The EPA CompTox Dashboard as a Data Integration Hub for Environmental Chemistry Data
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The EPA CompTox Dashboard serves as a comprehensive data integration hub for environmental chemistry, featuring approximately 762,000 chemicals with related property data and various search capabilities. This platform supports high-throughput screening through tools like ToxCast/Tox21 and provides access to bioactivity and hazard data, enhancing chemical safety assessments. Continuous development aims to improve functionality with real-time predictions and advanced search features, ultimately expanding the available data resources and integration of various chemical substances.
The EPA CompTox Dashboard as a Data Integration Hub for Environmental Chemistry Data
- 1. The EPA CompTox Dashboard as a Data Integration Hub for Environmental Chemistry Data Antony Williams1, Andrew McEachran2, Imran Shah1, Richard Judson1, John Wambaugh1, Nancy Baker3, George Helman2, Chris Grulke1, Kamel Mansouri4, Grace Patlewicz1, Ann Richard1, Jeremy Dunne1 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, RTP, NC 3) Leidos, RTP, NC 4) Integrated Laboratory Systems, Inc., RTP, NC August 2018 ACS Fall Meeting, Boston 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 http://orcid.org/0000-0003-1423-330X ENVR 152
- 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 • Researching computational approaches to quickly evaluate the safety of chemicals for potential risk. • Outputs: a lot of data, models, algorithms and software applications National Center for Computational Toxicology
- 3. The CompTox Chemistry Dashboard • A publicly accessible website delivering access: – New entry portal for all NCCT dashboards – ~762,000 chemicals with related property data – Searchable by chemical, product use, gene and assay (ToxCast) – Experimental and predicted physicochemical property data – “Bioactivity data” for the ToxCast/Tox21 project – Generalized Read-Across (GenRA) module – 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 2
- 7. CompTox Dashboard Products and Use Categories 6
- 8. CompTox Dashboard Assays and Genes 7
- 12. Detailed OPERA Prediction Reports 11
- 13. Access to Chemical Hazard Data 12
- 14. In Vitro Bioassay Screening ToxCast and Tox21 13
- 15. In Vitro Bioassay Screening ToxCast and Tox21 14
- 16. In Vitro Bioassay Screening ToxCast and Tox21 15
- 17. Sources of Exposure to Chemicals 16
- 18. Sources of Exposure to Chemicals 17
- 20. Identifiers to Support Searches 19
- 21. Literature Searches and Links 20
- 22. Abstract Sifter – PubMed Integration 21
- 23. Abstract Sifter for Excel 22
- 24. External Links to ~80 websites 23
- 26. Not just chemical “structures” • Chemicals in commerce, of interest to the EPA, are not all easily represented by structures • Different chemical substances supported – Chemical structures – “UVCB chemicals” - Unknown or Variable Composition, Complex Reaction Products and Biological Materials – Metabolites and transformation products – Homologous series as Markush Structures – Curated classes of chemicals 25
- 30. Not just chemical “structures” • Different chemical substances supported – Chemical structures – “UVCB chemicals” - Unknown or Variable Composition, Complex Reaction Products and Biological Materials – Metabolites and transformation products – Homologous series as Markush Structures – Curated classes of chemicals • Lists of chemicals – Submitted lists of chemicals – Federal, State, International and other general lists – Growing lists to support specific projects – e.g. ToxCast phases, algal toxins, our publication datasets 29
- 32. Algal Toxins 31
- 33. Mass and Formula Searches Supporting Mass Spectrometry 32
- 34. Advanced Searches Mass Based Search 33
- 35. Advanced Searches Mass Based Search 34
- 36. Batch Searching • Singleton searches are useful but we work with thousands of chemicals! • Typical questions – What are the SMILES strings for a list of 1000 chemicals? – Do any of this list of chemicals have XXX type of data? – What are the predicted logP values for a list of chemicals? – Can I get chemical lists in Excel files? In SDF files? 35
- 42. Crowdsourced Curation • Annotation of any table cell – admin panel views highlighted cell 41
- 43. Our support for FAIR Data 42
- 45. Work in Progress • Present work in development – Real time prediction using OPERA models – Structure/substructure/similarity search integration – Ongoing expansion of chemicals – Release of new ToxCast database (v3_2018) – Addition of products data from 10s of thousands of MSDS sheets – Analytical Data support • Integration of analytical data for ToxCast/Tox21 data • Spectral searching against predicted Mass Spectra 44
- 47. Predicted Mass Spectra http://cfmid.wishartlab.com/ • MS/MS spectra prediction for ESI+, ESI-, and EI • Predictions generated and stored for >700,000 structures, to be accessible via Dashboard 46
- 48. Conclusion • The EPA CompTox Dashboard provides access to data for ~762,000 chemicals, ToxCast assays and associated product use categories • 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 • Data and functionality increases with every release 47
- 49. Acknowledgments • The NCCT CompTox Chemistry Dashboard Development Team • NERL scientists (Jon Sobus, Elin Ulrich) – Mass Spectrometry • Kamel Mansouri – OPERA models • Todd Martin and Valery Tkachenko – TEST predictions • Nancy Baker – Abstract Sifter 48
- 50. Contact Andrew McEachran ORISE Postdoctoral Fellow US EPA Office of Research and Development [email protected] http://orcid.org/0000-0003-1423-330X Antony Williams US EPA Office of Research and Development National Center for Computational Toxicology (NCCT) [email protected] ORCID: https://orcid.org/0000-0002-2668-4821 49