AFPA "SonSa, Protection EPA/600/R-21/136 | August 2021 | aopdb.epa.gov
Lnl Agency
The EPA Adverse Outcome Pathway
Database (AOP-DB)
Application User Manual
Center for Public Health and Environmental Assessment
Office of Research and Development
U.S. Environmental Protection Agency
Research Triangle Park, NC
Last Update: August 25th, 2021
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Contents
1 Introduction 2
1.1 The Adverse Outcome Pathway Database in Context 3
2 Searching 4
2.1 Genes Query 5
2.2 Stressors Query 6
2.3 Diseases Query 7
2.4 Biological Pathways Query 8
2.5 Batch Search 9
3 How Data Are Maintained 11
3.1 New Records and Updates 11
4 How Content is Selected 14
5 References 16
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1 Introduction
There is a need for approaches to understand the biological mechanism of adverse outcomes
and human variability in response to environmental chemical exposure. A recent legislation,
the Frank R. Lautenberg Chemical Safety for the twenty-first Century Act of 2016 (114-182
2016 ), requires the US Environmental Protection Agency to evaluate new and existing toxic
chemicals with explicit consideration of susceptible populations of all types (life stage,
exposure, genetic, etc.). In addition, on September 10, 2019, EPA Administrator Andrew
Wheeler signed a directive that prioritizes efforts to reduce animal testing. In response to this
directive, the EPA has developed a 2019 Strategic Plan to Promote the Development and
Implementation of Alternative Test Methods Strategies (or New Approach Methodologies
(NAMs)) per TSCA Section 4(h)(2)(C). The EPA Adverse Outcome Pathway Database (AOP-
DB) is a decision support tool developed by the EPA's Center for Public Health and
Environmental Assessment, which contributes to NAMs (e.g. computational toxicology tools)
used for TSCA. The EPA Adverse Outcome Pathway Database (AOP-DB) is a database
resource that combines different datatypes (AOP, gene, chemical, disease, pathway, orthology,
and ontology) to characterize the impacts of chemicals to human health and the environment
(Pittman, et al., 2018), and for the characterization of human genetic susceptibility for the
purpose of human health risk assessment (Mortensen, et al., 2018). The AOP-DB was originally
developed with the primary aim of integrating AOP molecular target information with other
publicly available datasets and related toxicological data. Updates to the AOP-DB in version 2
(Mortensen, et al., 2021) were made primarily to facilitate and improve computational analyses
of AOP information. Near term goals for use of the AOP-DB are to address the biological and
mechanistic aspects of alternative test methods in terms of the adverse outcome pathway
construct to facilitate Integrated Approaches to Testing and Assessment (IATA) for regulatory
purposes (Delrue, Sachana et al. 2016, Patlewicz, Worth et al. 2016, Sakuratani, Horie et al.
2018), and serve as a decision support tool for case study development.
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1.1 The Adverse Outcome Pathway Database in Context
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Figure 1: How AOP-DB relates to other publicly available tools
the OECD has launched a project to develop the "Adverse Outcome Pathway Knowledge Base"
(AOP-KB) to enable the scientific community to share, develop and discuss AOP related
knowledge in one central location. The AOP-KB allows all interested parties and stakeholders to
build AOPs by entering and linking information about key events, molecular initiating events,
adverse outcomes and stressors, including chemical initiators. The AOP-DB is a part of the AOP-
KB third party toolset, contributing a resource to analyze AOP associations and construct putati ve
AOPs for further study. Figure 1 illustrates AOP-DB's connection to the AOP-KB, specifically the
AOP-Wiki, and other tools like EU supported OpenRiskNet's WikiPathways, and illustrates how
data are shared and transferred.
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2 Searching for Information using the AOP-DB User Interface
To query AOP-DB enter a term for any of the six parameters listed in Table 1 and select the
"Match By" boxes for the parameters of interest. Searching on any of the parameters will return a
list of AOPs with the matching term. Note that capitalization does not matter.
Domain
Parameter
AOP
AOP Name
AOP ID
Gene
Entrez ID
HUGO ID
Stressor
Stressor Name
DTXS ID
Disease
Disease Name
Table 1: Available search parameters.
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Adverse Outcome Pathway Database (AOP-DB)
Home | Basic Info | Search | Batch | Resources
Match By:
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Associated with each AOP are four types of information;; genes, diseases., stressors, and
I) I XID. To view these tables in the AOP-DB, click the radio button and enter associated
information of interest in the search window. Each table can be filtered by any of the column values
by entering a search term in the provided search box. The filtered results can then be exported as a
csv, Excel, or PDF file for local use by clicking the corresponding button or it can be copied to the
clipboard and pasted elsewhere. Second level queries can be performed by selecting information
of interest (e.g. select green arrow for individual AOP ID, as illustrated in Figure 3 below).
AEPAs
United Slates
Environmental Protection
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Environmental Topics Laws & Regulatioi
Related Topics: Safer Chemicals Research | Hea
Adverse Outcome
Home
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AOP ID Name AOPWiki
41 Sustained AhR Activation leading to Rodent Liver Tumours AOPWiki
57 AhR activation leading to hepatic steatosis AOPWiki
151 AhR activation leading to placental insufficiency AOPWiki
310 Embryonic Activation of the AHR leading to Reproductive failure, AOPWiki
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AOPWiki
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Showing 1 to 4 of 4 entries
AOPWiki
First Previous 1 Next 11 Last I
Figure 3: Screenshot of a sample query being exported and the resulting file.
2.1 AOP-DB Gene Query
AOP-gene links are only created by mapping protein IDs, provided by AOP-Wiki in the key
event component field, to gene IDs using UniProt source mapping for exact gene mapping. Genes
linked in this way can be viewed in the gene table.
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Adverse Outcome Pathway Database (AOP-DB)
Home | Basic Info J Search | Batch | Resources
Match By: ®AOPName OAOPID Oentrez ID ODisease Name OStressor Name ODTXSID
AHR
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Copy | Excel | CSV | PDF
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O 41 Sustained AhR Activation leading to Rodent Liver Tumours
® 57 AhR activation leading to hepatic steatosis
AOPWiki
AOPWiki
Gene I Stressor I Disease I Pathway
Copy Excel CSV PDF
Show 110 v | entries
Entrez * HUGO ID Object Name
Search J
Event ID
Event Process
Event
Action
Event Type
Tax Id
molecular-
increased
initiating-
9606
event
increased
key-event
9606
increased
key-event
9606
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9606
196
948
1543
3949
5105
6319
11622
16835
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CD36
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LDLR
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13076 Cyp1a1
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aryl hydrocarbon receptor
platelet glycoprotein 4
cytochrome P450 1A1
low-density lipoprotein
receptor
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acyl-CoA desaturase
aryl hydrocarbon receptor
platelet glycoprotein 4
cytochrome P450 1A1
low-density lipoprotein
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18
54
80
aryl hydrocarbon
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gene expression
gene expression
gene expression
216
gene expression
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9606
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gene expression
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gene expression
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10090
Showing 1 to 10 of 17 entries
I First 11 Previous |[T| [2] (Next [ | LastJ
AhR activation leading to placental insufficiency
AOPWiki
Figure 4: Screenshot of the filtered gene table associated with an AOP.
2.2 Stressors Query
Direct AOP-stressor associations in the AOP-DB are provided by AOP-Wiki. Stressors entered
into the AOP-Wiki can include a link to chemical stressors, via the DSSTox Substance Identifier
(DTXSID), which maps the stressor to substances registered in the DSSTox database (Richard and
Williams, 2002). The chemical DTXSID, a unique substance identifier, provides a link to the
Dashboard using the process described in Williams (2017). When no DTXSID is provided for
stressors imported from the AOP-DB, manual curation to the Dashboard has been performed on
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individual substances, on a substance-by-substance basis and using available identifiers (e.g. CAS
Registry Numbers and chemical names) according to the process described in Grulke (2019).
Adverse Outcome Pathway Database (AOP-DB)
Home | Basic Info | Search | Batch | Resources
Match By: ®AOP Name OAOPID OentrezlD ODisease Name OStressor Name ODTXSID
AHR
Search:
Mode: ©Contains OExact
Show 110 v I entries
AOPID * Name
Copy Excel CSV PDF
Search:
AOPWiki
O 41 Sustained AhR Activation leading to Rodent Liver Tumours
O 57 AhR activation leading to hepatic steatosis
Gene
Stressor
Disease
Pathway
Show 110 v I entries|
Stressor ID
Copy Excel CSV PDF
Stressor Name
Search;)
DTXID
AOPWiki
AOPWiki
62
147
148
149
150
250
Showing 1 to 6 of 6 entries
Benzidine
Dibenzo-p-dioxin
Polychlorinated hi phenyl
Polychlorinated dibenzofurans
Hexachlorobenzene
Polycydic aromatic hydrocarbons (PAHs)
DTXSID2020137
DTXSID3020410
DTXSID5024267
DTXSID2020682
DTXSID3044043
[First][Previousj |jJ [Next)[Last]
© 151 AhR activation leading to placental insufficiency AOPWiki
O 310 Embryonic Activation of the AHR leading to Reproductive failure, via epigenetic down-regulation of GnRHR AOPWiki
AOP ID Name
Showing 1 to 4 of 4 entries
AOPWiki
rirst Previous "l Next Last
Figure 5: Screenshot of the filtered stressor table associated with an AOP.
2.3 AOP-DB Diseases Query
The associations between genes and human disease phenotypes in the AOP-DB are sourced
from DisGeNET, which combines mined, curated, and inferred associations from ten sources for
Mendelian, complex, environmental, and rare diseases as well as disease traits. Due to the
redundancy of information across these ten data sources, a confidence score between 0 and 1 was
calculated for each association based on the proportion of the sources that recognize that
association.
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Adverse Outcome Pathway Database (AOP-DB)
Home | Basic Info | Search | Batch | Resources
Match By: DAOP Name OAOP ID Oentrez ID ODisease Name OStressor Name ODTXSID
AHR
Search:
Mode: ©Contains OExact
Show 110 v | entries
AOPID * Name
Copy | Excel | CSV | PDF
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AOPWiki
O 41 Sustained AhR Activation leading to Rodent Liver Tumours
O 57 AhR activation leading to hepatic steatosis
Show 110 v 1 entries
Disease
Entrez
ID
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Copy I Excel | CSV | PDF
Disease Name
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AOPWiki
AOPWiki
Score 0-
1
196 C0700501
196 C0678222
196 C0006142
196 C1458155
196 C0023903
196 C0376358
196 C0003873
196 C0152013
196 C0027627
196 C0024623
Showing 1 to 10 of 1,121 entries
Congenital nystagmus
Breast Carcinoma
Malignant neoplasm of breast
Mammary Neoplasms
Liver neoplasms
Malignant neoplasm of prostate
Rheumatoid Arthritis
Adenocarcinoma of lung (disorder)
Neoplasm Metastasis
Malignant neoplasm of stomach
0.5
0.4
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0.36
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AOP ID Name
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Figure 6: Screenshot of the filtered associated diseases table for an AOP.
2.4 AOP-DB Biological Pathways Query
Biological pathways represent the series of molecular and genetic interactions that amount to
the execution of a biological process. The AOP-DB directly extracts pathway information from
three sources: the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Consensus
Path DB. That data is associated with a given AOP via the Entrez ID
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Adverse Outcome Pathway Database (AOP-DB)
Home | Basic Info | Search | Batch | Resources
Match By: ®AOP Name OAOP ID Oentrez ID ODisease Name OStressor Name ODTXSID
Search: |ahr
Mode: (^Contains OExact
Show 110 v I entries
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O 41 Sustained AhR Activation leading to Rodent Liver Tumours
O 57 AhR activation leading to hepatic steatosis
Gene I Stressor I Disease I Pathway
Show
v entries!
Entrez
Path ID
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Path Name
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Path Source
AOPWiki
AOPWiki
Tax ID
196
196
196
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196
196
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Endogenous sterols
Xenobiotics
Aryl hydrocarbon receptor
signalling
Integrated Breast Cancer
Pathway
ConsensusPathDB
KEGG Pathways
KEGG Pathways
ConsensusPathDB
Reactome
Reactome
Reactome
Reactome
9606
9606
9606
9606
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9606
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ConsensusPathDB 9606
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AOP ID Name
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AOPWiki
First Previous I 1 Next Last
Figure 7: Screenshot of the filtered associated biological pathways table for an AOP.
2.5 AOP-DB Batch Search
In addition to the queries described above, data from a particular domain associated with
multiple AOPs can be retrieved in a single query using the AOPDB Batch query tool. There are
three options that must be selected: input type is the domain to search on (AOP, stressors, genes,
or diseases), output type is the data to be retrieved, and output format is the output file format (tsv,
csv, or json). Note that the input type and output selections cannot be the same, once an input type
is selected the output type of the same name will be greyed out and not available for selection.
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4>EPA
United States
Environmental Protection
Environmental Topics Laws & Regulations About EPA
Related Topics: Safer Chemicals Research | Health Research | Risk Assessment
Search EPA.gov
Adverse Outcome Pathway Database (AOP-DB)
Home | Basic Info | Search | Batch | Resources
0 Input Type: X
® Output Type: X
OAOP OGene OStressor ODisease
OAOP OGene OStressor ODisease
(?) Output Format: * OJSON OCSV OTSV
Figure 8. Screenshot of the Batch Search Tool.
The batch search tool provides help text for all fields which can be viewed by hovering the
mouse over the yellow question marks, help text, accepted parameters, and sample inputs for each
of the search domains are displayed in the input data text box. Search terms are entered either in
the input data text box directly or a file using the "Upload a File" button which will automatically
populate the text box with file data. Note, input file formats should be in csv, tsv, or txt format
with comma or tab delimiters and files should not have column headers. When using the input text
box all search terms should be comma seperated and terms that are names (e.g. the stressor
"ibuprofen") should be enclosed in double quotes.
Then final step before submitting the query is format validation, which is accomplished by
clicking the "Validate" button. Validation will verify that all terms match an expected format,
reformat them if possible or remove them otherwise.
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Domain
Parameter
AOP
AOP Name
AOP ID
Gene
Entrez ID
Stressor
Stressor Name
DTXS ID
CASRN
MESH ID
Disease
Disease Name
UMLS Disease Concept ID
Table 2: Available search parameters in Batch Search.
3 How Data Are Maintained
3.1 New Records and Updates to the AOP-DB
Because AOP-DB draws data from a number of sources each with release and update schedules
independent of one another, AOP-DB updates its records on a quarterly basis. Updates are
conducted by scripted routines that ensure data integrity and consistency across all tables, remove
duplicate records, and perform sample queries with known expected results to test the coherence
and fidelity of the database. A manual review of new data is not conducted.
Biological
Category
Data Source
Description
Gene
NCBI Gene
This source supplies all NCBI entrez genes in the gene
info table with associated gene information such as name,
symbol, location, etc.
STRING
This source gives protein-protein interaction data for the
gene interactions table. Each record from these networks is
stored with an entrez 1, entrez2, and an interaction score.
Taxonomy &
Orthology
NCBI
Taxonomy
All taxa available from NCBI, including nomenclature info
and divisions. This data is used to fill the species info.
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Homologene
Constructs and stores putative homology groups and
contributes and ortho group number, tax id, entrez id to the
homology gene table.
KEGG
Orthology
This database of functional orthologs contributes ortho
group ids, tax ids, and entrez ids describing an orthologous
group to the homology gene table.
metaPhOrs
This database of phylogeny based orthologs contributes
ortho group ids, taxonomy ids, and entrez ids to the
homology gene table, describing orthologous groups.
AOP
AOP-wiki
This is a collaborative set of AOPs regularly updated
with new details or new Adverse Outcome Pathways.
This source contributes to the central AOP info tables
and the AOP gene tables, supplying AOP names, key
events, descriptions, and information used to map key
events to genes.
Chemical
CTD
This source is a manually curated database of chemical
information, including many modules. The module of
interest for the AOPdb is the chemical gene interactions
module, which contributes chemical names and ids to
chemical info, as well as the chemical gene interactions
with contextual information to the chemical gene table.
AOP-wiki
In addition to being the source of AOPs for the AOPdb,
this source also adds chemical stressors related to the
MIE of each AOP. This data contributes chemical
names, as well is DTXSIDs, casrns, or other chemical
ID when available.
ToxCast
This is a collection of high-throughput screening assays
for chemicals that contributes assay identification
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information and assay context information as well as
gene target information in the form of entrez ids.
Pathway
KEGG Pathways
This source is a collection of biological molecular
interaction pathways that supplies entrez ids and
pathway names and ids, linking gene components to the
pathways in which they are involved.
Reactome
This curated and peer-reviewed source of molecular
pathways supplies entrez ids and their linked pathways
to the pathway gene table of the
AOPdb.
ConcensusPathDB
This source brings together pathway and interaction
data from 32 public resources and supplies entrez ids
and pathway ids that link genes to biological pathways
for the pathway gene table.
Disease
DisGeNET
This database compiles different data, both curated and
inferred from models, and supplies multiple
downloadable tables relating genes and variants to the
diseases in the database. The AOPdb uses DisGeNET's
gene-disease association table, adding all fields to the
disease-gene table. These include disease name and id,
entrez id, and a score for the association based on its
sources.
Ontology
NCBI Gene
In addition to being a source of taxonomy info and gene
info, NCBI Gene supplies gene ontology information.
This supplies gene ontology terms and any related
entrez ids to the GO gene table.
Tissues
HumanBase
This API is used to pull tissue specific gene interaction
network from HumanBase. The data imported into the
tissue networks table in the AOPdb include entrez 1 and
entrez2 fields to construct edges, as well as a probability
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score indicating the strength of the modeled gene
interaction.
Haplotypes
1000 Genomes
This is a collection of variant data for individuals from
a multitude of populations. This source contributes snp
frequencies for each function snp in the snps table for
each of 5 1000 Genomes major populations.
Ensemble
This API, allowing access to ensembl's gene and variant
information, is used to get genotype data for each
individual sample from the 1000 Genomes project.
These data are used to construct haplotypes for each
AOP and find differences in haplotype frequencies
within and between populations.
GWAS Catalog
This is a source used to filter SNPs into snps of interest
for variant analysis in different populations. Functional
snps are specifically targeted. It, along with GTEx,
supplies refsnp ids for these variants as well as
contextual information.
GTEx
This is a source used to filter SNPs into snps of interest
for variant analysis in different populations. Functional
snps are specifically targeted. It, along with GWAS
Catalog, supplies refsnp ids for these variants as well as
contextual information.
4 How Content is Selected for Inclusion in the AOP-DB
AOP-DB strives to be an aggregator and curator of toxicologically-relevant data from around
the globe. To that end, publicly available data sources are selected using an informal and expansive
criterion that emphasizes robust quality assurance measures, programmable access through an API
or FTP, and regular updates and maintenance where the data is not static. While sources from the
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United States were not preferentially included, sources maintained by an agency of the US federal
government were assumed to have implemented rigorous QA measures and generally were
selected.
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5 References
Public Law 114-182. (2016). Frank R. Lautenberg Chemical Safety for the 21st Century Act t.
Congress. Delrue, N., M. Sachana, Y. Sakuratani, A. Gourmelon, E. Leinala and R. Diderich
(2016). "The adverse outcome pathway concept: A basis for developing regulatory decision-
making tools." Altera Lab Anim 44(5): 417-429.
Patlewicz, G., A. P. Worth and N. Ball (2016). "Validation of Computational Methods." Adv Exp Med
Biol 856: 165-187.
Sakuratani, Y., M. Horie and E. Leinala (2018). "Integrated Approaches to Testing and Assessment:
OECD Activities on the Development and Use of Adverse Outcome Pathways and Case
Studies." Basic Clin Pharmacol Toxicol 123 Suppl 5:20-28.
Grulke, C.M., et al. EPA's DSSTox database: History of development of a curated chemistry resource
supporting computational toxicology research. Comput Toxicol 2019;12.
Mortensen, H.M., et al. Leveraging human genetic and adverse outcome pathway (AOP) data to inform
susceptibility in human health risk assessment Mamm Genome 2018;29(l-2):190-204.
Mortensen, H.M., et al The 2021 update of the EPA's adverse outcome pathway database. Sci Data
2021;8(1):169.
Pittman, M.E., et al AOP-DB: A database resource for the exploration of Adverse Outcome Pathways
through integrated association networks. Toxicol ApplPharmacol 2018;343:71-83.
Richard, A.M. and Williams, C.R Distributed structure-searchable toxicity (DSSTox) public database
network: a proposal. Mutat Res 2002;499(l):27-52.
Williams, A.J., et al The CompTox Chemistry Dashboard: a community data resource for
environmental chemistry./ Cheminform 2017;9(1):61.
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