AOP-Wiki access - OpenTox Summer School 2024

This slide deck was presented by Marvin Martens during the OpenTox Summer School 2024 as part of the session entitled "Streamlining Toxicological Assessments: Automated Access to Adverse Outcome Pathways with VHP4Safety Tools" (https://opentox.net/events/opentox-summer-school-2024/Marvin-Martens) Session description: In the rapidly advancing field of in silico toxicology, Adverse Outcome Pathways (AOPs) are essential for next-generation risk assessment and regulatory decision-making. Integrating AOPs with computational models and risk assessment workflows allows for efficient use of the framework to understand and predict toxicological effects. However, accessing and utilizing AOP data efficiently remains a challenge due to its vastness and lack of automated accessibility. The VHP4Safety project, a Dutch initiative, aims to develop a virtual, integrated platform to assist regulatory agencies with risk assessment and hazard characterization. This session will focus on automated access to AOPs through two services deployed in the VHP4Safety platform: the AOP-Wiki SPARQL endpoint with its SNORQL user interface and the AOP-Wiki API. These tools streamline the retrieval and application of AOP information, enhancing the efficiency and accuracy of in silico toxicological studies. The session will begin with an introduction to the Virtual Human Platform (VHP), its infrastructure, and the role of AOPs in risk assessment, providing participants with a basic understanding of the platform. Following this, we will showcase the relevant AOP services and ongoing efforts within the VHP4Safety project, offering an overview of the services, their intended use, implementation details, and benefits for toxicological research. The remainder of the session will be a hands-on workshop, with practical exercises to use the AOPservices, starting with an introduction to SPARQL, the query language for the AOP-Wiki SPARQL endpoint. Basic assignments will familiarize participants with the AOP services through their user interfaces, followed by exploring the application of these services in coding environments such as Python and R. By the end of this session, participants will have gained valuable insights into the automated access of AOPs and hands-on experience in utilizing these tools to enhance their toxicological research workflows. The hands-on session instructions can be found on https://marvinm2.github.io/AOP-Wiki-workshop/