Marvin Martens (0000-0001-7487-8615), originally trained as a biomedical scientist and developmental biologist at Maastricht University (NL) and Université Pierre et Marie Curie (FR), transitioned into bioinformatics during his master's projects. This shift led him to the Department of Bioinformatics (BiGCaT) at Maastricht University, where he received his PhD in 2024. Throughout his doctoral research, Marvin focused on Adverse Outcome Pathways (AOPs), data integration, FAIR principles, and semantic web approaches. Marvin has contributed to several significant toxicology projects, including EU-ToxRisk, OpenRiskNet, NanoSolveIT, RiskGONE, and CIAO, and the Dutch project VHP4Safety. His PhD work included AOP development, data and service integration, database FAIRification (notably the AOP-Wiki), semantic web applications, and in-depth transcriptomic data analysis. Currently, Marvin is a postdoctoral researcher at Maastricht University, continuing his work within the VHP4Safety project. He co-leads the ELIXIR Toxicology Community, a collaborative effort to advance toxicology through bioinformatics solutions. Additionally, he is involved in the EFSA-funded project TXG-MAP, which aims to make transcriptomics data applicable for the risk assessment of chemicals. In this project, he is responsible for data analysis and contextualizing transcriptomics data within AOPs. Marvin's passion and expertise are centered on optimizing the use of AOPs, which he envisions as central hubs for integrating toxicological data, knowledge, and tools. Also, his work continues to enhance the accessibility and applicability of toxicological data, with a particular emphasis on making transcriptomics data relevant for risk assessments, contributing to more informed decision-making and accelerated advancements in the field of toxicology.
OpenTox Summer School 2024
Streamlining Toxicological Assessments: Automated Access to Adverse Outcome Pathways with VHP4Safety Tools
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.