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New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA


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Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new CompTox Chemistry Dashboard and the developing architecture to support real-time property and toxicity endpoint prediction. This abstract does not reflect U.S. EPA policy.

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New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA

  1. 1. New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA Antony Williams1, Chris Grulke1, Andrew McEachran2, Grace Patlewicz1, Imran Shah1, John Wambaugh1, Ann Richard1, Richard Judson1 and Jeff Edwards1 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 March 2018 ACS Spring Meeting, New Orleans 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. • National Center for Computational Toxicology established in 2005 to integrate: – High-throughput and high-content technologies – Modern molecular biology – Data mining and statistical modeling – Computational biology and chemistry • Outputs: a lot of data, models, algorithms and software applications • Open Data – we want scientists to interrogate it, learn from it, develop understanding National Center for Computational Toxicology
  3. 3. Early Dashboard Applications 2
  4. 4. Earlier Dashboards • Chemistry data mashed together based on CAS Number/Names • Chemistry data quality issues • Multiple applications requiring maintenance • April 2016 – beta release of the CompTox Chemistry Dashboard as an integration hub 3
  5. 5. The CompTox Chemistry Dashboard • A publicly accessible website delivering access: – ~760,000 chemicals with related property data – Experimental and predicted physicochemical property 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 – DOWNLOADABLE Open Data for reuse and repurposing 4
  6. 6. CompTox Chemistry Dashboard 5
  7. 7. Detailed Chemical Pages 6
  8. 8. Access to Chemical Hazard Data 7
  9. 9. In Vitro Bioassay Screening ToxCast and Tox21 8
  10. 10. Sources of Exposure to Chemicals 9
  11. 11. Identifiers to Support Searches 10
  12. 12. Literature Searches and Links 11
  13. 13. External Links to Data and Services 12
  14. 14. Integrated Linkouts 13
  15. 15. Integrated Linkouts Comparative Toxicogenomics DB 14
  16. 16. Advanced Searches 15
  17. 17. Advanced Searches Mass Based Search 16
  18. 18. Advanced Searches 17
  19. 19. Batch Searches 18
  20. 20. Batch Search 19
  21. 21. Excel Output 20
  22. 22. Real-Time Predictions 21
  23. 23. Real-Time Predictions 22
  24. 24. Real-Time Predictions 23
  25. 25. Our support for FAIR Data 24
  26. 26. Downloadable Data 25
  27. 27. Prototype Development 26
  28. 28. Prototype Development 27
  29. 29. Future Development Real Time OPERA Predictions 28
  30. 30. Future Search Possibilities 29 Chemical Assay Gene Product Search Assay Endpoint Name
  31. 31. Conclusion • The CompTox Chemistry Dashboard provides access to data for ~760,000 chemicals • High quality data from ongoing curation efforts • An integration hub for multiple “modules” – Experimental and predicted properties – Human and Ecological Hazard data – Exposure data – products, data in the environment – In vitro bioassay data – ToxCast/Tox21 – Literature searching – Google Scholar and PubMed – Specialized searches – mass/formula for analytical support – Batch searching and Real Time Predictions • The primary architecture for NCCT data 30
  32. 32. Acknowledgments • The NCCT CompTox Chemistry Dashboard Development Team • NERL scientists (Jon Sobus, Elin Ulrich) – Mass Spectrometry • Kamel Mansouri – OPERA models • Todd Martin – TEST predictions • Nancy Baker – Abstract Sifter 31
  33. 33. Contact Antony Williams US EPA Office of Research and Development National Center for Computational Toxicology (NCCT) ORCID: 32