From AOP-Wiki to Knowledge Graphs: Enhancing accessibility and FAIR reuse of mechanistic knowledge

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-09-14
DOI
https://doi.org/10.5281/zenodo.22753470
Primary Topic
Biomedical Text Mining and Ontologies
Type
article
Field-Weighted Citation Impact
0.00
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article

From AOP-Wiki to Knowledge Graphs: Enhancing accessibility and FAIR reuse of mechanistic knowledge

Marvin Martens
Zenodo (CERN European Organization for Nuclear Research)
Biomedical Text Mining and Ontologies
article

From AOP-Wiki to Knowledge Graphs: Enhancing accessibility and FAIR reuse of mechanistic knowledge

Marvin Martens
article en

Abstract

Presentation (abstract #644) given by Marvin Martens at EUROTOX 2026, the 60th Congress of the European Societies of Toxicology in Vienna, in session S04 "Integrating Data and Intelligence: Building Next-Generation AOPs". Adverse Outcome Pathway knowledge in AOP-Wiki is written for human readers, which limits its computational reuse. The talk introduces linked data and knowledge graphs for a toxicology audience, and presents AOP-Wiki RDF: the complete AOP-Wiki as a weekly validated, versioned knowledge graph with a DOI per release, built on the AOP Ontology. It then shows the ways into the graph without programming (the SPARQL explorer, a REST API and the AOP-Wiki RDF dashboard with 34 quarterly snapshots), and three routes from a Key Event to a gene set: text mining, Gene Ontology annotation of Key Event components (curation by Sidra Adil) and curated mappings to molecular pathways in the molAOP Builder, used by the molAOP Analyser for Key Event enrichment of transcriptomics data. Numbers refer to AOP-Wiki RDF build 2026-08-29. Funding: Dutch Research Council (NWO), NWA-ORC 1292.19.272 (VHP4Safety); European Food Safety Authority (EFSA), GP/EFSA/ED/2022/01.

Zenodo (CERN European Organization for Nuclear Research)
Maastricht University (NL)
Openalex Percentile: Top 18%
Biomedical Text Mining and Ontologies
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