The Adverse Outcome Pathway Database (AOP-DB)

Toxicology database, Knowledge base and data mining, AOP related tools
The AOP-DB serves to link molecular targets identified as molecular initiating events (MIEs) and key events (KEs) in the AOP-Wiki (https://aopwiki.org) to publicly available data (e.g. gene-protein, pathway, species orthology, chemical, disease), in addition to ToxCast assay information. The database is not yet publicly available, and exists behind the EPA firewall currently. A web front-end is currently under development in node.js.
For end-users
Type:
Database / data source, Service
Categories:
Toxicology, chemical properties and bioassay databases, Processing and analysis
Applicability domain:
Computational modelling, Bioinformatics, Predictive toxicology, Ontology
Topic:
Bioassay, Predictive modelling, Information extraction
Biological area:
Omics
Targeted industry:
Chemicals
Targeted users:
Risk assessors, Researchers, Students, Software Developers, Regulators
Relevant OpenRiskNet case study:
AOPLink - Identification and Linking of Data related to AOPWiki
References and training materials:

Pittman, M.E., Edwards, S.W., Ives, C., Mortensen, H.M. (2018) AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. Toxicology and Applied Pharmacology Mar 15; 343:71-83. doi: 10.1016/j.taap.2018.02.006. Epub 2018 Feb 14.

Provided by:
US Environmental Protection Agency
Contact:
mortensen.holly@epa.gov
Login required:
No
Implementation status:
Graphical user interface available
Technology readiness level:
TRL 3 – experimental proof of concept
Integration status:
Integration in progress

Resources & Training

Webinar recording
Connecting Adverse Outcome Pathways, knowledge and data with AOPLink workflows
Marvin Martens (Department of Bioinformatics, Maastricht University, The Netherlands)
16 Jul 2019
Related services:
BridgeDb identifier mapping service
AOP-Wiki SPARQL Endpoint
ToxTargetLinks
The Adverse Outcome Pathway Database (AOP-DB)
Target audience: Risk assessors, Researchers, Students, Nanosafety community, Regulators, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: UM
Webinar recording
Presentation
Connecting Adverse Outcome Pathways, knowledge and data with AOPLink workflows
Marvin Martens (Department of Bioinformatics, Maastricht University, The Netherlands)
15 Jul 2019
Additional materials:
Slides
Related services:
BridgeDb identifier mapping service
AOP-Wiki SPARQL Endpoint
ToxTargetLinks
The Adverse Outcome Pathway Database (AOP-DB)
Target audience: Risk assessors, Researchers, Students, Nanosafety community, Data modellers, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: UM
Presentation
Webinar recording
AOP-DB: The Adverse Outcome Pathway Database
Holly Mortensen, Ph.D. (US EPA), Phillip Langley (ORAU-SSC) and Trevor Levey (ORAU-SSC)
16 Apr 2019
Related services:
AOP-DB SPARQL Endpoint
ToxTargetLinks
The Adverse Outcome Pathway Database (AOP-DB)
Target audience: Risk assessors, Researchers, Students, Developers, OpenRiskNet stakeholders, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: EwC, UM
Webinar recording
Presentation
AOP-DB: The Adverse Outcome Pathway Database
Holly Mortensen, Ph.D. (US EPA), Phillip Langley (ORAU-SSC) and Trevor Levey (ORAU-SSC)
8 Apr 2019
Additional materials:
Slides
Related services:
AOP-DB SPARQL Endpoint
The Adverse Outcome Pathway Database (AOP-DB)
Target audience: Risk assessors, Researchers, Students, OpenRiskNet stakeholders, Regulators, Data modellers
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: UM
Presentation