AOP-Wiki RDF

AOP-Wiki RDF converts AOP-Wiki content into Resource Description Framework (RDF) triples to semantically structure adverse outcome pathway (AOP) data for queryable integration and analysis.

Key Features:

• Semantic Structuring with RDF: Converts AOP-Wiki content into RDF triples to enable structured representation and automated parsing of AOP data.
• Extensive Ontological Annotation: Applies semantic annotations using over 20 ontologies, including the Chemical Information Ontology, Dublin Core, and AOP Ontology, to clarify property-object relationships.
• Comprehensive Data Representation: Produces more than 122,000 RDF triples describing over 158 unique properties across more than 15,000 unique subjects.
• Integration with External Databases: Provides link-outs including over 3,500 links to 12 chemical databases and more than 7,500 links to four gene and protein databases to enrich AOP records.
• SPARQL Interface for Advanced Queries: Exposes the RDF data via a SPARQL endpoint to support complex, domain-specific queries over AOP content.
• Federated Query Support: Enables federated SPARQL queries that combine AOP-Wiki RDF content with external database endpoints for integrated data retrieval.

Scientific Applications:

• Risk Assessment: Supports development of mechanistic risk assessment strategies by providing structured, queryable AOP evidence.
• Workflow Integration: Enables automated incorporation of AOP data into broader bioinformatics and computational toxicology workflows via RDF and SPARQL.
• Cross-domain Data Linking: Facilitates interdisciplinary studies by linking chemical, gene, and protein database identifiers to AOP entities for integrated analyses.

Methodology:

Systematic conversion of AOP-Wiki content into RDF triples, semantic annotation using over 20 ontologies including Chemical Information Ontology, Dublin Core, and AOP Ontology, creation of link-outs to external chemical and gene/protein databases, and exposure via a SPARQL endpoint with support for federated queries.