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Ontology authoring (Strixonomy v0.27)

Status: Documents behavior in Strixonomy v0.27.0. Pre-1.0 APIs may change. Canonical feature list: What ships today.

Strixonomy provides Turtle, OBO, RDF/XML, and OWL/XML write-back for simple edits and Manchester for complex class expressions. It is not a full Protégé replacement — see Known limitations and Protégé coexistence.

Supported operations

Operation LSP / patch op
Create class, property, individual create_entity
Delete entity delete_entity
Add / set / remove label add_label, set_label, remove_label
Add / set / remove comment add_comment, set_comment, remove_comment
Add / remove parent class (named IRI) add_sub_class_of, remove_sub_class_of
Add / remove complex SubClassOf (Manchester) add_complex_sub_class_of, remove_complex_sub_class_of
Add / remove / set equivalent class (Manchester) add_equivalent_class, remove_equivalent_class, set_equivalent_class
Add / remove disjoint class (named IRI) add_disjoint_class, remove_disjoint_class
Add / remove ontology import add_import, remove_import
Add / remove domain and range add_domain, remove_domain, add_range, remove_range
Property characteristics (functional, transitive, …) set_functional, set_transitive, …
Property chains add_property_chain, remove_property_chain
Individual assertions add_class_assertion, add_object_property_assertion, add_data_property_assertion
Generic annotations add_annotation, remove_annotation
Set deprecated flag set_deprecated

Full JSON reference: patch-reference.md.

Format policy

  • Write-back: Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), OWL/XML (.owx)
  • Read/index: Turtle, OBO, RDF/XML (.owl / .rdf), OWL/XML (.owx), JSON-LD, N-Triples, TriG
  • OWL/XML and RDF/XML support inspector/strixonomy patch write-back via Horned re-serialize (v0.21; not byte-identical layout)

VS Code workflow (simple edits)

Turtle (.ttl)

  1. Open a .ttl ontology and select an entity in the Strixonomy explorer.
  2. Use the Entity Inspector edit section: add labels, comments, parents, or delete.
  3. Use context menu Create Class/Property/Individual on explorer views.
  4. Changes apply via strixonomy/applyAxiomPatch and trigger a workspace reindex.
  5. VS Code undo works on saved file changes.

OBO (.obo)

  1. Open a .obo file and select a term in the Strixonomy explorer.
  2. Edit name, definition, synonyms, is_a, and related fields in the Entity Inspector.
  3. Preview and apply — see OBO authoring.

Manchester editor

For complex class expressions (restrictions, and/or, cardinality):

  1. Select a class in a .ttl file.
  2. In the Entity Inspector, click Edit in Manchester on a complex axiom row, or Add Manchester axiom.
  3. Choose axiom type: SubClassOf, EquivalentClasses, or DisjointClasses (named class IRI for disjoint).
  4. Enter a Manchester expression (e.g. ex:hasRecord some ex:MedicalRecord).
  5. Use Insert pickers for classes, object properties, data properties, and XSD datatypes.
  6. Validate shows parse diagnostics and an expression tree.
  7. Preview shows the Turtle fragment; Apply writes the patch.

Manchester covers OWL 2 class expressions used in complex SubClassOf / EquivalentClasses on Turtle — including and / or / not, some / only / value / Self, OneOf {…}, min / max / exact cardinality, nested restrictions, and data restrictions on XSD types (see SHIPPED — Manchester scope). DisjointClasses, domain/range, and property chains are editable via inspector and patch JSON. XML write-back supports core ops; richest Manchester authoring remains Turtle-first.

Manage Imports (v0.11)

Add or remove owl:imports in Turtle ontology headers:

  1. Ontologies view → right-click a .ttl file → Manage Imports
  2. Add an import IRI or remove an existing one; preview and apply

Guide: Manage Imports

Editor completion and quick fixes (v0.11)

In .ttl files, Strixonomy offers:

  • Completion — triggered on :, <, and @ for prefixes, QNames, and IRIs
  • Quick fixes — lightbulb actions for undefined_prefix, missing_label, and broken_import diagnostics

See LSP API and Troubleshooting.

Workspace refactoring

For multi-file changes (rename IRI, namespace migration, move entity, extract module), use the refactor commands and Refactor Preview panel — see Refactoring guide.

Query workbench

Run Strixonomy: Open Query Workbench from the Command Palette.

  • Toggle SQL, SPARQL, or DL Query mode
  • Run queries against the indexed workspace (DL mode: Manchester class expressions — DL Query honesty)
  • Export results as CSV or JSON
  • Save named queries and reload from history
  • Use the virtual table dropdown for SQL table names

CLI

Example patches.json

[
  {
    "op": "create_entity",
    "entity_iri": "http://example.org/people#Student",
    "kind": "class"
  },
  {
    "op": "add_label",
    "entity_iri": "http://example.org/people#Student",
    "value": "Student"
  },
  {
    "op": "add_sub_class_of",
    "entity_iri": "http://example.org/people#Student",
    "parent_iri": "http://example.org/people#Person"
  }
]

# From a folder containing example.ttl (e.g. strixonomy-tutorial from first-success)
strixonomy patch ./example.ttl patches.json --preview
strixonomy patch ./example.ttl patches.json
strixonomy validate .

More examples: patch-reference.md.

Horned-OWL dual stack

For Turtle files, catalog entities and axioms come from Horned-OWL via strixonomy-owl. Oxigraph remains authoritative for triple counts and SPARQL. CI runs owl_oxigraph_consistency tests on fixtures.

Unsaved buffers

When you apply a patch or Manchester edit in VS Code, the language server uses the open editor buffer as the source of truth (not only the file on disk). Unsaved edits in the buffer are preserved and patched in place. If reindex fails after a successful write, you may see APPLIED_NOT_INDEXED — run Index Workspace. See errors.md.

Limitations

  • Write-back is Turtle (.ttl), OBO (.obo), RDF/XML (.owl/.rdf), and OWL/XML (.owx); JSON-LD and line-oriented RDF remain read-only
  • Complex axioms appear in the inspector and Manchester editor but not as edges in the class hierarchy tree (named-parent edges only; use reasoner for inferred hierarchy)
  • Manchester autocomplete uses catalog Insert pickers (no inline buffer autocomplete yet)
  • No SQL/SPARQL editor autocomplete in the workbench (v0.8+)