AOP-Wiki RDF
AOP-Wiki RDF is an RDF representation of the AOP-Wiki, the authoring interface of the Adverse Outcome Pathway Knowledge Base. The AOP-Wiki XML export is converted to RDF/Turtle every week using the AOP Ontology (aopo) together with Dublin Core, CHEMINF and NCIT, and is enriched with gene mappings (gene names in key events matched to HGNC symbols and resolved to Ensembl, NCBI Gene, UniProt and Protein Ontology identifiers through BridgeDb) and chemical cross-references. AOPs, key events, key event relationships, biological events, stressors and chemicals get identifiers.org URIs and are linked to ChEBI, GO, PATO, UBERON, CL, NCBITaxon and HGNC. The 2026.08.15 release has about 340,000 triples, covering 595 AOPs, 1,595 key events, 2,360 key event relationships, 754 stressors and 430 chemicals. The data is served from a public SPARQL endpoint with a SNORQL query interface on top of it. A grlc REST API built from the same curated query library, a second endpoint holding every quarterly AOP-Wiki snapshot since 2018 as named graphs, and a dashboard for version-over-version trends are also available.
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Distributed as Turtle files in the data/ directory of the conversion repository (AOPWikiRDF.ttl, AOPWikiRDF-Genes.ttl, AOPWikiRDF-Enriched.ttl); all of them are loaded together into the SPARQL endpoint and are meant to be used as one dataset. 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Every plot exposes the SPARQL query behind it and offers CSV export.", "format": "http", "id": "aopwiki-rdf.dashboard", "name": "AOP-Wiki RDF Dashboard", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://aopwiki-dashboard.vhp4safety.nl", "repository": "https://github.com/marvinm2/AOP-Wiki-RDF-dashboard"}, {"category": "ProgrammingInterface", "connection_url": "https://aopwiki.api.bigcat-bioinformatics.org/", "description": "grlc-generated REST API that exposes the curated AOP-Wiki SPARQL example queries as parameterized HTTP endpoints with a Swagger/OpenAPI description, for users who prefer REST over writing SPARQL.", "format": "http", "id": "aopwiki-rdf.grlc-api", "is_public": true, "name": "AOP-Wiki RDF grlc REST API", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://aopwiki.api.bigcat-bioinformatics.org/", "repository": "https://github.com/marvinm2/AOP-Wiki-Queries"}, {"category": "DocumentationProduct", "description": "Curated library of documented SPARQL example queries for AOP-Wiki RDF, organised by category (metadata, AOPs, key events, KERs, stressors, chemicals, data export, federated queries). 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AOPs, key events, key event relationships, biological events, stressors and chemicals get identifiers.org URIs and are linked to ChEBI, GO, PATO, UBERON, CL, NCBITaxon and HGNC. The 2026.08.15 release has about 340,000 triples, covering 595 AOPs, 1,595 key events, 2,360 key event relationships, 754 stressors and 430 chemicals. The data is served from a public SPARQL endpoint with a SNORQL query interface on top of it. 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Distributed as Turtle files in the data/ directory of the conversion repository (AOPWikiRDF.ttl, AOPWikiRDF-Genes.ttl, AOPWikiRDF-Enriched.ttl); all of them are loaded together into the SPARQL endpoint and are meant to be used as one dataset. 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Willighagen"], "doi": "10.1089/aivt.2021.0010", "id": "doi:10.1089/aivt.2021.0010", "journal": "Applied In Vitro Toxicology", "preferred": true, "title": "Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content", "year": "2022"}, {"authors": ["Marvin Martens", "Egon Willighagen", "Chris Evelo"], "doi": "10.5281/zenodo.13353286", "id": "doi:10.5281/zenodo.13353286", "journal": "Zenodo", "title": "Adverse Outcome Pathway Wiki RDF", "year": "2026"}], "repository": "https://github.com/marvinm2/AOPWikiRDF", "synonyms": ["AOPWikiRDF", "AOP-Wiki RDF Explorer"], "version": "2026.08.15"}