Adverse Outcome Pathway Knowledge Base · Adverse Outcome Pathway Knowledge Base Stephen Edwards US...
Transcript of Adverse Outcome Pathway Knowledge Base · Adverse Outcome Pathway Knowledge Base Stephen Edwards US...
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U.S. Environmental Protection Agency
Adverse Outcome Pathway Knowledge Base
Stephen EdwardsUS EPA National Health & Environmental Effects
Research Laboratory
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BiologicInputs
NormalBiologicFunction
Morbidityand
Mortality
Cell Injury
Adaptive StressResponses
Early CellularChanges
Exposure
Tissue Dose
Biologic Interaction
Perturbation
Dan Krewski & National Research Council Committee on Toxicity Testing in the 21st Century
A New Paradigm: Activation of Toxicity Pathways
Toxicity Pathway: A cellular response pathway that, when sufficiently perturbed, is expected to result in an adverse health effect.
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Application of Research to Levels of Organization Based on Source to Outcome
Toxicity Pathway, NRC 2007
Aggregate Exposure Pathway, Teeguarden 2016 Adverse Outcome Pathway, Ankley 2010, Villeneuve 2014
Mode of Action, IPCS/EPA/ILSI 2001-2008
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AOP Components
• Key Events (KEs) - nodes– Change in biological state – Measurable and essential for progression – Molecular Initiating Event (MIE): Initial point of chemical interaction– Adverse Outcome (AO): Adverse outcome of regulatory significance
• Key Event Relationships (KERs) - edges– Connections between two key events– Critical for assembling evidence in support of the AOP
• Does not explicitly include chemicals Villeneuve, et al. Tox Sci., 2014, 142:312-320
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OECD AOP Development Programme
• Extended Advisory Group for Molecular Screening & Toxicogenomics (EAGMST)
• Guidance & Training– Guidance, User Handbook, many training options
• International Knowledgebase to capture information– >100 AOPs at various stages of development
http://www.oecd.org/chemicalsafety/testing/adverse-outcome-pathways-molecular-screening-and-toxicogenomics.htm
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AOP-KBe.AOP.portal
Third party Applications,
plugins
AOP-XML
Intermediate Effects DB
Put chemical-related AOP components in a regulatory
context
AOP XplorerVisualize attribute
networks to discover & explore AOPs in a broader
context
EffectopediaDetailed development of
structured & computational AOPs
AOP WikiCollaborative development of AOP descriptions & evidence
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Five Principles of AOP Development
1. AOPs are not chemical specific2. AOPs are modular (consisting of KEs and KERs)3. An individual AOP is a pragmatic unit of development and
evaluation4. For most real-world applications, AOP networks are the
functional unit of prediction5. AOPs are living documents
Villeneuve, et al. Tox Sci., 2014, 142:312-320
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Five Principles of AOP Development
1. AOPs are not chemical specific2. AOPs are modular (consisting of KEs and KERs)3. An individual AOP is a pragmatic unit of development and
evaluation4. For most real-world applications, AOP networks are the
functional unit of prediction5. AOPs are living documents
Villeneuve, et al. Tox Sci., 2014, 142:312-320
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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
ToxicantsMacro-
Molecular Interactions
Cellular Responses
Organ Responses
Organism Responses
Population Responses
Time between exposure and effect increases
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Overlapping Phases of AOP Development
Define the AOP
Evaluate the AOP
Quantitatively describe the AOP
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AOP-KBe.AOP.portal
Third party Applications,
plugins
AOP-XML
Intermediate Effects DB
Put chemical-related AOP components in a regulatory
context
AOP XplorerVisualize attribute
networks to discover & explore AOPs in a broader
context
EffectopediaDetailed development of
structured & computational AOPs
AOP WikiCollaborative development of AOP descriptions & evidence
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AOP PageSection 1 – Title
Section 2 – Authors
Section 3 - Status
Section 4 – AbstractBackground (Optional)
Section 5a – Summary of the AOPMIE
KEs
AO
Key Event Relationships
Section 6 – Scientific evidence supporting the linkages in the AOP
Applicability domain(s) of the AOPLife-stageTaxonomic
Sex
Section 7 – Overall Assessment of the AOP
Modified Bradford Hill Considerations
KE Pages
KER Pages
AO Page
• Description• Measurement/
detection• Taxonomic
applicability
• Description• Measurement/
detection• Taxonomic
applicability• Regulatory
relevance
Section 5b – MIE, KE, and AO descriptions
• Title• Description• Biological
plausibility• Empirical support• Inconsistencies
and uncertainties• Quantitative
understanding
Linkage table
MIE Page
• Description• Measurement/
detection• Taxonomic
applicability• Evidence for
chemical initiation
Chemical initiator(s)
Section 8 – Considerations for Potential Applications of the AOP
OECD HandbookStep by step guide to AOP development
https://aopkb.org/common/AOP_Handbook.pdf
AOP-WikiProvides consistent structure based on the OECD handbook and facilitates collaborative AOP development
http://aopwiki.org/
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Carole Yauk –https://aopwiki.org/wiki/index.php/Aop:15
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ToxicantsMacro-
Molecular Interactions
Cellular Responses
Organ Responses
Organism Responses
Population Responses
AOP Provides Understanding & Scaffold for Data
Toxicity Pathways Regulatory Endpoints
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ToxicantsMacro-
Molecular Interactions
Cellular Responses
Organ Responses
Organism Responses
Population Responses
AOP Provides Understanding & Scaffold for Data
Mechanistic Toxicology DataBioindicators (e.g. Molecular Epi)
EpidemiologyEco Field Studies
Toxicity Pathways Regulatory Endpoints
High Throughput Tox Guideline Studies
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AOP-KBe.AOP.portal
Third party Applications,
plugins
AOP-XML
Intermediate Effects DB
Put chemical-related AOP components in a regulatory
context
AOP XplorerVisualize attribute
networks to discover & explore AOPs in a broader
context
AOP WikiCollaborative development of AOP descriptions & evidence
EffectopediaDetailed development
of structured & computational
AOPs
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mix
ed
molecular organelle cellularLevel of Biological Organisation
FadrozoleAromatase Inhibition
amphioxus vertebrates
Reduced E2 synthesis
amphioxus vertebrates
Pathway Elements and quantitative information
Sex
In-VitroH295R
human cells Fadrozole
f(x)
In-Vivo Aromatase inhibition in
primary tissueFathead minnow
Fadrozole
f(x)
Ex-VivoAromatase inhibition
Fathead minnowFadrozole
f(x)
In-VitroTox21
Aromatase Inhibition
Fadrozole
f(x)
In-SilicoPetko Petkov’s
model• Applicability
domain• Executable
source code
f(x)
In-vivo Radio Immuno
Assay
Fathead minnowFadrozole
f(x)
In-SilicoModel
• Applicability domain
• Executable source code
f(x)
EffectopediaHristo Aladjov
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In v
ivo
effe
ct,
% B
ound
ER
s
In vivo Concentration, [Log M]
Pathway elements –
test response mapping
Test response mapping / set of transformation function(s)
Concentration, [log M]
E2
Chem
3 H-E
2 B
indi
ng
%Mea
sure
d E
ffect
EffectopediaHristo Aladjov
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Five Principles of AOP Development
1. AOPs are not chemical specific2. AOPs are modular (consisting of KEs and KERs)3. An individual AOP is a pragmatic unit of development and
evaluation4. For most real-world applications, AOP networks are the
functional unit of prediction5. AOPs are living documents
Villeneuve, et al. Tox Sci., 2014, 142:312-320
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AOP networks emerge as AOPs are entered into the AOP-Wiki
Courtesy of Dan Villeneuve
AOP:30
AOP:25
AOP:23
Key Events Shared by Multiple AOPs
Linkages Shared by Multiple AOPs
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AOP Network as Stored in the AOP-Wiki
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AOPs in a Systems Biology Context
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Chemical Interactions Emerge from AOP Networks
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Modifying Factors Emerge from AOP Networks
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Too many AOPs, too little time…
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Accelerating AOP Development
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AOP-KBe.AOP.portal
Third party Applications,
plugins
AOP-XML
Intermediate Effects DB
Put chemical-related AOP components in a regulatory
context
EffectopediaDetailed development of
structured & computational AOPs
AOP WikiCollaborative development of AOP descriptions & evidence
AOP XplorerVisualize attribute
networks to discover & explore AOPs
in a broader context
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Current Status of AOP Development
> 100 putative AOPs in the AOP-Wiki (Most not under active development)
13 formal AOPs undergoing OECD review& 6 endorsed
Increasing number of quantitative AOPs under development
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OECD Endorsed AOPsWorking Group of the National Coordinators for the Test Guidelines (WNT)
Task Force on Hazard Assessment (TFHA)
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OECD AOP-KB Working Group• Clemens Wittwehr• Brigitte Landesmann• Ivana Campia• Sharon Munn• Ahmed Sayed• Maurice Whelan
• Ed Perkins• Lyle Burgoon• Natalia Garcia
Reyero
• Hristo Aladjov• Magda Sachana• Joop DeKnecht
• Stephen Edwards• Dan Villeneuve• Kevin Crofton• Gary Ankley• Robert Kavlock
• David Lyons• Max Felsher• Rose Combs• Landon Grindheim• Cataia Ives• Brendan Ferreri-Hanberry• Evgeniia Kazymova
• Collaborative Partners– OECD External Advisory Group on
Molecular Screening & Toxicogenomics
– IPCS/WHO Mode of Action Steering Committee
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AOP-Wiki 2.0 Release – November 2016
• Ability to provide more information through web services– Most new web services will come online in 2017
• Will incorporate ontologies to better characterize key events• Improved snapshots for OECD reviews • Improved help• Will include better handling of chemicals
– Connection with the EPA CompTox Dashboard (https://comptox.epa.gov/dashboard)
• Test version available in September
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Core AOP Ontology Describes AOP components only
Chemical Initiator
Key Event Key Event Key Event
AOP
KER KER
MIE AO
AOP Ontology Developed & Maintained by Lyle Burgoon: https://github.com/DataSciBurgoon/aop-ontology
Lyle BurgoonKyle Painter
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Extending the Core AOP Ontology• Core AOP Ontology is extended by incorporating existing chemical and biological
ontologies• US ACE – Extending core ontology to illustrate proof of concept for reasoners in risk
assessment• US EPA – Extending core ontology to capture AOP-Wiki information• EC JRC – Extending core ontology to inform OECD 201 and the Intermediate Effects
Database• OECD Ontology Working Group – Oversees efforts and ensures compatibility with other
related ontology efforts
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AOP-Wiki ExtensionsInitial Focus on
Key Events Chemical Initiator
Key Event Key Event Key Event
AOP
KER KER
MIE AO
Event Component
ProcessObjectAction
EventTitle
Level of OrgComponent(s)
Context
Level of Organization
MolecularCellularTissueOrgan
IndividualPopulation
ContextCellular (CL)
Organ (Uberon)Species (NCBI)
ProcessGO, etc. Object
GO, etc.Action
IncreasedDecreased
AlteredAccelerated
DelayedCataia Ives
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Organ
Cellular
Taxonomy/Sex/Life Stage
Context changes across levels of biological organization
Cataia Ives
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Using ontology to tag existing wiki
entry
Event Component
ProcessObjectAction
EventTitle
Level of OrgComponent(s)
Context
Level of Organization
MolecularCellularTissueOrgan
IndividualPopulation
ContextCL, UBERON,
NCBITaxon, etc.
ProcessGO, etc. Object
GO, etc.Action
IncreasedDecreased
AlteredAccelerated
Delayed
Cataia Ives
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Event Component
ProcessObjectAction
EventTitle
Level of OrgComponent(s)
Context
Level of Organization
Cellular
ContextCL
“hepatocyte”
ProcessGO
“gene expression and translation”
ObjectPR
“vitellogenins”
ActionDecreased
AOP: “Aromatase inhibition leading to reproductive dysfunction (in fish)”KE: Title “Transcription and Translation of Vitellogenin in Liver, Reduction”
Cataia Ives
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Granulosa cellsE2 synthesis,
reduction FemaleCumulative
fecundity and spawning, reduction
AromataseInhibition
HepatocyteTranscription and
translation of VTG, reduction
OocytesVTG accumulation,
oocyte growth/development,
reduction
CirculationPlasma E2
concentrations, reduction Population
Trajectory, decrease
Molecular Cellular Organ Organism Population
CirculationPlasma VTG,
reduction
Process: catalytic activityObject: cytochrome p450 19A1Action: DecreasedContext: granulosa cell
Process: biosynthetic processObject: 17beta-estradiolAction: DecreasedContext: granulosa cell
Process: gene expression AND translation
Object: vitellogeninsAction: DecreasedContext: hepatocyte
Process: receptor-mediated endocytosis
Object: vitellogeninsAction: DecreasedContext: oocyte
Process: blood circulationObject: 17beta-estradiolAction: DecreasedContext: blood plasma
Process: blood circulationObject: vitellogeninsAction: DecreasedContext: blood plasma
Process: fecundityObject: eggAction: DecreasedContext:
Process: population growth rateObject: Action: DecreasedContext:
Process: gene expression, translationObject: vitellogeninsAction: DecreasedContext: hepatocyte
Cataia Ives
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Ontologies that describe key events in existing AOPs
Stressor
EventTitle
Level of Org
Event(s)Tissue
Key Event Key Event Key Event
AOP
KER KER
(MIE
)
(AO
)
Level of Organization
MolecularCellularTissueOrgan
IndividualPopulation Event
ComponentProcessObjectAction
ProcessGO, etc Object
GO, etc.ContextCellular (CL)
Organ (Uberon)Species (NCBI)
AOPComponents
Lyle BurgoonCataia Ives
ActionPATO
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OECD AOP Ontology Efforts
• AOP-KB Ontology Effort
• Stephen Edwards• Cataia Ives
• Clemens Wittwehr• Ivana Campia• Brigitte Landesmann• Ahmed Abdelaziz
• Hristo Aladjov• Magda Sachana
• Lyle Burgoon
• OECD Ontology WG
• Richard Currie (chair)• Annamaria Colacci• George Fotakis• Ignacio Tripodi• Nikolai Georgiev Nikolov• Nina Jeliazkova• Olga Tcheremenskaia
• AOP-KB Representatives
•Cataia Ives•Rong-Lin Wang•Lyle Burgoon•Kyle Painter
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Links to OECD & SAAOP AOP Pages:
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User Roles• Gardener
– Experienced AOP developers to help ensure consistency with published principles and OECD guidelines
• Author– Can create new AOPs and edit AOP components
• Authenticated User (self created account)– Can comment on AOPs, KEs, & KERs
• Anonymous– Read only
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Gardenersonly
Edited on this pageby Gardeners
Edited on AOP pageby Authors
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AOP Authors
• Corresponding author– Controls access– Point of contact for
questions/comments• Contributors
– Able to edit the AOP• Author list
– Free text field as in current wiki
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Authors& Gardeners
GardenersOnly
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WYSIWYG Easily create tables and add images
Edit all text sections from a single page
Save changes to allsections with one click
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Ontology Tags for Key Events• Event Components
– Process– Object– Action
• Event Context– Tied to level of organization– Cellular, Organ, Taxonomy
• All terms driven by biological ontologies
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Comments
• Modern look & feel• Allows comments on
comments
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Acknowledgements
• Rose Combs• Landon Grindheim• Cataia Ives• Brendan Ferreri-
Hanberry• Evgeniia Kazymova
OECD AOP-KB Working Group• Clemens Wittwehr• Brigitte Landesmann• Ivana Campia• Sharon Munn• Ahmed Sayed• Maurice Whelan
• Ed Perkins• Lyle Burgoon• Natalia Garcia
Reyero
• Hristo Aladjov• Magda Sachana• Joop DeKnecht
• Stephen Edwards• Dan Villeneuve• Kevin Crofton• Gary Ankley• Robert Kavlock
• David Lyons• Max Felsher• Rose Combs• Landon Grindheim• Cataia Ives• Brendan Ferreri-Hanberry• Evgeniia Kazymova
• Collaborative Partners– OECD External Advisory Group on
Molecular Screening & Toxicogenomics
– IPCS/WHO Mode of Action Steering Committee
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AOP-KBe.AOP.portal
Third party Applications,
plugins
AOP-XML
Intermediate Effects DB
Put chemical-related AOP components in a regulatory
context
AOP XplorerVisualize attribute
networks to discover & explore AOPs in a broader
context
EffectopediaDetailed development of
structured & computational AOPs
AOP WikiCollaborative development of AOP descriptions & evidence
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Questions?
SYSTEMS TOXICOLOGY