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US-EPA Chemicals Dashboard: an integrated data hub for environmental science Antony Williams Center for Computational Toxi...
Contact Antony Williams Williams.Antony@epa.gov 1 https://doi.org/10.1186/s13321-017-0247-6
Overview • The CompTox Chemicals Dashboard - web- based database of 875k substances • Associated data including: – Experim...
A single application integrating… 3 SEARCH TOX DATA BIOACTIVITY SIMILARITY READ-ACROSS PUBMED BATCH SEARCH
CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 4 875k Chemical Substances
BASIC Search 5
Detailed Chemical Pages 6
An “Executive Summary” Quick Look Tox Info 7
Access to Chemical Hazard Data 8
Hazard Data from “ToxVal_DB” • ToxVal Database contains following data: –~800,000 toxicity values –~30 sources of data –~2...
Experimental and Predicted Data 10
Transparency for prediction models 11
In Vitro Bioassay Screening ToxCast and Tox21 12
In Vitro Bioassay Screening ToxCast and Tox21 13
Bioactivity: Downloadable Data https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data 14
Sources of Exposure to Chemicals 15
Sources of Exposure to Chemicals 16
Identifiers to Support Searches 17
Quality Control of the Database • We have full time curators checking data 18
Built-in “Modules” 19
Literature Searching 20
Literature Searching 21
Literature Searching 22
Abstract Sifter for Excel 23
Generalized Read-Across (GenRA) 24
Related Publications 25
Mapped Relationships 26
Relationships in the Data 27
28
Bisphenol A 27 Total Mappings 29
Chemical Lists and Categories 30
Category example – PAHs 31
EPAHFR: Hydraulic Fracturing 32
List of Assays
From Assay to Chemicals… 34
Other Searches 35
Product/Use Categories 36
Lubricant 37
Lots of UVCBS in Commerce…. 38
Other Searches Chemical-Biology 39
Assay/Gene Search 40
Assay/Gene Search Finds associated assays/chemicals 41
Batch Searching 42
Batch Searching • Singleton searches are useful but people generally want data on LOTS of chemicals! • Typical questions –...
Aggregate data for a list of chemicals 44
Batch Search Names 45 Excel Download
Add Other Data of Interest 46
Conclusion • An integrated hub for environmental chemistry data to serve computational toxicology • Transparent access to ...
Acknowledgements EPA-RTP • An enormous team of contributors from CCTE, especially the IT software development team • Our c...
SLIDE DECK ALREADY ONLINE https://www.slideshare.net/AntonyWilliams/ LIVE DEMO TIME!!! 49
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US-EPA Chemicals Dashboard – an integrated data hub for environmental science

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The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. 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. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data for over 4000 chemicals and ~1500 assays, and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include an interactive read-across module, real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

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US-EPA Chemicals Dashboard – an integrated data hub for environmental science

  1. 1. US-EPA Chemicals Dashboard: an integrated data hub for environmental science Antony Williams Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, RTP, NC June 25th 2020 PCRM: 2020 Summer School on Innovative Approaches in Science 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. Contact Antony Williams Williams.Antony@epa.gov 1 https://doi.org/10.1186/s13321-017-0247-6
  3. 3. Overview • The CompTox Chemicals Dashboard - web- based database of 875k substances • Associated data including: – Experimental and predicted physicochemical data – In vivo hazard data – In vitro bioactivity screening data – Link farm to tens of public resources • Integrated modules – read-across, lit search • Data mappings and searches supporting Mass Spectrometry & structure identification 2
  4. 4. A single application integrating… 3 SEARCH TOX DATA BIOACTIVITY SIMILARITY READ-ACROSS PUBMED BATCH SEARCH
  5. 5. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 4 875k Chemical Substances
  6. 6. BASIC Search 5
  7. 7. Detailed Chemical Pages 6
  8. 8. An “Executive Summary” Quick Look Tox Info 7
  9. 9. Access to Chemical Hazard Data 8
  10. 10. 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 9
  11. 11. Experimental and Predicted Data 10
  12. 12. Transparency for prediction models 11
  13. 13. In Vitro Bioassay Screening ToxCast and Tox21 12
  14. 14. In Vitro Bioassay Screening ToxCast and Tox21 13
  15. 15. Bioactivity: Downloadable Data https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data 14
  16. 16. Sources of Exposure to Chemicals 15
  17. 17. Sources of Exposure to Chemicals 16
  18. 18. Identifiers to Support Searches 17
  19. 19. Quality Control of the Database • We have full time curators checking data 18
  20. 20. Built-in “Modules” 19
  21. 21. Literature Searching 20
  22. 22. Literature Searching 21
  23. 23. Literature Searching 22
  24. 24. Abstract Sifter for Excel 23
  25. 25. Generalized Read-Across (GenRA) 24
  26. 26. Related Publications 25
  27. 27. Mapped Relationships 26
  28. 28. Relationships in the Data 27
  29. 29. 28
  30. 30. Bisphenol A 27 Total Mappings 29
  31. 31. Chemical Lists and Categories 30
  32. 32. Category example – PAHs 31
  33. 33. EPAHFR: Hydraulic Fracturing 32
  34. 34. List of Assays
  35. 35. From Assay to Chemicals… 34
  36. 36. Other Searches 35
  37. 37. Product/Use Categories 36
  38. 38. Lubricant 37
  39. 39. Lots of UVCBS in Commerce…. 38
  40. 40. Other Searches Chemical-Biology 39
  41. 41. Assay/Gene Search 40
  42. 42. Assay/Gene Search Finds associated assays/chemicals 41
  43. 43. Batch Searching 42
  44. 44. 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? 43
  45. 45. Aggregate data for a list of chemicals 44
  46. 46. Batch Search Names 45 Excel Download
  47. 47. Add Other Data of Interest 46
  48. 48. Conclusion • An integrated hub for environmental chemistry data to serve computational toxicology • Transparent access to data and models • Ongoing expansion of data on a daily basis • Data QUALITY is a key focus - careful curation 47
  49. 49. 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
  50. 50. SLIDE DECK ALREADY ONLINE https://www.slideshare.net/AntonyWilliams/ LIVE DEMO TIME!!! 49

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