The US EPA CompTox Chemicals Dashboard website provides access to various data types associated with ~900,000 chemical substances and supports the needs of the National Center for Computational Toxicology. The dashboard both consumes data, models and open source code from open as well as delivering data and services back to the community. The dashboard offers access to various types of aggregated and integrated chemistry, biology and toxicology data. The dashboard provides web-based access to data hosted in multiple databases, integrates to an underlying chemical registration system and utilizes both commercial and open QSAR/QSPR models to deliver predicted data for the chemicals. Some of the open source software that we utilize is used for InChI generation, for structure drawing and for real time prediction of both toxicity and physicochemical endpoints. This presentation will provide an overview of the dashboard, review our usage of open source code to deliver the web application, and discuss our present and planned contributions to open science. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

1. Using open data, open services, and open
source software to deliver the EPA
CompTox Chemicals Dashboard
Antony Williams1, Chris Grulke1, Kamel Mansouri2, Jeremy Dunne1
and Jeff Edwards1
1) National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC
2) Integrated Laboratory Systems, Research Triangle Park, NC
Fall 2019
ACS Fall Meeting, San Diego
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. CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
1
875k Chemical Substances

3. BASIC Search
2

4. Detailed Chemical Pages
3

5. CompTox Chemicals Dashboard
• Total data landscape includes:
– ~875,000 chemical substances
– Experimental & predicted physchem property data
– Experimental Human and Ecological hazard data
– Bioactivity data for 1000s of chemicals
– Consumer products containing chemicals
– “Literature” searches for chemicals using PubMed
– Real time prediction of physchem/toxicity endpoints
4

6. CompTox Chemicals Dashboard
• To make this happen we CONSUME open data
and open source software
• We also PRODUCE open data and both free and
open source software
• This presentation is an overview of what we
consume and what we produce…
5

7. CONSUMER
Integrated Wikipedia Snippet
6
• Integrated Wikipedia snippet linked out to
full article

8. PhysChem Data
and Predictions
7

9. CONSUMER: Available Data
2010 files underlying EPI Suite
8

10. Data required thorough curation
9

11. CONSUMER
KNIME workflows for curation
10

12. PRODUCER
All curated data available
11

13. PRODUCER
TEST and OPERA Predictions
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14. Transparency for prediction models
13

15. PRODUCER
OPERA Standalone Application
14

16. PRODUCER: Open Source
https://github.com/kmansouri/OPERA
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17. PRODUCER: Other prediction models
TEST Desktop Software
16

18. Bioactivity Data:
Tox21 and
Toxcast
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19. PRODUCER
In Vitro Bioassay Screening
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20. PRODUCER
Bioactivity: Downloadable Data
19

21. CONSUMER
PubChem Widgets - Bioactivities
20

22. Literature
Data
21

23. CONSUMER
PubChem Widgets - Articles
22

24. CONSUMER
PubChem Widgets – Patents
23

25. CONSUMER: Pubmed Services
Literature Searching
24

26. CONSUMER: Pubmed Services
Literature Searching
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27. CONSUMER: Pubmed Services
Literature Searching
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28. PRODUCER
Abstract Sifter for Excel
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29. Real-Time
Predictions
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30. CONSUMER
epam Ketcher
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31. CONSUMER: Ketcher Drawing
TEST Real Time Predictions
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32. Ketcher Drawing
TEST Real Time Predictions
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33. TEST detailed calculation reports
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34. PRODUCER: TEST Software
https://www.epa.gov/chemical-research/toxicity-
estimation-software-tool-test
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35. PRODUCER: TEST Web Services
https://www.epa.gov/sites/production/files/2018-08/documents/
webtest_users_guide.pdf
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36. PRODUCER
Web Services
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37. PRODUCER: Web Services
https://actorws.epa.gov/actorws/
• Dozens of web services to provide access
to data
• Data in UI, JSON and XML format
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38. PRODUCER
InChIKey to DTXCIDs
37
https://actorws.epa.gov/actorws/dsstox/v02/msready?identifier
=UVOFGKIRTCCNKG-UHFFFAOYSA-N

39. CONSUMER of our services
MassBank mapping to Dashboard
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40. Open Data
Sharing
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41. CONSUMER
NORMAN Suspect List Exchange
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42. PRODUCER
Curated Chemical Lists
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43. PRODUCER
EPAHFR: Hydraulic Fracturing
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44. PRODUCER
Publishing Open Data: CPDat
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45. …and then reused in PubChem
44

46. PRODUCER
Downloadable Data
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47. Work in Progress
• Multiple projects in progress that use Open
Source software
– Structure, substructure and similarity searching
– MS-Ready and QSAR-Ready data preparation
– WebTEST “Batch” predictions
– OPERA model predictions
– Prediction of MS fragmentation patterns and matching
to searched experimental spectra
• New services and Full API will be openly
available (in future releases)
46

48. CONSUMER: Prototype Development
epam Ketcher + Bingo NoSQL
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49. CONSUMER
Epam Bingo NoSQL
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50. August 26, 2019
Nontargeted screening of wastewater for water reuse using mass spectrometry Current Advances in Water
Analysis
49
CONSUMER
CFM-ID Fragmentation Prediction
4x10
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1.1
1.2
1.3
1.4
1.5
1.6
1.7
Cpd 101: Pseudoephedrine 12.111: (M+H)+: +ESI Product Ion (rt: 12.111 min) Frag=125.0V CID@20.0 (166.1226[z=1] -> **) HI1.d
148.1120
117.0697
133.0888
91.0539
70.0644
106.0655
120.0814
79.0535
100.1109
93.0679
NH
OH
H3C
H3C
Counts vs. Mass-to-Charge (m/z)
60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150 155 160 165
Ephedrine

51. • Predictions generated and stored for >700,000 structures
• Python code to score experimental vs predicted spectra
• Cosine dot product match score calculation
August 26, 2019
Nontargeted screening of wastewater for water reuse using mass spectrometry Current Advances in Water
Analysis
50
PRODUCER
CFM-ID Predicted Library

52. PRODUCER
Published data is on FigShare
51

53. Conclusion
• Dashboard access to data for ~875,000 chemicals
• Dashboard CONSUMES a lot of open source
libraries and open data
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• We PRODUCE open
models and data to the
community in exchange
• We are committed to an
open API to provide more
complete data access and
real time predictions

54. Acknowledgements
• NCCT IT development team
• Tommy Cathey, ACTOR Web Services
• Nancy Baker, Abstract Sifter
• Todd Martin & Valery Tkachenko,
WebTEST
• Kathie Dionisio & Kristin Isaacs, CPDat
• Thanks to Emma Schymanski, University
of Luxembourg, for coordinating all efforts
with the NORMAN Network for curation of
lists on the Suspect Exchange

55. Contact
Antony Williams
NCCT, US EPA Office of Research and Development,
Williams.Antony@epa.gov
ORCID: https://orcid.org/0000-0002-2668-4821
54
https://doi.org/10.1186/s13321-017-0247-6