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The Adverse Outcome Pathway Ontology (AOPO) provides a formal semantic representation of the AOP framework and has been used in the AOP-Wiki RDF to model core AOP relations across AOPs, Key Events, Molecular Initiating Events, Adverse Outcomes, and Key Event Relationships. However, the current public AOPO repository (https://github.com/DataSciBurgoon/aop-ontology) does not yet package itself as a modern community ontology project.
Visibility on ontology registries is limited. Standard ontology practices, such as versioning and metadata practices, are sparse. The current version of the ontology does not yet cover all AOP-specific concepts needed for AOP harmonisation and AOP-Wiki RDF. At the same time, the AOP-Wiki RDF ecosystem has matured substantially and now provides maintained RDF datasets, a public SPARQL endpoint, weekly updates, and quality-control workflows, making this an ideal moment to align the ontology and RDF layers more systematically.
Our project will bring together ontology engineers, FAIR data specialists, and AOP domain scientists to uplift AOPO into a registry-ready and deployment-ready ontology and demonstrate its value through improved integration with AOP-Wiki RDF. The project has three tightly linked aims.
- First, we will perform a gap analysis of the current AOPO, focusing on requirements exposed by the AOP-Wiki RDF and by standard ontology registry expectations.
- Second, we will align the ontology with top-level ontologies such as BFO (Basic Formal Ontology), RO (Relation Ontology), as per OBO Foundry principles, bringing AOPO under the umbrella of biological ontologies, allowing automated submission of the ontology to major ontology discovery portals such as BioPortal, FAIRsharing, OLS, and Bioregistry. This includes preparing the metadata and governance material needed for an OBO Foundry submission path.
- Third, we will apply the improved ontology in the AOP-Wiki RDF workflow by identifying high-priority AOP-specific concepts modelled with generic predicates or incomplete semantics, implementing ontology improvements, and demonstrating the result with RDF regeneration and SPARQL queries.
The project is aligned with BioHackathon Germany priorities in FAIR data integration, identifier management, metadata standards, ontologies, and metadata catalogues. It also aligns with PARC WP 7 interests in FAIR data policy, data libraries, and innovative analyses for chemical risk assessment.
The expected outputs are practical and reusable: a curated AOPO metadata package, registry submission materials, ontology pull requests or issue sets defining the priority improvements, a demonstrator application in AOP-Wiki RDF, validation and quality-control outputs, and example SPARQL queries and documentation to support reuse by the AOP and ELIXIR Toxicology communities. Our minimal deliverable is a registry-ready AOPO package plus a pilot AOPO-driven enhancement of AOP-Wiki RDF. Our stretch goal is to add selected mappings to reused OBO ontologies, improve release and validation automation, and document a path toward sustainable community stewardship of AOPO.
This project is designed not only to improve a single ontology but to strengthen the semantic backbone connecting AOP curation, RDF-based integration, and FAIR computational toxicology workflows.