ArticleApplied in vitro toxicology2017
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations.
Article in Applied in vitro toxicology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Organizing mechanism-related information on chemical interactions using a framework based on the aggregate exposure and adverse outcome pathways.Environment international · 2020Pooled it
- Filling the mechanistic and methodological gaps for predicting cytokine release syndrome in humans.Frontiers in pharmacology · 2026Article
- Enhancing toxicological interpretation and reporting ofFrontiers in toxicology · 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
- Methods2AOP: A Collaboration to Strengthen the Integration of Test Methods into the Adverse Outcome Pathway Framework.F1000Research · 2025Review
- Article
- Building an Adverse Outcome Pathway network for COVID-19.Frontiers in systems biology · 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
- The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond.Journal of biomedical semantics · 2023Article
- Application of AOPs to assist regulatory assessment of chemical risks - Case studies, needs and recommendations.Environmental research · 2023Review
- The ECOTOXicology Knowledgebase: A Curated Database of Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment.Environmental toxicology and chemistry · 2022Article
- Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content.Applied in vitro toxicology · 2022Article
- 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
- Application of evidence-based methods to construct mechanism-driven chemical assessment frameworks.ALTEX · 2022Article
- The Human Salivary Proteome Wiki: A Community-Driven Research Platform.Journal of dental research · 2021Article
- AOP Report: Uncoupling of Oxidative Phosphorylation Leading to Growth Inhibition via Decreased Cell Proliferation.Environmental toxicology and chemistry · 2021Article
- Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
introductionThe Adverse Outcome Pathway framework is increasingly used to integrate data generated based on traditional and emerging toxicity testing paradigms. As the number of AOP descriptions has increased, so has the need to define the AOP in computable terms. MATERIALS AND
methodsHerein, we present a comprehensive annotation of 172 AOPs housed in the AOP-Wiki as of December 4, 2016 using terms from existing biological ontologies.
resultsAOP Key Events (KEs) were assigned ontology terms using a concept called the Event Component, which consists of a Process, an Object, and an Action term, with each term originating from ontologies and other controlled vocabularies. Annotation of KEs with ontology classes from fourteen ontologies and controlled vocabularies resulted in a total of 685 KEs being annotated with a total of 809 Event Components. A set of seven conventions resulted, defining the annotation of KEs via Event Components. DISCUSSION: This expanded annotation of AOPs allows computational reasoners to aid in both AOP development and applications. In addition, the incorporation of explicit biological objects will reduce the time required for converting a qualitative AOP description into a conceptual model that can support computational modeling. As high throughput genomics becomes a more important part of the high throughput toxicity testing landscape, the new approaches described here for annotating key events will also promote the visualization and analysis of genomics data in an AOP context.
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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.