Enhancing the AOP-Wiki usability and accessibility with semantic web technologies
There is a need for faster and more efficient use of existing data to assemble effective assessment strategies for the ever growing number of chemicals. Therefore, a framework to organize existing mechanistic information, the Adverse Outcome Pathway (AOP), was introduced. The main repository for such AOPs is the AOP-Wiki. However, it is challenging to automatically and systematically parse, filter, and use its captured knowledge.
We explored the use of semantic web technologies to link the AOP-Wiki with chemical and biological databases, allowing more detailed exploration of the database, thereby better supporting risk assessment workflows.
The created RDF and its accessibility through a SPARQL endpoint and Web API assist in the expansion and usability of the knowledge of the AOP-Wiki and AOP-DB. Furthermore, the use of ontologies and persistent identifiers allow new ways to explore the AOP knowledge, and makes the integration of this database in workflows possible. For example, federated SPARQL queries or integration in Jupyter notebooks can answer complex questions that require multiple information sources.
Funding
OpenRiskNet: Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment
European Commission
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