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EPA CompTox chemicals dashboard: An online resource for environmental chemists Antony Williams, Chris Grulke, Jeremy Dunne...
CompTox Portal 1
CompTox Chemicals Dashboard • A publicly accessible website delivering access: – ~875,000 chemicals with related property ...
CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 3 875k Chemical Substances
BASIC Search 4
Detailed Chemical Pages 5
THE POWER OF BATCH SEARCHING 6
Batch Access to Underlying Data https://comptox.epa.gov/dashboard/dsstoxdb/batch_search 7
Inputs 8
CAS Numbers… 9
Display Chemicals 10
CAS Numbers… 11
Possible Outputs… 12
13
“MS-Ready Structures” https://doi.org/10.1186/s13321-018-0299-2 14
MS-Ready SMILES 15
Possible Outputs… 16
TEST and OPERA Predictions 17
Transparency for prediction models 18
TEST Real-Time Predictions 19
TEST Real-Time Predictions with detailed calculation reports 20
TEST Real-Time Predictions with detailed calculation reports 21
TEST/OPERA Batch Download 22
Possible Outputs… 23
Curation Level Details • We have full time curators checking data 24
Possible Outputs… 25
Hazard Data from “ToxVal_DB” • ToxVal Database contains following data: –30,050 chemicals –772,721 toxicity values –29 sou...
Access to Chemical Hazard Data 27
Possible Outputs… 28
In Vitro Bioassay Screening ToxCast and Tox21 29
Possible Outputs… 30
Sources of Exposure to Chemicals 31
Possible Outputs… 32
IRIS Report 33
Integrated Data in Excel Sheet 34
Possible Outputs… 35
Literature Searching 36
Literature Searching 37
Literature Searching 38
Abstract Sifter for Excel 39
Possible Outputs… 40
Identifiers to Support Searches 41
Possible Outputs… 42
Transformation Products 43
Related Substance Relationships
CASRN Checking 45
Batch Searching Formula/Mass 46
Searching batches using MS-Ready Formula (or mass) searching 47
AN EXAMPLE APPLICATION 48
Aggregate data for a list of chemicals 49
Batch Search Names 50 Excel Download
Add Other Data of Interest 51
Possible Outputs – Chemical Lists 52
Batch Search in specific lists 53
Conclusion • Dashboard access to data for ~875,000 chemicals • Batch search capability for integrated search for thousands...
Acknowledgements EPA-RTP • An enormous team of contributors from NCCT, especially the IT software development team • Our c...
Contact Antony Williams NCCT, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/...
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EPA CompTox chemicals dashboard: An online resource for environmental chemists

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The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

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EPA CompTox chemicals dashboard: An online resource for environmental chemists

  1. 1. EPA CompTox chemicals dashboard: An online resource for environmental chemists Antony Williams, Chris Grulke, Jeremy Dunne and Jeff Edwards National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC Spring 2019 ACS Spring Meeting, Orlando 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. CompTox Portal 1
  3. 3. CompTox Chemicals Dashboard • A publicly accessible website delivering access: – ~875,000 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 2
  4. 4. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 3 875k Chemical Substances
  5. 5. BASIC Search 4
  6. 6. Detailed Chemical Pages 5
  7. 7. THE POWER OF BATCH SEARCHING 6
  8. 8. Batch Access to Underlying Data https://comptox.epa.gov/dashboard/dsstoxdb/batch_search 7
  9. 9. Inputs 8
  10. 10. CAS Numbers… 9
  11. 11. Display Chemicals 10
  12. 12. CAS Numbers… 11
  13. 13. Possible Outputs… 12
  14. 14. 13
  15. 15. “MS-Ready Structures” https://doi.org/10.1186/s13321-018-0299-2 14
  16. 16. MS-Ready SMILES 15
  17. 17. Possible Outputs… 16
  18. 18. TEST and OPERA Predictions 17
  19. 19. Transparency for prediction models 18
  20. 20. TEST Real-Time Predictions 19
  21. 21. TEST Real-Time Predictions with detailed calculation reports 20
  22. 22. TEST Real-Time Predictions with detailed calculation reports 21
  23. 23. TEST/OPERA Batch Download 22
  24. 24. Possible Outputs… 23
  25. 25. Curation Level Details • We have full time curators checking data 24
  26. 26. Possible Outputs… 25
  27. 27. Hazard Data from “ToxVal_DB” • ToxVal Database contains following data: –30,050 chemicals –772,721 toxicity values –29 sources of data –21,507 sub-sources –4585 journals cited –69,833 literature citations 26
  28. 28. Access to Chemical Hazard Data 27
  29. 29. Possible Outputs… 28
  30. 30. In Vitro Bioassay Screening ToxCast and Tox21 29
  31. 31. Possible Outputs… 30
  32. 32. Sources of Exposure to Chemicals 31
  33. 33. Possible Outputs… 32
  34. 34. IRIS Report 33
  35. 35. Integrated Data in Excel Sheet 34
  36. 36. Possible Outputs… 35
  37. 37. Literature Searching 36
  38. 38. Literature Searching 37
  39. 39. Literature Searching 38
  40. 40. Abstract Sifter for Excel 39
  41. 41. Possible Outputs… 40
  42. 42. Identifiers to Support Searches 41
  43. 43. Possible Outputs… 42
  44. 44. Transformation Products 43
  45. 45. Related Substance Relationships
  46. 46. CASRN Checking 45
  47. 47. Batch Searching Formula/Mass 46
  48. 48. Searching batches using MS-Ready Formula (or mass) searching 47
  49. 49. AN EXAMPLE APPLICATION 48
  50. 50. Aggregate data for a list of chemicals 49
  51. 51. Batch Search Names 50 Excel Download
  52. 52. Add Other Data of Interest 51
  53. 53. Possible Outputs – Chemical Lists 52
  54. 54. Batch Search in specific lists 53
  55. 55. Conclusion • Dashboard access to data for ~875,000 chemicals • Batch search capability for integrated search for thousands of chemicals across diverse data 54 • Future capabilities will include batch prediction • Ongoing data expansion continues day to day • We are committed to open API development for data access and predictions
  56. 56. 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
  57. 57. Contact Antony Williams NCCT, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 56 https://doi.org/10.1186/s13321-017-0247-6

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