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Accessing information for chemicals in
hydraulic fracturing fluids using the US
EPA CompTox Chemistry Dashboard
Antony Wil...
The CompTox Chemistry Dashboard
• A publicly accessible website delivering access:
– ~760,000 chemicals with related prope...
CompTox Chemistry Dashboard
https://comptox.epa.gov/dashboard
2
1 of ~761,000 Chemical Pages
3
Advanced Searches
4
Batch Searches
5
Real-Time Predictions
6
Real-Time Predictions
7
Real-Time Predictions
8
What’s under the Data Tabs?
Focus on Hydraulic Fracturing Chemicals
9
Surfacing Lists of Chemicals
• Specific subsets of chemicals, “lists”, can
be displayed on the dashboard
• If there are ch...
EPA’s Hydraulic Fracturing Site
https://www.epa.gov/hfstudy
11
Draft Database
• Early draft database is available
associated with the June 2015 draft report
• Contained list of CAS Numb...
What were the original sources?
• Federal- and state-collected data sets
• Databases maintained by federal and state
gover...
Delivering a Better Database
• An improved database would provide:
– Curated CAS Number-Name mappings
– Chemical structure...
Registration and Curation
• Consolidation and registration of the original
chemical lists into the underlying database
(DS...
Names to CASRN Mappings
16
Subtleties
17
E/Z-stereochemistry E-stereochemistry
“4-Decene”
Registration and Curation
• Registration of the chemical list into the
underlying database (DSSTox)
• Careful (and time-co...
CAS Registry Numbers
19
Registration and Curation
• Registration of the chemical list into the
underlying database (DSSTox)
• Careful (and time-co...
Alternative Synonyms
21
Registration and Curation
• Registration of the chemical list into the
underlying database (DSSTox)
• Careful (and time-co...
A List of Lists of Chemicals
https://comptox.epa.gov/dashboard/chemical_lists
23
The EPA List of
Hydraulic Fracturing Chemicals
24
The List as “Structures”
25
Browsing the List of Chemicals
26
Detailed Chemical Pages
27
Access to Chemical Hazard Data
28
In Vitro Bioassay Screening
ToxCast and Tox21
29
Sources of Exposure to Chemicals
30
Identifiers to Support Searches
31
Literature Searches and Links
32
External Links to Data and Services
33
Integrated Linkouts
34
Integrated Linkouts
Comparative Toxicogenomics DB
35
Batch Access to Dashboard Data
36
Batch Search Through Dashboard
37
Batch Search Through Dashboard
38
Batch Access to Dashboard Data
39
Many Hydraulic Fracturing
Chemicals are “Complex”
40
UVCB Chemicals
41
Di-sec-butylphenol
42
CAS Representation
Dashboard Representation
“Markush Structures”
https://en.wikipedia.org/wiki/Markush_structure
43
AFTER CURATION
1640 Chemicals
• 528/1640 chemicals without explicit structures
• 483/1640 chemicals examined in ToxCast – ...
Curated Database for Download
https://www.epa.gov/hfstudy
45
Download Files from EPA Site
46
Suspect Screening and Non-Targeted
Analysis Workflow
47
DSSTox Chemical Database
“Molecular Features”
Extracted Samples
Ra...
The Dashboard to Support
MS-Analysis
48
MS-Ready
Structures
Underpin
Analysis
Specific Data-Mappings
“MS-Ready Structures”
49
MS-Ready Mappings
• Input Formula: C10H16N2O8
• EXACT Formula Search: 3 Chemicals
50
MS-Ready Mappings
• Same Input Formula: C10H16N2O8
• MS Ready Formula Search: 88 Chemicals
51
Complexity to Simplicity
88 Chemicals – 7 in EPAHFR
52
Complexity to Simplicity
88 Chemicals – 7 in the list
53
Searching batches
Formula (or mass) searching
54
Conclusions
• The CompTox Chemistry Dashboard is
useful for delivering access to lists
– The EPA Hydraulic Fracturing Chem...
Conclusions
• Registering chemical lists gives access to:
– Human and Ecological Hazard data
– ToxCast/Tox21 in vitro scre...
Acknowledgments
• Hydraulic Fracturing Drinking Water Study Team
• The CompTox Chemistry Dashboard team
• Todd Martin (TES...
Contact
Antony Williams
US EPA Office of Research and Development
National Center for Computational Toxicology (NCCT)
Will...
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Accessing information for chemicals in hydraulic fracturing fluids using the US EPA CompTox Chemistry Dashboard

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EPA’s National Center for Computational Toxicology is developing automated workflows for curating large databases and providing accurate linkages of data to chemical structures, exposure and hazard information. The data are being made available via the EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard), a publicly accessible website providing access to data for almost 760,000 chemical substances, the majority of these represented as chemical structures. The web application delivers a wide array of computed and measured physicochemical properties, in vitro high-throughput screening data and in vivo toxicity data as well as integrated chemical linkages to a growing list of literature, toxicology, and analytical chemistry websites. In addition, several specific search types are in development to directly support the mass spectroscopy non-targeted screening community, who are generating important data for detecting and assessing environmental exposures to chemicals contained within DSSTox. The application provides access to segregated lists of chemicals that are of specific interests to relevant stakeholders including, for example, scientists interested in algal toxins and hydraulic fracturing chemicals. This presentation will provide an overview of the challenges associated with the curation of data from EPA’s December 2016 Hydraulic Fracturing Drinking Water Assessment Report that represented chemicals reported to be used in hydraulic fracturing fluids and those found in produced water. The data have been integrated into the dashboard with a number of resulting benefits: a searchable database of chemical properties, with hazard and exposure predictions, and open literature. The application of the dashboard to support mass spectrometry non-targeted analysis studies will also be reviewed. This abstract does not reflect U.S. EPA policy.

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Accessing information for chemicals in hydraulic fracturing fluids using the US EPA CompTox Chemistry Dashboard

  1. 1. Accessing information for chemicals in hydraulic fracturing fluids using the US EPA CompTox Chemistry Dashboard Antony Williams1, Andrew McEachran2, Jon Sobus3, Chris Grulke1 and Ann Richard1 1) National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC 2) Oak Ridge Institute of Science and Education (ORISE) Research Participant, Research Triangle Park, NC 3) National Exposure Research Laboratory, U.S. Environmental Protection Agency, RTP, NC March 2018 ACS Spring Meeting, New Orleans 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. 2. The CompTox Chemistry Dashboard • A publicly accessible website delivering access: – ~760,000 chemicals with related property data – Experimental and predicted physicochemical property data – Experimental Human and Ecological hazard data – Integration to “biological assay data” for 1000s of chemicals – Information regarding consumer products containing chemicals – Links to other agency websites and public data resources – “Literature” searches for chemicals using public resources – “Batch searching” for thousands of chemicals – Real time prediction of physchem and toxicity endpoints – DOWNLOADABLE Open Data for reuse and repurposing 1
  3. 3. CompTox Chemistry Dashboard https://comptox.epa.gov/dashboard 2
  4. 4. 1 of ~761,000 Chemical Pages 3
  5. 5. Advanced Searches 4
  6. 6. Batch Searches 5
  7. 7. Real-Time Predictions 6
  8. 8. Real-Time Predictions 7
  9. 9. Real-Time Predictions 8
  10. 10. What’s under the Data Tabs? Focus on Hydraulic Fracturing Chemicals 9
  11. 11. Surfacing Lists of Chemicals • Specific subsets of chemicals, “lists”, can be displayed on the dashboard • If there are chemicals that map together then these link to existing: – Property data – Hazard data – Exposure data – In vitro bioassay data – Documents and Literature 10
  12. 12. EPA’s Hydraulic Fracturing Site https://www.epa.gov/hfstudy 11
  13. 13. Draft Database • Early draft database is available associated with the June 2015 draft report • Contained list of CAS Numbers/Names aggregated from various sources 12
  14. 14. What were the original sources? • Federal- and state-collected data sets • Databases maintained by federal and state government agencies • Publicly available data (e.g ) • Industry data provided to the EPA - two information requests to oil and gas service companies and production well operators (some data claimed as CBI under TSCA) • http://ofmpub.epa.gov/eims/eimscomm.getfile?p_download_id=530159 13
  15. 15. Delivering a Better Database • An improved database would provide: – Curated CAS Number-Name mappings – Chemical structures – Access to related data of interest 14
  16. 16. Registration and Curation • Consolidation and registration of the original chemical lists into the underlying database (DSSTox) • Careful (and time-consuming) curation – Confirming mappings of chemical names and CASRNs 15
  17. 17. Names to CASRN Mappings 16
  18. 18. Subtleties 17 E/Z-stereochemistry E-stereochemistry “4-Decene”
  19. 19. Registration and Curation • Registration of the chemical list into the underlying database (DSSTox) • Careful (and time-consuming) curation – Confirming mappings of chemical names and CASRNs – CASRN checking – Active, Alternate and Deleted 18
  20. 20. CAS Registry Numbers 19
  21. 21. Registration and Curation • Registration of the chemical list into the underlying database (DSSTox) • Careful (and time-consuming) curation – Confirming mappings of chemical names and CASRNs – CASRN checking – Active, Alternate and Deleted – Misspellings, alternative synonyms, misassociations 20
  22. 22. Alternative Synonyms 21
  23. 23. Registration and Curation • Registration of the chemical list into the underlying database (DSSTox) • Careful (and time-consuming) curation – Confirming mappings of chemical names and CASRNs – CASRN checking – Active, Alternate and Deleted – Misspellings, alternative synonyms, misassociations – Iterative checking on how the list was assembled 22
  24. 24. A List of Lists of Chemicals https://comptox.epa.gov/dashboard/chemical_lists 23
  25. 25. The EPA List of Hydraulic Fracturing Chemicals 24
  26. 26. The List as “Structures” 25
  27. 27. Browsing the List of Chemicals 26
  28. 28. Detailed Chemical Pages 27
  29. 29. Access to Chemical Hazard Data 28
  30. 30. In Vitro Bioassay Screening ToxCast and Tox21 29
  31. 31. Sources of Exposure to Chemicals 30
  32. 32. Identifiers to Support Searches 31
  33. 33. Literature Searches and Links 32
  34. 34. External Links to Data and Services 33
  35. 35. Integrated Linkouts 34
  36. 36. Integrated Linkouts Comparative Toxicogenomics DB 35
  37. 37. Batch Access to Dashboard Data 36
  38. 38. Batch Search Through Dashboard 37
  39. 39. Batch Search Through Dashboard 38
  40. 40. Batch Access to Dashboard Data 39
  41. 41. Many Hydraulic Fracturing Chemicals are “Complex” 40
  42. 42. UVCB Chemicals 41
  43. 43. Di-sec-butylphenol 42 CAS Representation Dashboard Representation
  44. 44. “Markush Structures” https://en.wikipedia.org/wiki/Markush_structure 43
  45. 45. AFTER CURATION 1640 Chemicals • 528/1640 chemicals without explicit structures • 483/1640 chemicals examined in ToxCast – 94 not active in any assay • 1036/1640 chemicals with Hazard Data • 141/1640 chemicals with IRIS Assessment Reports (Integrated Risk Information System) 44
  46. 46. Curated Database for Download https://www.epa.gov/hfstudy 45
  47. 47. Download Files from EPA Site 46
  48. 48. Suspect Screening and Non-Targeted Analysis Workflow 47 DSSTox Chemical Database “Molecular Features” Extracted Samples Raw Samples Raw Features Matched Formulas Mapped Structures Prioritized Structures (using ToxPi) Confirmed Structures (using ToxCast standards) Processed Features Prioritized Features Predicted Formulas Candidate Structures Sorted Structures Predicted Retention Times Predicted/Observed Functional Use Top Candidate Structure(s) Suspect Screening Non-Targeted Analysis Predicted Concentrations Predicted/Observed Media Occurrence Predicted Mass Spectra Methodological Concordance Red = Analytical Chemistry Blue = Data Processing & Analysis Green = Informatics & Web Services Purple = Mathematical & QSPR Modeling Color Key Content from J. Sobus, US-EPA-NERL
  49. 49. The Dashboard to Support MS-Analysis 48 MS-Ready Structures Underpin Analysis
  50. 50. Specific Data-Mappings “MS-Ready Structures” 49
  51. 51. MS-Ready Mappings • Input Formula: C10H16N2O8 • EXACT Formula Search: 3 Chemicals 50
  52. 52. MS-Ready Mappings • Same Input Formula: C10H16N2O8 • MS Ready Formula Search: 88 Chemicals 51
  53. 53. Complexity to Simplicity 88 Chemicals – 7 in EPAHFR 52
  54. 54. Complexity to Simplicity 88 Chemicals – 7 in the list 53
  55. 55. Searching batches Formula (or mass) searching 54
  56. 56. Conclusions • The CompTox Chemistry Dashboard is useful for delivering access to lists – The EPA Hydraulic Fracturing Chemical List – The ToxCast Bioassay Screening List – NIOSH International Chemical Safety Cards – Algal Toxins • Lists can be updated with new chemicals 55
  57. 57. Conclusions • Registering chemical lists gives access to: – Human and Ecological Hazard data – ToxCast/Tox21 in vitro screening data – Exposure data – consumer products & functional use – Physicochemical and environmental fate and transport experimental and predicted data – Integrated mappings into multiple public sites • Curation is time-consuming, iterative and high-value 56
  58. 58. Acknowledgments • Hydraulic Fracturing Drinking Water Study Team • The CompTox Chemistry Dashboard team • Todd Martin (TEST Predictions), US-EPA-NRMRL • NERL colleagues: – Jon Sobus, Elin Ulrich, Mark Strynar, Seth Newton (NTA Analysis) – Katherine Phillips, Kathie Dionisio, Kristin Isaacs (Consumer Products Database) • Emma Schymanski – Luxembourg Center for Systems Biomedicine (MS-ready/NTA) 57
  59. 59. Contact Antony Williams US EPA Office of Research and Development National Center for Computational Toxicology (NCCT) Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 58

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