Delivering chemical-associated data via EPA web applications
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The document discusses the Comptox Chemicals Dashboard, developed by the U.S. EPA, as a central hub for environmental chemical data, integrating over 900,000 chemical substances and various predictive models. It emphasizes the need for efficient access to chemical hazard and exposure data to aid decision-making and chemical risk assessments. Additionally, the dashboard features batch searching and real-time data retrieval from literature, aiming to streamline the research process related to chemical safety.
Delivering chemical-associated data via EPA web applications
- 1. Center for Computational Toxicology and Exposure, US-EPA, RTP, NC http://www.orcid.org/0000-0002-2668-4821 Delivering chemical-associated data via EPA web applications The views expressed in this presentation are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA Antony J. Williams Cheminformatics Resources of U.S. Governmental Organizations– May 11th 2022
- 2. The State of Internet Chemistry… • The past two decades has seen an explosion in online data • There are so many resources to choose from…so much data • In our world there are dominant aggregating resources done well: PubChem, ChEMBL, eChemPortal, ECHA • Do we need yet another online chemistry database?
- 3. 20 Years of Curating Data in Our Team
- 4. The Charge for the CompTox Chemicals Dashboard • Develop a “first-stop-shop” for environmental chemical data to support EPA and partner decision making: – Centralized location for chemical data (DSSTox foundation) – Chemistry, exposure, hazard and dosimetry – Combination of existing data and predictive models – Publicly accessible, periodically updated, curated • Easy access to data improves efficiency and ultimately accelerates chemical risk assessment
- 5. CompTox Chemicals Dashboard https://comptox.epa.gov/dashboard 5 SEARCH TOX DATA BIOACTIVITY SIMILARITY READ-ACROSS PUBMED BATCH SEARCH
- 6. Detailed Chemical Pages • Chemical page: Wikipedia snippet when available, intrinsic properties, structural identifiers, linked substances
- 7. “Executive Summary” regarding chemical toxicity • Overview of toxicity- related info • Quantitative values • Physchem. and Fate & Transport • Adverse Outcome Pathway links • In vitro bioactivity summary plot
- 8. Experimental and Predicted Data • Physchem and Fate & Transport experimental and predicted data • Data extracted (somewhat curated) from literature and databases • Multiple prediction algorithms used: OPERA, TEST, ACD/Labs, EPI Suite • Data can be downloaded as Excel, TSV and CSV files
- 9. Chemical Hazard Data ToxVal Database • >50k chemicals • >770k tox. values • >30 sources of data • ~5k journals cited • ~70k citations
- 10. Safety Data – Thank you PubChem! Bring together resources
- 11. Sources of Exposure to Chemicals
- 12. A recent focus on PFAS chemicals
- 13. Similar Compounds Simple cheminformatics search
- 14. Relationships in the data Manual curation and mapping
- 15. Markush Chemical representations • PFOS is a member of linear perfluoroalkyl sulfonates 15
- 16. …and their Markush Children… • Linear perfluoroalkyl sulfonates has children…
- 17. Bioactivity Data
- 18. ToxCast
- 20. Full transparency in terms of data • Concentration Response data
- 21. Full access to concentration-response curves
- 22. Use Models Derived from the Data
- 23. Searching Literature and the Internet
- 24. Literature Searching • Real-time retrieval of data from PubMed ~30 million abstracts and growing) • Choose from set of pre-defined queries • Adjust and fine tune queries based on interests
- 25. Literature Searching • “Sifting” of results using multiple terms • Frequency counting terms • Color highlighting of terms • Download list to Excel • Send list to PubMed for downloading ref. file • Direct link via PubMed ID
- 26. What’s the best way to search the internet for chemical data? • We know how complex chemicals identifiers are… • CASRN(s) • Hundreds of names (maybe) • SMILES • InChIs • EINECS, EC numbers • What can WE do to help you navigate the internet?
- 27. External Links – Also use Identifiers Names, CASRN, PubChem IDs, InChIs… 27
- 28. External Links • Links to ~90 websites providing access to additional data on the chemical of interest
- 30. A List of Lists of Chemicals https://comptox.epa.gov/dashboard/chemical_lists
- 31. The OECD List of PFAS http://www.oecd.org/chemicalsafety/portal-perfluorinated-chemicals/ 31
- 33. PFAS List Paper https://doi.org/10.3389/fenvs.2022.850019 • What makes our efforts different? • MANUAL curation work • Building lists, cross- referencing, mapping relationships, sourcing and curating data
- 34. Batch Searching
- 35. Batch Searching • Singleton searches are great but… • …we generally want data on LOTS of chemicals! • Typical questions • What are the structures for a set of chemical names? Set of CASRNs? • Can I get chemical lists in Excel files? As a list of SMILES strings? Can I get an SDF file? • Can I include predicted properties? OPERA? TEST? • Are “these chemicals” screened in Toxcast? • I need masses and formulae for a list of chemicals
- 36. Batch Search
- 37. Batch Search – Excel, CSV, SDF file
- 38. Batch Search
- 40. Since our data are Open… • They flow into other systems for benefit … • ECHA eChemPortal • ChemSpider • EBI’s UniChem • PubChem
- 42. Six Modules • Hazard Comparison Profiling – profile chemicals based on hazard • Alerts – structure, substructure, SMARTS based alerts and flags • Predict – batch prediction using WebTEST (100s of structures) • Search – structure/substructure/similarity searches • Standardize – convert structures into QSAR/MS-Ready forms • ToxPrints – generate ToxPrint substructural fragments and profile
- 43. Module 1: Hazard Module
- 44. Module 2: Alerts
- 45. Module 3: WebTEST Batch Prediction
- 47. Summary and Conclusion • CompTox Chemicals Dashboard - a central hub for environmental data • ~900k chemical substances (1.2M soon) • Integrating property data, hazard data, exposure data, in vitro bioactivity data • Interrogation of bioactivity data - • Multiple types of searches • Batch search for thousands of chemicals • Real-time property and toxicity predictions • Downloadable files – CSV, TSV and Excel
- 48. Some Related Publications of Interest
- 49. You want to know more… • Lots of resources available • Presentations: https://tinyurl.com/w5hqs55 • Communities of Practice Videos: https://rb.gy/qsbno1 • Manual: https://rb.gy/4fgydc • Latest News: https://comptox.epa.gov/dashboard/news_info 49
- 50. Acknowledgments • Contact: Williams.Antony@epa.gov • Feedback and follow-up is welcomed! Your questions help. • The dashboard is based on the efforts of many more team members than us • Many collaborators provide data also 50 EPA’s Center for Computational Toxicology and Exposure
- 51. THANK YOU Panel Discussion Ideas… • Thank you to the organizers for the conference. It was very beneficial to catch up on what’s going on across the groups • For the Panel Discussion today…selfish wants • How do we limit rework in terms of repeat curation? • How do we coordinate development of QSAR data sets (because QSAR modeling is not the hard part) – DILI data, Log Kow, Solubility • There would be so much benefit to InChI-Markush. It’s doable…how can we collectively fund it?