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US-EPA Cheminformatics Support for Delivering Data Related to Chemicals of Emerging Concern

This presentation was given at the "Department of Defense's (DoD) Energy and Environment Innovation Symposium" in Arlington, Virginia on December 1st 2023 (https://serdp-estcp.org/events/details/04d444f1-aa19-4e66-bb5c-5163964cc4dd/symposium-2023)

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US-EPA Cheminformatics Support for
Delivering Data Related to Chemicals
of Emerging Concern
Antony Williams
Center for Computational Toxicology and Exposure, US-EPA, RTP, NC
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
The role of cheminformatics at EPA
• I am from the EPA Center for Computational Toxicology and Exposure
• We develop lots of prediction models and web-based applications
• Today’s presentation: how do our efforts support data dissemination
regarding chemicals of emerging concern and MS-NTA
2
2
Chemical Monitoring Needs
Exposure
Assessment
Dose-
Response
Assessment
Risk
Characterization
Hazard
Identification
Free-Access Cheminformatics Tools
• The Center for Computational Toxicology and Exposure many tools
• CompTox Chemicals Dashboard
• Proof-of-Concept cheminformatics modules
• Chemicals Hazard Profiling
• Chemical Transformations database (ChET)
• Analytical Methods and Open Spectra database (AMOS)
• All chemicals are stored/curated in DSSTox
3
DSSTox Database
4
Accessing DSSTox chemistry:
CompTox Chemicals Dashboard
•A publicly accessible website delivering:
• 1.2M chemicals with related property data
• Related substances: transformation products, mono/polymer
• Experimental/predicted physicochemical property data
• Experimental Human and Ecological hazard data
• Integration to “biological assay data”
• Information regarding chemicals in consumer products
• Links to other agency websites and public data resources
• “Batch searching” for tens to thousands of chemicals
5
CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
6

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US-EPA Cheminformatics Support for Delivering Data Related to Chemicals of Emerging Concern

  • 1. US-EPA Cheminformatics Support for Delivering Data Related to Chemicals of Emerging Concern Antony Williams Center for Computational Toxicology and Exposure, US-EPA, RTP, NC 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. The role of cheminformatics at EPA • I am from the EPA Center for Computational Toxicology and Exposure • We develop lots of prediction models and web-based applications • Today’s presentation: how do our efforts support data dissemination regarding chemicals of emerging concern and MS-NTA 2 2 Chemical Monitoring Needs Exposure Assessment Dose- Response Assessment Risk Characterization Hazard Identification
  • 3. Free-Access Cheminformatics Tools • The Center for Computational Toxicology and Exposure many tools • CompTox Chemicals Dashboard • Proof-of-Concept cheminformatics modules • Chemicals Hazard Profiling • Chemical Transformations database (ChET) • Analytical Methods and Open Spectra database (AMOS) • All chemicals are stored/curated in DSSTox 3
  • 5. Accessing DSSTox chemistry: CompTox Chemicals Dashboard •A publicly accessible website delivering: • 1.2M chemicals with related property data • Related substances: transformation products, mono/polymer • Experimental/predicted physicochemical property data • Experimental Human and Ecological hazard data • Integration to “biological assay data” • Information regarding chemicals in consumer products • Links to other agency websites and public data resources • “Batch searching” for tens to thousands of chemicals 5
  • 7. 1 of ~1.2M Chemical Pages 7
  • 9. Experimental Data 9 • Experimental data harvested from public domain databases and journal articles • Data link back to provenance • Data are used to build QSAR models for real time predictions • Data are available for download and reuse
  • 10. What is PFOS Called? Synonyms, CASRNs and more 10
  • 11. Substance Relationship Mappings • Similar compounds - based on structure “fingerprints” 11
  • 12. Relationships in the data 12 • Structure mappings - between parent and salts, multicomponent chemicals, isotopomers • Related substances – monomer to polymer, parent to transformation products
  • 13. Batch Searching is a big enabler https://pubs.acs.org/doi/10.1021/acs.jcim.0c01273 13
  • 14. Batch Searching • Singleton searches are useful but people work with groups of chemicals • Typical questions • Find me all data based on the input of 1000 CASRNs, or 1000 names • What are the physicochemical properties for a set of identifiers? • 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? 14
  • 17. Batch Search • All data can be downloaded into Excel files, CSV files or SDF files and reused • All data are Open
  • 18. Chemical Lists https://comptox.epa.gov/dashboard/chemical_lists • Chemical lists are focused on regulations, research efforts and categories • 425 lists and growing • TSCA Inventory • Clean Water Act Hazardous Substances • Consumer Products database • Chemicals of Emerging Concern • PFAS lists • Extractables and Leachables • Lists are versioned and updated and new lists added regularly 18
  • 23. PFAS Lists of Chemicals (51/426) 23
  • 25. Applications at the EPA •We have ongoing efforts applying NTA to multiple challenges including • PFAS identification • Pesticides in various matrices • CECs in water • Biosolids •Examples include… 25
  • 26. Example 1: Consumer Product Analysis 26
  • 27. 27 Many chemicals observed in consumer product extracts More observed chemicals not known to be in consumer products Why might the ‘other’ chemicals be in the products? Many observed chemicals known to be in consumer products Example 1: Consumer Product Analysis
  • 28. 28 Example 2: Recycled Product Analysis
  • 29. 29 Significant differences between chemicals in recycled vs. virgin products for certain product & use categories Most differences observed in paper products and construction materials Some uses (e.g., fragrances) highly represented across all product/use categories Example 2: Recycled Product Analysis
  • 30. Example 3: Placental Tissue Analysis 30
  • 31. Lots of “proof-of-concept” tools in development • PoCs are research software builds to prove approaches before moving into production software environments • Assemble data, develop data model(s), test user interface approaches, work with test user base to garner feedback • Since PoCs are internal access data refreshes and application updates can be more 31
  • 33. Easy Export of all data to Excel 33
  • 34. AMOS: Analytical Methods and Spectra Database • Three types of data in the database: • Methods (regulatory, lab manuals and SOPs, publications, tech notes) • Spectra (from public domain and our own laboratories) • Fact Sheets (harvested from SWGDRUG and other sites) • Currently contains >210,000 spectra, >700,000 external links, 4000 “Fact Sheets” and ~4000 methods • ALL data are growing in number weekly at present 34
  • 37. Linking to actual spectra 37
  • 38. Linking to actual spectra 38 • We are doing a lot of chemical curation as we build the database
  • 39. Why not just Regulatory Methods? 39
  • 40. Why not just Regulatory Methods? Because we need methods faster 40
  • 42. Our Data via services https://api-ccte.epa.gov/docs/ 42
  • 43. Conclusions • Our data resources underpin our research efforts – data quality is key • Our web-based applications deliver our data to the community • Our support for identifying chemicals of emerging concern is multi-fold • Curated chemistry data streams • Non-targeted analysis tool development and cheminformatics support • NTA WebApp in development uses all data streams to support analysis 43
  • 44. Acknowledgements and Contact Information • The work presented here represents an enormous team of contributors • Chemical curators • Software developers and contractors • Postdocs, SMEs and PIs • Contact info: williams.antony@epa.gov • Slides will be available at: https://www.slideshare.net/AntonyWilliams/ 44