Ontology Artifacts

This project publishes ontology-oriented artifacts generated from the LinkML schema.

The primary schema source remains:

src/reactome_ontology/schema/reactome_ontology.yaml

From that source, the project generates ontology distribution files that can be used for browsing, reuse, and downstream validation.

Published TTL Files

• OWL ontology (Turtle)
• SHACL shapes (Turtle)

These files are published with the documentation under docs/schema/ and are copied there from the tracked artifacts in the ontology/ folder during just gen-doc.

Protégé View

The following screenshot shows the ontology opened in Protégé. The left panel shows the class hierarchy, while the right panel shows an OntoGraf visualization of the ontology structure.

Notes

• The LinkML schema is the source of truth.
• The OWL and SHACL files are generated artifacts derived from that schema.
• When the schema changes, regenerate the ontology outputs before publishing updates.