical questions
• What are the structures for a set of chemical names? Set of
CASRNs?
• Can I get chemical lists in Excel files? As a list of SMILES strings?
Can I get an SDF file?
• Can I include predicted properties? OPERA? TEST?
• Are “these chemicals” screened in Toxcast?
• I need masses and formulae for a list of chemicals

41. Batch Search

42. Batch Search – Excel, CSV, SDF file

43. Batch Search

44. Open Data
Exchange

45. Since our data are Open…
• They flow into other systems for benefit …
• ECHA eChemPortal
• ChemSpider
• EBI’s UniChem
• PubChem

46. Cheminformatics
“PoC Modules”
https://www.epa.gov/chemical-
research/cheminformatics

47. Six Modules
• Hazard Comparison Profiling – profile chemicals based on hazard
• Alerts – structure, substructure, SMARTS based alerts and flags
• Predict – batch prediction using WebTEST (100s of structures)
• Search – structure/substructure/similarity searches
• Standardize – convert structures into QSAR/MS-Ready forms
• ToxPrints – generate ToxPrint substructural fragments and profile

48. Module 1: Hazard Module

49. Module 2: Alerts

50. Module 3: WebTEST Batch Prediction

51. Module 4: Structure/Substructure/Similarity

52. Chemical Transformation Database
(Work in Progress)

53. Chemical Transformation Database

54. Chemical Transformation Database
• The database of reactions under the Chemical Transformation Simulator
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55. Chemical Transformation Database
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56. Reaction, Original References etc
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57. Migrating MetaPath data

58. Work in Progress: MetaPath migration

59. What’s Next?
• Adding Thousands of Parent-Product mappings from the Dashboard
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60. Supporting Analytical Chemistry
1) Non-Targeted Analysis
2) Open Spectral Data
3) Analytical Methods
(Work in Progress)

61. Chemical Identification and Exposure

62. Rudimentary NTA Workflow

63. Non-Targeted Analysis Informatics

64. The Next Phase
Assembling Public Domain Spectra
• Assemble data from
MoNA, MassBank,
internal EPA data
• Already have CFM-ID
data for 1.2M chemicals
• Experimental searching

65. Integrated Methods Database
• Simple Vision: Find the best method(s) for a particular chemical
• Approach:
• Aggregate MS method documents
• Extract chemistry (mostly CASRN and Names)
• Map CASRN and Names to structures
• Build a searchable database of chemicals mapped to methods
• Chemical identifier search
• Structure/substructure and similarity search
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66. Where are there methods?
• 900 method documents
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67. Embedding old Method PDFs
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68. Vendor Methods
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69. Structure Tables/Tiles view
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70. How many methods do we have?
• We have 2785 method documents to extract
• 40% have been extracted – ca. 25 documents per day
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71. Summary and Conclusion
• CompTox Chemicals Dashboard - a central
hub for environmental data
• 1.2M chemical substances integrating property
data, hazard data, exposure data, in vitro
bioactivity data
• Batch search for thousands of chemicals
• Real-time property and toxicity predictions
• Proof-of-concept cheminformatics modules
• Informatics support for Non-Targeted Analysis
• Open Spectral data
• Analytical Methods database

72. Some Related Publications of Interest

73. You want to know more…
• Lots of resources available
• Presentations: https://tinyurl.com/w5hqs55
• Communities of Practice Videos: https://rb.gy/qsbno1
• Manual: https://rb.gy/4fgydc
• Latest News: https://comptox.epa.gov/dashboard/news_info
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74. Acknowledgments
• Contact:Williams.Antony@epa.gov
• Feedback and follow-up is
welcomed! Your questions help
• If anyone wants a deep dive into
any of the software applications
feel free to contact me
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EPA’s Center for Computational Toxicology and Exposure