ArticleApplied in vitro toxicology2022
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content.
Article in Applied in vitro toxicology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed.
- pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources.Bioinformatics (Oxford, England) · 2026Article
- De-risking seizure liability: integrating adverse outcome pathways (AOPs), new approach methodologies (NAMs), and in silico approaches while highlighting knowledge gaps.Toxicological sciences : an official journal of the Society of Toxicology · 2025Review
- The FAIR AOP roadmap for 2025: Advancing findability, accessibility, interoperability, and re-usability of adverse outcome pathways.Computational toxicology (Amsterdam, Netherlands) · 2025Article
- AOP-networkFinder-a versatile tool for the reconstruction and visualization of Adverse Outcome Pathway networks from AOP-Wiki.Bioinformatics advances · 2025Article
- Article
- ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation.International journal of molecular sciences · 2024Article
- NNI Nanoinformatics Conference 2023: Movement Toward a Common Infrastructure for Federal nanoEHS Data Computational Toxicology: Short Communication.Computational toxicology (Amsterdam, Netherlands) · 2024Article
- From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials.Journal of cheminformatics · 2024Article
- Why adverse outcome pathways need to be FAIR.ALTEX · 2024Article
- Comprehensive mapping of the AOP-Wiki database: identifying biological and disease gaps.Frontiers in toxicology · 2024Article
- A curated gene and biological system annotation of adverse outcome pathways related to human health.Scientific data · 2023Article
- Application of AOPs to assist regulatory assessment of chemical risks - Case studies, needs and recommendations.Environmental research · 2023Review
- Development of a data-driven approach to Adverse Outcome Pathway network generation: a case study on the EATS-modalities.Frontiers in toxicology · 2023Article
- Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Towards a qAOP framework for predictive toxicology - Linking data to decisions.Computational toxicology (Amsterdam, Netherlands) · 2022Article
- The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework.Frontiers in toxicology · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Introduction: The AOP-Wiki is the main platform for the development and storage of adverse outcome pathways (AOPs). These AOPs describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content, and to link it with chemical and biological resources. Together, this allows more detailed exploration, which can be automated. Materials and Methods: We converted the complete AOP-Wiki content into resource description framework (RDF) triples. We used >20 ontologies for the semantic annotation of property-object relations, including the Chemical Information Ontology, Dublin Core, and the AOP Ontology. Results: The resulting RDF contains >122,000 triples describing 158 unique properties of >15,000 unique subjects. Furthermore, >3500 link-outs were added to 12 chemical databases, and >7500 link-outs to 4 gene and protein databases. The AOP-Wiki RDF has been made available at https://aopwiki.rdf.bigcat-bioinformatics.org. Discussion: SPARQL queries can be used to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries. Conclusion: Overall, the AOP-Wiki RDF allows new ways to explore the rapidly growing AOP knowledge and makes the integration of this database in automated workflows possible, making the AOP-Wiki more FAIR.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.