Tools
All 55 tools the MCP server exposes, grouped by task. Each category page documents every tool with its arguments and returns.
Table of contents
Conventions
These hold for every tool:
- Structured JSON output. Every tool returns a structured JSON object, delivered as MCP
structuredContentand mirrored as a JSON text block — so every client, and a human reading the transcript, see the same result. - Entities by IRI or name. You may reference an entity by its full IRI or by its display name
(the active renderer). Where noted, class/data-range operands also accept Manchester syntax
expressions (e.g.
hasPart some Cell). - Edits are GUI-visible and undoable. Every model edit goes through
OWLModelManager.applyChanges, so it appears in Protégé immediately and joins the shared Edit ▸ Undo stack. (Document open/save operations use Protégé’s own load/save APIs and are not undoable.) - Safety gates. Mutating tools obey the read-only and confirm-each-write preferences (Settings ▸ MCP). Read/query tools work even in read-only mode.
- Minting signal. Many create/add tools report
new_entities(the entities the call introduced) and acceptstrict— set it to fail instead of minting a brand-new entity from an unrecognized IRI/name (a typo guard). - Active ontology + imports. Tools act on the active ontology (the current edit target). Where a
tool accepts
include_imports, it can widen to the imports closure.
A typical flow
A safe natural-language editing loop:
Orient (get_ontology_context / get_entity_context) → resolve names to IRIs
(search_entities / get_entity) → preview an edit (preview_changes) → apply (an edit tool
or apply_changes) → verify (run_reasoner, validate_ontology).
The guided prompts package these flows for one-click use in an MCP client.
Tool index
Explore & search
list_ontologies · get_active_ontology · summarize_ontology · list_classes · search_entities ·
get_entity · get_axioms_for_entity
Context & validation
get_ontology_context · get_entity_context · validate_ontology · validate_governance ·
diff_ontologies
Editing — entities & axioms
preview_changes · apply_changes · create_class · create_entity · create_term ·
create_property · add_subclass_of · add_annotation · set_label · add_axiom · remove_axiom ·
rename_entity · delete_entity · deprecate_entity · move_class
Ontology metadata & imports
set_ontology_id · set_prefix · add_import · remove_import · add_ontology_annotation ·
remove_ontology_annotation
Documents
load_ontology · set_active_ontology · merge_ontology_document · create_ontology ·
write_catalog
Rules (SWRL)
list_rules · add_rule · remove_rule
Reasoning
list_reasoners · set_reasoner · run_reasoner · get_unsatisfiable_classes ·
get_inferred_superclasses · execute_dl_query · explain_entailment · get_explanations
SPARQL
sparql_query · sparql_schema · sparql_validate
History & persistence
undo_change · redo_change · save_ontology
Cross-cutting reference
- Axiom types — the structured
axiom_typeoperand catalog used byadd_axiom,remove_axiom,preview_changes,apply_changes,explain_entailment, andget_explanations. - Guided workflows (prompts) — the 6 MCP prompts.