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Informatics Approaches supporting UVCB
Chemicals in the US-EPA CompTox
Chemicals Dashboard
Antony Williams1, Chris Grulke1 and Emma Schymanski2
Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, RTP, NC
Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg, Europe
November 2019
SETAC, Toronto, Canada
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
Overview
• The CompTox Chemicals Dashboard - web-
based database of 875k substances
• Associated data including:
– Experimental and predicted physicochemical data
– In vivo hazard data
– In vitro bioactivity screening data
– Link farm to tens of public resources
• Integrated modules – read-across, lit search
• Data mappings and searches supporting
Mass Spectrometry & structure identification
1
CompTox Chemicals Dashboard
https://comptox.epa.gov/dashboard
2
875k Chemical Substances
BASIC Search
3
Detailed Chemical Pages
4
Human and Eco Hazard Data
• ToxVal Database contains following data:
–~700,000 toxicity values
–~30 sources of data
–~22,000 sub-sources
–~5000 journals cited
–~70,000 literature citations
5
In Vitro Bioassay Screening
ToxCast and Tox21
6
Related Substances – Transformation
Products, “Monomer-Polymer”
7
What No
Structures???
“UVCB”
Chemical
Substances
8
UVCB Chemicals
9
Lots of UVCBS in Commerce….
10
Example UVCBs with no structures
11
• Aroclor 1254
• Toxaphene
• Xylenes
• Demeton
• Aroclor 1248
• Asbestos
• Technical chlordane
• Coke oven emissions
• Creosote
• Diesel engine exhaust
• Nickel refinery dust
• Nickel, soluble salts
• Refractory ceramic fibers
• Toluene diisocyanate
What is Toxaphene?
“Complex, but reproducible mixture of at least 175
distinct C10-chloro compounds, having an approximate
overall empirical formula of C10H10Cl8.; the 2 most
active components are a C10H10Cl8 compound and a
C10H11Cl7 compound which had been elucidated as
2,2,5-endo,6-exo,8,9,10-heptachlorobornane.
Produced by the chlorination of camphene to 67-69%
chlorine by weight and made up of compds. of C10 H8
Cl10, C10 H18-n Cl n (mostly poychloroboranes) and
C10 H16-n Cl n (oychloroboranes and/or
polychlorotricyclenes) with n = 6 to 9”
12
Toxaphene has rich data
13
UVCB: Mapped Chemicals
Polymer individual components
Linear Alkylbenzenesulfonates
15
• Ambiguous representations of
some structures are possible
• “Markush” representations
can be valuable for describing
and mapping chemicals
“Markush Structures”
https://en.wikipedia.org/wiki/Markush_structure
16
Chemical “grouping” – PCBs, PBDEs
17
PCBs
PBDEs
Some Markush chemicals
are bounded
18
Previously 1-1 mapping
Now Markush Enumeration
19
UVCB: Complex Surfactants
20
UVCB: Complex Surfactants
21
Chemical Lists
and Categories
22
EPAHFR: Hydraulic Fracturing
23
TSCA Inventory
24
TSCA Inventory List
Active Non-confidential portion
25
Over 11,500 out of 23,500 have NO STRUCTURES
Batch
Searching
26
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?
27
Batch Search Names
28
Excel
Download
Add Other Data of Interest
29
Related Substance Relationships
Conclusion
• Building an integrated hub for environmental chemistry
data to serve computational toxicology
• Transparent access to data and models – file
downloads, SQL data dumps and web services
• Expansion of functionality to serve all data streams
generated by NCCT across the agency & community
31
• Data QUALITY is a key
focus - ongoing curation
• Ongoing API development
will provide enhanced
access to data streams
Acknowledgements
EPA-RTP
• An enormous team of contributors
from CCTE, especially the IT
software development team
• Our curation team for their care
and focus on data quality
• Multiple centers and laboratories
across the EPA
• Many public domain databases
and open data contributors
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

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Informatics Approaches supporting UVCB Chemicals in the US-EPA CompTox Chemicals Dashboard