AOP-DB SPARQL Endpoint
This service is a Virtuoso SPARQL endpoint that is loaded with RDF of the EPA Adverse Outcome Pathway Database (AOP-DB) from the US EPA, who won the implementation challenge. The AOP-DB is currently an internal EPA SQL database that supports discovery and development of putative and potential AOPs. The AOP-DB aggregates relationships between AOP-gene targets, chemical, disease, tissue, pathway, species orthology information, ontologies and gene interactions to characterise the impacts of chemicals on human health and the environment. The AOP-DB serves as a hypothesis generation and decision support tool for case study development. Associations are sourced from public annotation to provide biological context and are integrated with AOP information centralised in the AOP-Wiki. The AOP-DB allows for fast, automatic AOP profiling and exploration that gives a broad, systems-level overview of the biological context of AOPs, thus dramatically expediting predictive toxicology efforts. The long-term significance and impact of the AOP-DB tool is the continued translation of AOP biological context, and the ability to associate these data between and across AOPs, and with assay, chemical, and disease endpoints.
For end-users
For developers
Type:
Database / data source
API Type:
SPARQL
Categories:
Toxicology, chemical properties and bioassay databases, Knowledge bases and data mining
Applicability domain:
Toxicology, Bioinformatics
Topic:
Risk assessment, Information extraction
Targeted industry:
Chemicals, Nanotechnology, Drugs, Cosmetics, Food, Other consumer products
Targeted users:
Risk assessors, Researchers, Software Developers, Data managers, Regulators
Relevant OpenRiskNet case study:
AOPLink - Identification and Linking of Data related to AOPWiki
Provided by:
Maastricht University
Login required:
No
Implementation status:
Containerised, Available as web service
Integration status:
Integration in progress
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.
Resources & Training
AOP-DB: The Adverse Outcome Pathway Database
16 Apr 2019
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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
AOP-DB: The Adverse Outcome Pathway Database
8 Apr 2019
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Additional materials:
Slides
Slides
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
AOPLink - Linking experimental data to Adverse Outcome Pathways
27 Mar 2019
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Additional materials:
Slides
Slides
Related services:
BridgeDb identifier mapping service
AOP-DB SPARQL Endpoint
AOP-Wiki SPARQL Endpoint
ToxTargetLinks
BridgeDb identifier mapping service
AOP-DB SPARQL Endpoint
AOP-Wiki SPARQL Endpoint
ToxTargetLinks
Publisher: OpenRiskNet
Target audience: Risk assessors, Researchers, Students, Data modellers, Bioinformaticians
Open access: yes
Licence: Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Organisations involved: UM