protege-mcp v0.3.3

Ontology-development hardening: project-governance validation, high-level curation macros, broader
reasoner explanations, and a headless end-to-end smoke test. 50 → 55 tools.

New tools

• validate_governance — audit the active ontology against project policy (complements validate_ontology's generic quality checks and run_reasoner's logic checks). Each rule is opt-in: OWL 2 profile conformance (owl_profile = DL (default) / EL / QL / RL — reports the axioms that leave the profile), an IRI policy (required_namespaces / iri_pattern — every owned entity's IRI must conform), a required annotation suite (required_annotations, incl. the specials label and definition — every owned class/property must carry each), and module ownership / import layering (check_ownership, default on — the active module must not assert logical axioms about imported terms — including via a property chain that re-axiomatises an imported super-property). The expensive profile computation runs off the UI thread (on a snapshot taken on it), so conformance-checking a large ontology does not block Protégé for the analysis.
• create_term — create a class with its curation suite in one undoable step: label, a definition (definition, default rdfs:comment), an arbitrary annotation suite, parent(s) (named or a Manchester restriction such as hasPart some Cell), and optional equivalent_to class expressions for a defined class.
• create_property — create an object/data property with its axioms in one step: label, definition, domain, range (a class expression for object; a datatype / Manchester data range for data), super_properties, characteristics (functional, transitive, symmetric, …), and an inverse_of.
• deprecate_entity — the standard obsolescence pattern in one step: owl:deprecated true plus an optional "term replaced by" pointer (IAO_0100001 by default) and any extra curation annotations. Idempotent (re-deprecating is a no-op).
• move_class — reparent a class (its subtree follows): replace the class's asserted named superclasses with a new parent, preserving anonymous restriction superclasses; keep_other_parents adds without removing, and omitting new_parent detaches the class to a root.

Improved

• get_explanations now handles any axiom_type: for a kind the justification generator cannot minimally explain (e.g. a property-hierarchy or property-characteristic entailment), it falls back to confirming whether the axiom is entailed and returning the asserted axioms that mention the same entities as structural context (clearly labelled not a minimal justification) instead of rejecting the request.
• validate_ontology gains a timeout_ms budget — the structural checks run on the model thread and are not interrupted mid-run, so this bounds how long the call waits before returning a timeout error, not the on-thread work itself.
• preview_changes description now points at apply_changes (apply the whole batch in one undoable call) alongside the single-axiom edit tools, matching the README workflow.

Notes

• New: a headless, CI-runnable pipeline smoke test (ToolPipelineTest) that drives the tool cores end-to-end — load → edit → validate → govern → diff → SPARQL — plus a manual live-Protégé checklist in docs/smoke-test.md for the GUI/reasoner/transport legs the unit tests cannot reach. Test count 84 → 97.
• Requires a Java 17+ JVM (unchanged). The OWL 2 profile checker is the OWL API's own (org.semanticweb.owlapi.profiles), already on the Protégé platform.

Install: download protege-mcp-0.3.3.jar below, or use Protégé ▸ File ▸ Check for plugins.