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EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental Chemistry Data

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The CompTox Chemicals Dashboard (available at https://comptox.epa.gov/dashboard) is the latest in a suite of dashboards that have been delivered to the community by EPA’s National Center for Computational Toxicology. The dashboard delivers access to data for >875,000 chemicals and includes experimental and predicted physicochemical properties, hazard and exposure data, access to Toxcast/Tox21 bioactivity screening data and provides a link farm to dozens of other online resources. The dashboard delivers access to data with a variety of powerful search capabilities including searching by chemical identifier (e.g. CAS Number or Name), by commercial product type, or by mass or formula. Searches can be performed one chemical at a time or in batches of thousands. Whether you are a chemist, an analytical scientist or a toxicologist the dashboard is of value as it seamlessly integrates data from dozens of databases into a web-based user experience. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed and almost 30 million publication abstracts. The data and functionality available via the dashboard can be of value in terms of decontamination by providing access to data to assist in detection (specifically via mass spectrometric detection), accessing literature and potential decontamination approaches associated with specific chemicals, and access to toxicity values for chemicals such as Military Exposure Guidelines. 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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EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental Chemistry Data

  1. 1. EPA CompTox Chemicals Dashboard as a Data Integration Hub for Environmental Chemistry Data Antony Williams Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, RTP, NC November 2019 Decontamination Conference, Norfolk, VA 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 Chemicals Dashboard https://comptox.epa.gov/dashboard • Freely accessible website and integration hub – Chemical substances – the majority with structures – Searchable by chemical, product use and gene – Experimental and predicted physicochemical property data – Experimental and predicted fate and transport data – Bioactivity data for the ToxCast/Tox21 project – Literature searches for chemicals using public resources – Links to other agency websites and public data resources – Batch searching for thousands of chemicals – Chemical lists of interest – pesticides, leachables, PFAS 1
  3. 3. A single application integrating… 2 SEARCH TOX DATA BIOACTIVITY SIMILARITY READ-ACROSS PUBMED BATCH SEARCH
  4. 4. A data integration hub LOTS of data! • >875,000 chemicals curated over 20 years • >700,000 toxicity data points from >30 sources • Millions of synonyms and identifiers • Tens of thousands of experimental data points • Millions of QSAR prediction reports • Millions of bioactivity data points for >4000 chemicals and hundreds of assay end points • Searching of Pubmed’s 29 million abstracts 3
  5. 5. DEMO AND QUESTIONS Live Demo at Table 11 Later 4
  6. 6. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 5 875k Chemical Substances
  7. 7. BASIC Search 6
  8. 8. Detailed Chemical Pages 7
  9. 9. An “Executive Summary” Quick Look Tox Info 8
  10. 10. Experimental and Predicted Data 9
  11. 11. Transparency for prediction models 10
  12. 12. Access to Chemical Hazard Data 11
  13. 13. 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 12
  14. 14. In Vitro Bioassay Screening ToxCast and Tox21 13
  15. 15. Sources of Exposure to Chemicals 14
  16. 16. Sources of Exposure to Chemicals 15
  17. 17. Identifiers to Support Searches 16
  18. 18. What if we have nothing for you? “EXTERNAL LINKS” 17
  19. 19. External Links 18
  20. 20. External Links 19
  21. 21. External Links 20
  22. 22. Built in “Modules” 21
  23. 23. Literature Searching 22
  24. 24. Literature Searching 23
  25. 25. Literature Searching 24
  26. 26. Chemical Lists 25
  27. 27. EPAHFR: Hydraulic Fracturing 26
  28. 28. Emergency Response List 27
  29. 29. WebWISER List 28
  30. 30. Batch Searching 29
  31. 31. 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? 30
  32. 32. Batch Search Names 31 Excel Download
  33. 33. Conclusion • An integrated hub for environmental chemistry data to serve computational toxicology • Serving multiple use cases and needs – let’s talk! 32
  34. 34. Contact Antony Williams CCTE, US EPA Office of Research and Development, Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 33 https://doi.org/10.1186/s13321-017-0247-6 Live Demo at Table 11 Later

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