| name | ontology-protocol |
| tools | ["inspect_ontology.py","edit_ontology.py"] |
| description | Use when enforcing OWL ontology terms, adding or modifying OWL classes and object/data properties in the RDF, updating node_types or edge_types in project.yaml, or managing disease scope. Provides scripts/inspect_ontology.py to verify valid names and scripts/edit_ontology.py to add or remove declarations while keeping project.yaml in sync. Owns data/ontology/ontology.rdf and config/project.yaml. Does not manage ontology_mappings.yaml (mapping-protocol's scope) or Python source files. |
You manage the OWL schema and the project configuration:
| File | Your responsibility |
|---|
data/ontology/ontology.rdf | OWL schema: classes, object properties, data properties |
config/project.yaml | node_types, edge_types, disease_scope, ontology paths |
Strict constraints:
- Only modify
data/ontology/ontology.rdf on explicit user request.
- Never edit Python source files.
project.yaml as the Published OWL Name Table
project.yaml node_types and edge_types are the single source of truth for valid OWL names available to the rest of the pipeline:
mapping-protocol reads them to confirm a class or property name is valid before writing a mapping entry.
Keeping these lists in sync with the RDF is the primary ongoing responsibility of this skill. A name present in the RDF but absent from project.yaml is invisible to the rest of the pipeline.
Active entries are uncommented. Inactive entries (defined in ontology but no data source produces them yet) are commented out — preserve them.
Activating an Existing OWL Class or Property
Uncomment the entry in node_types or edge_types in project.yaml. No RDF change needed — the class or property already exists in the ontology.
Reference Tools
Checking valid names — scripts/inspect_ontology.py
Before writing any mapping or parser entry, confirm the class or property name exists in the ontology:
from scripts.inspect_ontology import get_classes, get_object_properties, get_datatype_properties, crossref_project_yaml
crossref_project_yaml("data/ontology/ontology.rdf", "config/project.yaml")
Run crossref_project_yaml after any ontology or project.yaml edit to verify they are in sync. Use get_classes, get_object_properties, and get_datatype_properties to list valid names by type.
Adding or removing declarations — scripts/edit_ontology.py
Use when a required class or property does not yet exist in the RDF. Each function writes the RDF and, when project_yaml_path is provided, updates project.yaml in the same call. Pass dry_run=True to preview without writing.
from scripts.edit_ontology import add_class, add_object_property, add_datatype_property
add_class("data/ontology/ontology.rdf", "MyNode", parent="GeneticEntity",
project_yaml_path="config/project.yaml")
add_object_property("data/ontology/ontology.rdf", "myRelatesTo",
domain="Gene", range_="Disease",
project_yaml_path="config/project.yaml", active=False)
Declarations are inserted alphabetically. active=False adds a commented-out inactive entry; the default is active. Datatype properties are not listed in project.yaml — only the RDF is updated. Run python3 scripts/edit_ontology.py --help for full CLI usage.
Disease Scope
See references/project_yaml_format.md for disease_scope field semantics and which parsers consume each field.
