1. Adverse Outcome Pathway Networks and the AOP Knowledgebase
Stephen Edwards
U.S. Environmental Protection Agency
Integrated Systems Toxicology Division

2. Outline Knowledge management AOP Networks Evidence assembly
Data organization
Computational modeling
AOP Networks
Automatic assembly by design
Basis for decision support tools
Challenges and opportunities

3. AOPs Connect Toxicity Pathways to Regulatory Endpoints
Predictivity of measurement for AO decreases
Time between exposure and effect increases

4. Factors Determining Predictivity of Early Key Events
Evidence supporting the KERs between that KE and the AO
Quantitative understanding of the downstream KERs
Modifying factors that influence downstream KEs & KERs

5. AOP-KB AOP-XML http://aopkb.org/ https://aopwiki.org/
AOP Wiki
Collaborative development of AOP descriptions & evidence
Effectopedia
Detailed development of structured & computational
AOPs
AOP Xplorer
Visualize attribute networks to discover & explore AOPs in a broader context
e.AOP.portal
Intermediate Effects DB
Put
chemical-related
AOP components
in a regulatory
context
AOP-KB
Third party Applications, plugins
AOP-XML

6. Factors Determining Predictivity of Early Key Events
Evidence supporting the KERs between that KE and the AO
Quantitative understanding of the downstream KERs
Modifying factors that influence downstream KEs & KERs

7. Carole Yauk –
Yauk et al., Environ Mol Mutagen (2015) 56: doi: /em

8. Ontologies that describe key events in existing AOPs
(MIE)
(AO)
AOP
Components
Stressor
Key Event
Key Event
Key Event
KER
KER
Level of Organization
Molecular
Cellular
Tissue
Organ
Individual
Population
Event
Title
Level of Org
Event(s)
Tissue
Event Component
Process
Object
Action
Process
GO, etc
Object
GO, etc.
Context
Cellular (CL)
Organ (Uberon)
Species (NCBI)
Lyle Burgoon
Cataia Ives
Action
PATO

9. Event components-Definitions
Process
Biological process, dynamics of the underlying biological system (e.g. receptor signaling). Ideally this represents the normal biology that is perturbed as part of the AOP not the perturbation itself.
Object
Biological object (e.g. specific biological receptor that is activated or inhibited). This term again represents the object only and is associated with the normal biology of the system.
There are a few cases where the process term from the ontology alludes to the abnormal state, so these definitions are more of an ideal than the actual reality. I think they serve as a reasonable starting point for term selection though. At the end of the day we will not get into the business of developing biological ontologies, so we have to work with the results from the people who are willing to do that work.
Action
This represents the perturbation of this system described by the other two terms that results in this key event (e.g. ‘decreased’ in the case the a receptor is inhibited to indicate a decrease in the signaling by that receptor).

10. Alkylation of DNA in male pre-meiotic germ cells leading to heritable mutations
Molecular
Cellular
Organism
Heritable mutations in offspring, Increase
DNA, Alkylation
Insufficient or incorrect DNA repair
MIE- DNA alkylation in male pre-meiotic germ cells. Parent metabolite is uptaken and interacts with DNA in spermatagonia.
KE1- insufficient or incorrect dna repair.
KE2- Mutations, male premieotic germ cells and eventually mature sperm.
AO- Mutations transmitted to offspring (all tissues)
Mutations, Increase
Cataia Ives

11. Alkylation of DNA in male pre-meiotic germ cells leading to heritable mutations
Molecular
Cellular
Organism
Heritable mutations in offspring, Increase
DNA, Alkylation
Insufficient or incorrect DNA repair
Process: DNA alkylation
Object: DNA
Action: increased
Context: eukaryotic cell
Process: dna repair
Object: DNA
Action: functional change
Context: eukaryotic cell
Process: induced mutation
Object: DNA
Action: increased
Context:
Using the Example of AOP:15, these fields of Process, Object, Action, and Context are being used to describe KE’s using existing ontology terms from GO, PATO, CL, Uberon, and NCBI Taxon.
Mutations, Increase
Process: induced mutation
Object: DNA
Action: increased
Context: eukaryotic cell
Cataia Ives

12. What's new in the AOP Wiki
The AOP Wiki now provides authors the ability to tag AOPs with terms from controlled vocabularies and ontologies.
In order to harmonize the tagging of existing AOPs in the Wiki, we worked with authors to annotate all AOPs in the AOP-Wiki as of December 4, 2016.
Currently working on instructions for authors to annotate their own AOPs in the future.
Ivana Campia

13. Factors Determining Predictivity of Early Key Events
Evidence supporting the KERs between that KE and the AO
Quantitative understanding of the downstream KERs
Modifying factors that influence downstream KEs & KERs

14. AOP Provides Understanding & Scaffold for Data

15. Pathway Elements and quantitative information
In-Vitro
Tox21 Aromatase Inhibition
Fadrozole
f(x)
In-Silico
Petko Petkov’s model
Applicability domain
Executable source code
f(x)
In-vivo
Radio Immuno Assay
Fathead minnow
Fadrozole
f(x)
Pathway Elements and quantitative information
Fadrozole
Aromatase Inhibition
amphioxus vertebrates
Reduced E2 synthesis
amphioxus vertebrates
Sex
mixed
In-Vitro
H295R
human cells
Fadrozole
f(x)
In-Vivo Aromatase inhibition in primary tissue
Fathead minnow
Fadrozole
f(x)
Ex-Vivo
Aromatase inhibition
Fathead minnow
Fadrozole
f(x)
In-Silico
Model
Applicability domain
Executable source code
f(x)
Effectopedia
Hristo Aladjov
molecular
organelle
cellular
Level of Biological Organisation

16. Transformation of Dose-Response to Response-Response
Key Event 2
Key Event 2
These transformation function describe how the measured test results can be mapped to the observed in vivo effects
Key Event 1
Key Event 1
Concentration, [log M]

17. Factors Determining Predictivity of Early Key Events
Evidence supporting the KERs between that KE and the AO
Quantitative understanding of the downstream KERs
Modifying factors that influence downstream KEs & KERs

18. AOP networks emerge as AOPs are entered into the AOP-Wiki
Key Events Shared by Multiple AOPs
AOP:30
AOP:25
AOP:23
Linkages Shared by Multiple AOPs
Courtesy of Dan Villeneuve

19. AOP Network as Stored in the AOP-Wiki

20. Dan Villeneuve –

21. Chemical Interactions Emerge from AOP Networks
Nelms, M.D., et al. (2017)
in Chemical Mixtures and Combined Chemical and Nonchemical Stressors: Exposure, Toxicity, Analysis and Risk

22. AOP Networks Incorporate “Effect Modifiers”
Gallagher, et al., (2010) in “Biomarkers in Medicine, Drug Discovery and Environmental Health”

23. Factors Determining Predictivity of Early Key Events
Evidence supporting the KERs between that KE and the AO
Quantitative understanding of the downstream KERs
Modifying factors that influence downstream KEs & KERs

24. Too many AOPs, too little time…

25. Bell et al. (2016) Toxicol. Sci., 150:510-520
doi: /toxsci/kfw017
Oki & Edwards (2016)
Toxicology, 350–352:49–61
doi: /j.tox
Oki et al. (2016)
Current Environmental
Health Reports,
3(1):53-63
doi: /s y
This figure shows at a very high level the work that Shannon Bell and Noffisat Oki have done so far in using HTS data to develop a cpAOP network. Oki is currently working on how we can extract out cpAOP subnetworks from this global network.
Noffisat Oki, Shannon Bell

26. Accelerating AOP Development

27. AOP-KB AOP-XML https://github.com/DataSciBurgoon/aop_networks AOP Wiki
Collaborative development of AOP descriptions & evidence
Effectopedia
Detailed development of structured & computational
AOPs
AOP Xplorer
Visualize attribute networks to discover & explore AOPs in a broader context
e.AOP.portal
Intermediate Effects DB
Put
chemical-related
AOP components
in a regulatory
context
AOP-KB
Third party Applications, plugins
AOP-XML

28. OECD AOP-KB (http://aopkb.org/) Supports All Stages of Development
AOP-Xplorer – AOP-Wiki – Effectopedia –

30. Translate research for decision makers
Focus experimental work
Facilitate computational modeling
Level of resolution determined by information needs

31. Environmental/Personal
Measurement Understanding
Environmental/Personal
Exposure Monitoring
Biomarkers of
Exposure
Bioindicators of
Key Events
Apical Endpoints/
Adverse Outcomes
Toxicity Pathway, NRC 2007
Aggregate Exposure Pathway, Teeguarden 2016
Adverse Outcome Pathway, Ankley 2010, Villeneuve 2014

32. CSS AOP Discovery & Development Project Team
Acknowledgements
CSS AOP Discovery & Development Project Team

33. Additional Information Available Online
Reference
Training