Connecting Adverse Outcome Pathways, knowledge and data with AOPLink workflows
Monday, 15 July 2019, 16:00 CEST
Presenters: Marvin Martens (Department of Bioinformatics, Maastricht University, The Netherlands)
This webinar is a follow-up of the previous “Identification and linking of data related to AOPWiki (an OpenRiskNet case study)” webinar on March 26th, in which the OpenRiskNet project and AOPLink case study were introduced.
The objectives of the AOPLink case study are to explore Adverse Outcome Pathway (AOP) knowledge, and the validation and linking of existing knowledge to support AOPs. Another goal is the establishment of links between AOPs and experimental data to support the biological plausibility of Key Events, and identify Key Events based on an experimental dataset.
The central component in this case study is the RDF-converted AOP-Wiki, the main repository for qualitative AOPs. The RDF is exposed in a SPARQL endpoint and with an API that allows us to ask a wide variety of questions. This webinar will highlight the functionalities of the AOP-Wiki SPARQL endpoint, demonstrated with several example queries to extract specific information from the database. Also, federated queries between the AOP-Wiki RDF with SPARQL endpoints of other databases, such as Rhea, DisGeNET, and WikiPathways, will be shown.
In order to answer the main research questions of the AOPLink case study, the AOP-Wiki SPARQL endpoint is used in Jupyter notebooks to find data related to AOPs in a variety of databases, and extend the knowledge that is captured in the AOP-Wiki. Furthermore, a notebook on nanomaterial-related AOP identification will be shown, and the near future of the AOPLink case study will be described for the final months of the OpenRiskNet project.