Adverse Outcome Pathway Ontology (AOPO)

A BFO-aligned ontology of the adverse outcome pathway framework: key events as processes, MIE and adverse outcome as defined classes, key-event components carrying the (process, object, action) triple — with the AOP-Wiki record model as a pluggable module.

Status: pre-release

The artefacts in this repository are a pre-release. They are committed and usable, but they carry no version IRI, are not tagged, and are not a release. 213 identifiers from an earlier migration of the legacy aopkb.org ontology are not yet represented in the rewrite; the final version follows once each is re-modelled or deprecated — see docs/pre-release.md for what has to be true first, and docs/term-backlog.md for the terms still to come.

The AOPO_ PURLs in these artefacts are provisional and do not resolve. Do not cite them, import this ontology elsewhere, or treat the identifiers as stable until the first release.

Products

Rebuilt with make -C src/ontology products and committed at the repository root:

Product	Contents
aopo.owl / .obo / .json	Main product. Core + AOP-Wiki module, reasoned.
aopo-full.owl / .obo	Everything merged, import closure collapsed.
aopo-base.owl / .obo	AOPO axioms only; external terms referenced, not defined.
aopo-core.owl	The domain-agnostic backbone alone. Self-contained.
aopo-aopwiki.owl	The AOP-Wiki module alone, owl:imports core rather than merging it. Requires the core PURL to resolve, so it is only usable once the ID space is registered.

Take aopo.owl unless you specifically want the layering. aopo-core.owl if you want the AOP framework without the Wiki record model; aopo-aopwiki.owl if you are building on the Wiki model and want core to arrive as an import you can version independently.

Editors' version

Editors work on two files, never on the root artefacts:

• src/ontology/aopo-edit.owl — the AOP-Wiki module
• src/ontology/components/aopo-core.owl — the reusable core, imported by the module

The root artefacts are generated and CI checks they match the sources. Editing one by hand is how the delivered aopo-full.ttl drifted — see docs/known-issues.md #4.

Build

Requires Java 17+ and ROBOT.

make -C src/ontology test        # report + ELK reasoning + SPARQL constraints
make -C src/ontology products    # rebuild the root artefacts

Contact

Use the issue tracker to request terms or report errors.

Acknowledgements

Repository layout follows the Ontology Development Kit convention, mirroring PBPKO.