The US EPA’s National Center for Computational Toxicology (NCCT) has been both measuring and aggregating data to support our research efforts for over a decade. We have delivered these data via a number of publicly accessible websites, so-called dashboards, to provide transparent access to the outputs of the center. Since the inception of our research, software projects technologies have changed dramatically, as have the expectations regarding the methods by which to access data. Our informatics efforts provide access to millions of dollars of high-throughput screening data available in open, downloadable formats, via web services and through a rich web interface. Similarly, we provide access to experimental and predicted data associated with ~760,000 substances to serve the environmental chemistry community, and open source code for predictive models. This presentation will provide an overview of the efforts of NCCT to provide transparent access to our research and data via our publications (and accompanying supplementary data), via our Open Data policies, and through our databases, software tools and web services. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

1. Progress in Delivering Transparency in
Research Data by the National Center for
Computational Toxicology at the US-EPA
Antony J. Williams, Jeff Edwards, Chris Grulke and John Cowden
National Center for Computational Toxicology, U.S. Environmental Protection Agency, RTP, NC
August 2018
ACS Fall Meeting, Boston
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. Disclaimer of Endorsement
• Mention of or referral to commercial
products or services, and/or links to non-
EPA sites does not imply official EPA
endorsement of or responsibility for the
opinions, ideas, data, or products
presented at those locations, or guarantee
the validity of the information provided.
1

3. • 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,
software applications and publications
• Open Data – we want scientists to interrogate
it, learn from it, develop understanding
National Center for
Computational Toxicology

4. The CompTox Portal
https://comptox.epa.gov/
3

5. Downloadable CompTox Data
https://www.epa.gov/chemical-research/downloadable-computational-toxicology-data
4

6. Deliver Data for Reuse:
DIFFERENT formats
https://www.epa.gov/chemical-research/toxicity-forecaster-toxcasttm-data

7. Open Data means Reuse
For Science
6

8. Open Data means Reuse
For Software
7

9. CompTox Dashboard
https://comptox.epa.gov/dashboard
8

10. CompTox Dashboard
Chemicals
9

11. CompTox Dashboard
Products and Use Categories
10

12. CompTox Dashboard
Assays and Genes
11

13. Downloadable data in
useful formats
12

14. EPA FigShare Page
https://epa.figshare.com/
13

15. Datasets with versioning
14

16. Measuring Our IMPACT
15

17. The impact of our paper versus the
impact of our data…187 downloads
16

18. FAIR Data
17

19. FAIRsharing.org
18

20. Examples of our transparency
1. OPERA Prediction Models
19

21. What are OPERA Models?
20

22. What are OPERA Models?
Detailed QMRF reports
21

23. How Transparent in the Publication?
22

24. On FigShare
23

25. How Transparent with the Code?
https://github.com/kmansouri/OPERA
24

26. How widely do we share?
25

27. How widely do we share?
26

28. Journals for Data Articles
27

29. Data Journals Hold Promise
28

30. Examples of our transparency
2. The Chemical and Products Database
29

31. Examples of our transparency
2. The Chemical and Products Database
30

32. What chemicals are in
Arts and Crafts Paint?
31

33. Examples of our transparency
2. The Chemical and Products Database
32

34. Are we oversharing?
• We share our datasets
• We share our models
• We share our code
• We share our database schemas
• We share our database dumps
• We are not yet sharing all code under an
application like the CompTox Dashboard..
33

35. A Recurring Plea for Formats
• Chemical data exchange formats are critical
• We all know it’s imperfect, that there are
efforts afoot, and it’s taking time
34
2015
2018

36. Use APPROPRIATE formats
• Our databases use chemical structures
• Many journal articles deliver poor data
35

37. Chemical structures as text
36

38. How do I extract structures?
• Copy and paste into Excel as a start point
• Assume no loss of formatting!
• Convert SMILES to structures
• But Copy-Paste doesn’t work
37

39. How do I extract structures?
• Copy and paste into Excel as a start point
• Assume no loss of formatting!
• Convert SMILES to structures
• Copy-Paste doesn’t work
38

40. Structure Drawings Are Worse
39

41. Names and CASRNs
are NOT structures
• In our domain most chemicals are text –
chemical names and CAS Numbers
40

42. And generally problematic…
41

43. So this is how we publish our
chemical substance data
42

44. Publish data for your domain
• Push data out in immediately useful formats
– Make multiple formats available as appropriate – SQL
database dumps, Excel files, etc.
– For chemistry - SDF files – includes LAYOUT and data
(but requires cheminformatics tools), Excel files generally
handled at any desktop.
43

45. So this is how we publish our
chemical substance data
44

46. When we publish now…
• Add the data as a “list” to our Lists of Chemicals
• Generally store files on our FTP site PLUS
copies in a repository (or two)
• Multiple formats of data as appropriate
– Can be as supplementary data or DOI’ed data files
• DOI’ed data gives altmetrics also..
45

47. PERSONAL affection for
Open Peer Review
46

48. Will my data always be available?
• There are no guarantees our data will
always be on all sites. They come and go.
• Some organizations are just as concerned
as you about your data…
47

49. Future Work
• We have a lot more models to make
available – Open and free web services
• We are planning for embeddable widgets
to access our Open data
• The challenge of versioning – ongoing
curation of data requires version tracking
48

50. NCCT “InvitroDB_v3”
• The last public release of ToxCast data
(invitroDB_v2) was in 3rd Quarter of 2015
• The next release invitroDB_v3 is Fall 2018
• Data includes new assays, new chemicals,
new pipelining, results of data curation
• Data will also release via CompTox Dashboard
• Data will be available at https://www.epa.gov/chemical-
research/exploring-toxcast-data-downloadable-data
49

51. NCCT Transcriptomics Data will Deliver
50 Terabytes of Data for Analysis
TruSeq
r2 0.74
TempO-Seq
r2 0.75
Low Coverage
r2 0.83
Currently capable of assigning to >40
MOAs based on transcriptional
responses
MOA Analysis Pipeline
• Large scale screen of 1,000 chemicals (ToxCast I/II)
Additional screens across multiple cell types/lines
• Additional reference chemicals and genetic
perturbations (RNAi/CRISPR/cDNA)

52. Conclusions
• For publications and for applications deliver
your data in “fit-for-purpose” form
• Multiple formats of data are appropriate
• Consider your audience(s) and “how would
YOU want the data”???
• Not everything can be put in a supplementary
file – use repositories and DOI your data
• Take the benefits of DOIs to measure
altmetrics
51

53. Conclusion
• NCCT works with transparency in mind – our
data is released for community usage – as data
and in apps
• The CompTox Dashboard is the new application
to surface all data as the architecture expands
• We attempt to deliver data in as transparent a
form as possible for our scientific publications
• We consider long-term access and versioning
in our releases. Lots of work to do…
52

54. …and let other people use it…

55. Contact
Antony Williams
US EPA Office of Research and Development
National Center for Computational Toxicology (NCCT)
Williams.Antony@epa.gov
ORCID: https://orcid.org/0000-0002-2668-4821
54