AOP-Wiki SPARQL Endpoint

This service is a Virtuoso SPARQL endpoint that is loaded with RDF of the Adverse Outcome Pathway (AOP)-Wiki database (https://aopwiki.org/), based on the quarterly XML dumps that are provided. The AOP-Wiki serves as the primary repository of qualitative information for AOPs and is a central component in the AOP development effort coordinated by the Organisation for Economic Co-operation and Development (OECD). The database contains AOP which are described in terms of key events (KEs). An AOP is initiated by a stressor (e.g. a chemical) that causes a Molecular Initiating Event, which is followed by KEs (measurable, essential steps) along a pathway towards an adverse outcome for an organism or population. KEs are connected through Key Event Relationships (KERs), which capture the evidence supporting the AOP in a structured way. The AOP-Wiki website provides access to the AOP information via a web interface to look up AOPs, KEs, KERs, and stressors.

For end-users
For developers
Type:
Database / data source
API Type:
SPARQL
Categories:
Knowledge bases
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
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

Webinar recording
Identification and linking of data related to AOPWiki
Marvin Martens and Egon Willighagen (Department of Bioinformatics, Maastricht University, The Netherlands), Thomas Exner (Edelweiss Connect GmbH, Switzerland)
27 Mar 2019
Related services:
AOP-Wiki SPARQL Endpoint

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: EwC, UM
Webinar recording
Presentation
AOPLink - Linking experimental data to Adverse Outcome Pathways
Marvin Martens, Egon Willighagen, Chris Evelo (Department of Bioinformatics, Maastricht University, The Netherlands)
27 Mar 2019
Additional materials:
Slides

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
Presentation
Poster
Expanding Adverse Outcome Pathway knowledge by creating AOP-Wiki RDF with semantic annotations to facilitate risk assessment of chemicals.
Marvin Martens, Chris Evelo, Egon Willighagen
19 Feb 2019
Abstract:
1. Introduction With the ever-growing number of chemicals that require toxicological risk assessment, there is a need for faster, more efficient use of existing data to assemble effective assessment strategies [1]. Therefore, the concept of Adverse Outcome Pathways (AOPs) was introduced [2], a framework to organize existing mechanistic information about toxicological processes into a chain of smaller pieces of knowledge, called Key Events (KEs). These allow the structuring of toxicological knowledge and reduce the effort needed to capture all information before performing risk assessment [2, 3]. In order to facilitate a community effort in gathering toxicological knowledge, the AOP-Wiki was created by the European Commission JRC and the US EPA. To integrate this knowledge base more easily with other resources, we explored the use of semantic web technologies to link AOP-Wiki with other chemical and biological databases. 2. Approach The AOP-Wiki provides quarterly permanent downloads for the full database XML (https://aopwiki.org/downloads/). We parsed the AOP-Wiki knowledge with Python 3.5 and the ElementTree XML API and converted it into a semantic web RDF format, which allows for accurate description with ontological annotations, including the AOPO, CHEMINF, and Dublin Core. Chemical compounds are identified in the AOP-Wiki with CAS numbers and biological processes with a variety of ontologies, e.g. GO, Mammalian Phenotype Ontology, and Molecular Interactions ontology. These annotations are used to create Internationalized Resource Identifiers. To integrate and test the RDF, a variety of federated SPARQL queries were written and executed in Blazegraph (build version 2.1.4). 3. Results We created an AOP-Wiki RDF scheme and converted the XML into Turtle syntax. The RDF was tested with a variety of SPARQL queries to answer biological question relevant to risk assessment, such as: - What measurement / test-method information is available for a given AOP? - Which of the stressor chemicals on the AOP-Wiki can be linked molecular pathways on WikiPathways? 4. Discussion The RDF transformation of AOP-Wiki content can assist in the accessibility and expansion of toxicological knowledge by allowing semantic interoperability. The created RDF of the AOP-Wiki allows the querying and providing of additional information for stressor chemicals, genes, and proteins involved in KEs, the underlying molecular pathways, but also for the applicability of AOPs by cell types or species. This semantic approach allows novel ways to explore the rapidly growing AOP knowledge with every new publication related to toxicological studies. There is work in progress on a Virtuoso SPARQL endpoint Docker image to simplify the use of the data, and integrate the database in the OpenRiskNet e-infrastructure to provide AOP knowledge useful for automated risk assessment workflows. Funding This project has received funding from the European Union’s Horizon 2020 (EU 2020) research and innovation program under grant agreement no. 681002 (EU-ToxRisk) and EINFRA-22-2016 program under grant agreement no. 731075 (OpenRiskNet).
Related services:
AOP-Wiki SPARQL Endpoint

Target audience: Risk assessors, Researchers, Data managers, Data owners, OpenRiskNet stakeholders, Regulators, Bioinformaticians, Software developers, Data providers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UM
Poster
Peer-reviewed publication
Introducing WikiPathways as a data-source to support Adverse Outcome Pathways for regulatory risk assessment of chemicals and nanomaterials
Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T. Evelo, Egon L. Willighagen
4 Dec 2018
Abstract:
A paradigm shift is taking place in risk assessment to replace animal models, reduce the number of economic resources, and refine the methodologies to test the growing number of chemicals and nanomaterials. Therefore, approaches such as transcriptomics, proteomics, and metabolomics have become valuable tools in toxicological research, and are finding their way into regulatory toxicity. One promising framework to bridge the gap between the molecular-level measurements and risk assessment is the concept of Adverse Outcome Pathways (AOPs). These pathways comprise mechanistic knowledge and connect biological events from a molecular level towards an adverse effect outcome after exposure to a chemical. However, the implementation of omics-based approaches in the AOPs and their acceptance by the risk assessment community is still a challenge.

Published in: Frontiers in Genetics
Publisher: Frontiers
Target audience: Risk assessors, Researchers, Regulators, Bioinformaticians
Organisations involved: UM
Peer-reviewed publication