AOP-helpFinder 3.0: from text mining to network visualization of key event relationships, and knowledge integration from multiple sources

• Published in: Bioinformatics (Oxford, England) Vol. 41; no. 7
• Main Authors: Jaylet, Thomas, Jornod, Florence, Capdet, Quentin, Armant, Olivier, Audouze, Karine
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2025; Oxford Publishing Limited (England)
• Subjects: Adverse Outcome Pathways; Applications Note; Availability; Computational Biology - methods; Data mining; Data Mining - methods; Data sources; Humans; Internet; Natural Language Processing; Radon; Servers; Software; Toxicology
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btaf381

Abstract Motivation The Adverse Outcome Pathways (AOP) framework advances alternative toxicology by prioritizing the mechanisms underlying toxic effects. It organizes existing knowledge in a structured way, tracing the progression from the initial perturbation of a molecular event, caused by various stressors, through key events across different biological levels, ultimately leading to adverse outcomes that affect human health and ecosystems. However, the increasing volume of toxicological data presents a significant challenge for integrating all available knowledge effectively. Results Text mining techniques, including natural language processing and graph-based approaches, provide powerful methods to analyze and integrate large, heterogeneous data sources. Within this framework, the AOP-helpFinder TM tool, accessible as a web server, was created to identify stressor-event and event-event relationships by automatically screening scientific literature in the PubMed database, facilitating the development of AOPs. The proposed new version introduces enhanced functionality by incorporating additional data sources, automatically annotating events from the literature with toxicological database information in a systems biology context. Users can now visualize results as interactive networks directly on the web server. With these advancements, AOP-helpFinder 3.0 offers a robust solution for integrative and predictive toxicology, as demonstrated in a case study exploring toxicological mechanisms associated with radon exposure. Availability and implementation AOP-helpFinder is available at https://aop-helpfinder-v3.u-paris-sciences.fr.