AOP-Wiki
The AOP-Wiki is the primary collaborative authoring and curation interface for the Adverse Outcome Pathway Knowledge Base (AOP-KB). It enables the community to develop, review, browse, and export Adverse Outcome Pathways (AOPs) linking molecular initiating events through key events to adverse outcomes relevant to human and ecological risk assessment. Structured exports (XML and tabular subsets) support computational toxicology, ontology mapping, and integration into predictive assessment workflows.
[{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://aopwiki.org/info_pages/10"}], "label": "AOP-Wiki Coordination Group"}]
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Supports SELECT, CONSTRUCT, ASK and DESCRIBE over HTTP GET/POST with JSON, XML, CSV and Turtle result serializations, and federated queries via SERVICE. Reloaded weekly from the generated Turtle files.", "format": "http", "id": "aopwiki-rdf.sparql", "is_public": true, "name": "AOP-Wiki RDF SPARQL Endpoint", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://aopwiki.rdf.bigcat-bioinformatics.org/sparql"}, {"category": "GraphicalInterface", "description": "SNORQL web interface (\"AOP-Wiki RDF Explorer\") for interactive SPARQL querying of the AOP-Wiki RDF endpoint. Provides a CodeMirror SPARQL editor with syntax highlighting, a browsable library of curated and parameterized example queries, endpoint health indication, result browsing with dereferenceable URIs, and CSV/JSON/XML export.", "format": "http", "id": "aopwiki-rdf.snorql", "name": "AOP-Wiki RDF SNORQL Interface", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://aopwiki.rdf.bigcat-bioinformatics.org/", "repository": "https://github.com/marvinm2/AOP-Wiki-Snorql-UI"}, {"category": "GraphProduct", "description": "The AOP-Wiki RDF dataset in RDF/Turtle, covering AOPs, key events, key event relationships, biological events, stressors and chemicals converted from the AOP-Wiki XML export, together with the gene mappings (HGNC approved symbols resolved to Ensembl, NCBI Gene, UniProt and Protein Ontology identifiers via BridgeDb) and the chemical and protein cross-reference enrichments. 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. Regenerated weekly.", "format": "ttl", "id": "aopwiki-rdf.ttl", "latest_version": "2026.08.15", "license": {"id": "https://creativecommons.org/licenses/by-sa/4.0/", "label": "CC BY-SA 4.0"}, "name": "AOP-Wiki RDF Turtle Dataset", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}, {"relation_type": "prov:used", "source": "ensembl"}, {"relation_type": "prov:used", "source": "hgnc"}, {"relation_type": "prov:used", "source": "ncbigene"}, {"relation_type": "prov:used", "source": "pr"}, {"relation_type": "prov:used", "source": "uniprot"}], "product_url": "https://github.com/marvinm2/AOPWikiRDF/tree/master/data", "repository": "https://github.com/marvinm2/AOPWikiRDF"}, {"category": "Product", "description": "VoID metadata describing the AOP-Wiki RDF dataset, its triple counts, licence, provenance, update frequency and SPARQL endpoint.", "format": "ttl", "id": "aopwiki-rdf.void", "name": "AOP-Wiki RDF VoID Description", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_file_size": 1055, "product_url": "https://raw.githubusercontent.com/marvinm2/AOPWikiRDF/master/data/AOPWikiRDF-Void.ttl"}, {"category": "ProcessProduct", "description": "Python conversion pipeline that transforms the AOP-Wiki XML export into RDF/Turtle, performs the three-stage gene-mapping algorithm, and runs Turtle syntax and URI-resolvability quality control. Executed weekly by GitHub Actions (Saturdays 08:00 UTC). Code is MIT licensed.", "format": "http", "id": "aopwiki-rdf.converter", "license": {"id": "https://opensource.org/licenses/MIT", "label": "MIT License"}, "name": "AOP-Wiki XML to RDF Conversion Tool", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://github.com/marvinm2/AOPWikiRDF", "repository": "https://github.com/marvinm2/AOPWikiRDF"}, {"category": "ProgrammingInterface", "connection_url": "https://aopwiki-multirdf.vhp4safety.nl/sparql", "description": "Companion SPARQL endpoint holding every quarterly AOP-Wiki snapshot from 2018-04-01 onwards as separate named graphs (http://aopwiki.org/graph/YYYY-MM-DD), 33 versions at present, for tracking how AOP-Wiki content evolves over time.", "format": "http", "id": "aopwiki-rdf.multiversion-sparql", "is_public": true, "name": "AOP-Wiki RDF Multi-Version SPARQL Endpoint", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://aopwiki-multirdf.vhp4safety.nl/sparql", "repository": "https://github.com/marvinm2/AOP-Wiki_multi-endpoint"}, {"category": "GraphicalInterface", "description": "Web dashboard visualizing the content and growth of AOP-Wiki RDF across all quarterly versions, with entity counts, key event component and ontology usage breakdowns, network statistics, completeness metrics and an interactive AOP network view. 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). Consumed by both the SNORQL interface and the grlc REST API.", "format": "http", "id": "aopwiki-rdf.queries", "name": "AOP-Wiki SPARQL Query Library", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://github.com/marvinm2/AOP-Wiki-Queries", "repository": "https://github.com/marvinm2/AOP-Wiki-Queries"}]
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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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Executed weekly by GitHub Actions (Saturdays 08:00 UTC). Code is MIT licensed.", "format": "http", "id": "aopwiki-rdf.converter", "license": {"id": "https://opensource.org/licenses/MIT", "label": "MIT License"}, "name": "AOP-Wiki XML to RDF Conversion Tool", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://github.com/marvinm2/AOPWikiRDF", "repository": "https://github.com/marvinm2/AOPWikiRDF"}, {"category": "ProgrammingInterface", "connection_url": "https://aopwiki-multirdf.vhp4safety.nl/sparql", "description": "Companion SPARQL endpoint holding every quarterly AOP-Wiki snapshot from 2018-04-01 onwards as separate named graphs (http://aopwiki.org/graph/YYYY-MM-DD), 33 versions at present, for tracking how AOP-Wiki content evolves over time.", "format": "http", "id": "aopwiki-rdf.multiversion-sparql", "is_public": true, "name": "AOP-Wiki RDF Multi-Version SPARQL Endpoint", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://aopwiki-multirdf.vhp4safety.nl/sparql", "repository": "https://github.com/marvinm2/AOP-Wiki_multi-endpoint"}, {"category": "GraphicalInterface", "description": "Web dashboard visualizing the content and growth of AOP-Wiki RDF across all quarterly versions, with entity counts, key event component and ontology usage breakdowns, network statistics, completeness metrics and an interactive AOP network view. 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). Consumed by both the SNORQL interface and the grlc REST API.", "format": "http", "id": "aopwiki-rdf.queries", "name": "AOP-Wiki SPARQL Query Library", "original_source": [{"relation_type": "prov:wasDerivedFrom", "source": "aop-wiki"}, {"relation_type": "prov:hadPrimarySource", "source": "aopwiki-rdf"}], "product_url": "https://github.com/marvinm2/AOP-Wiki-Queries", "repository": "https://github.com/marvinm2/AOP-Wiki-Queries"}], "taxon": ["NCBITaxon:9606"], "version": "2.8"}