ontology-editor

name

ontology-editor

description

Read, edit, and manage OWL ontologies with OWL-MCP (axioms, prefixes, metadata, pitfall scanning). Use whenever the user wants to add or remove axioms, search axioms, add prefixes, set the ontology IRI, inspect ontology metadata, scan for pitfalls, or formalize an ontology in OWL—e.g. "add this axiom", "find axioms for class X", "add prefix", "check for pitfalls". Align with Ontology Builder workflow (formalization step); use absolute paths for OWL files. Never edit OWL files by hand.

Ontology Editor Skill

Use this skill when you need to inspect or modify OWL ontology files in this project. Never edit OWL files directly—use these tools for all axiom, prefix, and metadata changes. The tools are provided by the OWL-MCP server and operate on OWL files by absolute file path.

When to Use

• Step 6 (Formalization) in the Ontology Builder workflow: add axioms, prefixes, and annotations to an OWL file after the user has approved the draft.
• Ontology navigation: find axioms, get all axioms, or read ontology metadata for an existing file.
• Ontology editing: add/remove axioms in OWL functional syntax; add prefix mappings; set the ontology IRI.
• Quality checking: scan for common modeling pitfalls (OOPS!-style checks).

Align with the project's INSTRUCTIONS.md: work top-down, get user approval before large edits, and keep changes in formal OWL (functional syntax recommended).

How the Server Works

• File path: Every tool takes owl_file_path — an absolute path to the OWL file (e.g. C:\Users\...\ontology.owl or /path/to/ontology.owl). The server loads the file on first access and syncs in-memory state with disk on writes.
• Syntax: Axioms are strings in OWL functional syntax (e.g. SubClassOf(:Dog :Animal), Declaration(Class(:Cat))).

Tools Overview

Axioms

Tool	Purpose
add_axiom	Add one axiom (e.g. SubClassOf(:A :B)). Params: owl_file_path, axiom_str.
add_axioms	Add multiple axioms in one call. Params: owl_file_path, axiom_strs (array).
remove_axiom	Remove one axiom (exact match). Params: owl_file_path, axiom_str.
find_axioms	Search axioms by regex pattern; optional labels, limit, custom annotation property. Params: owl_file_path, pattern, limit, include_labels, annotation_property (nullable).
get_all_axioms	Return all axioms (up to limit); optional labels, custom annotation property. Params: owl_file_path, limit, include_labels, annotation_property (nullable).

Prefixes, Metadata, and IRI Management

Tool	Purpose
add_prefix	Add a prefix mapping (e.g. prefix ex: → http://example.org/). Params: owl_file_path, prefix, uri.
ontology_metadata	Get ontology-level annotation axioms (metadata header). Params: owl_file_path.
get_labels_for_iri	Get label(s) for a given IRI or CURIE; optional custom annotation property. Params: owl_file_path, iri, annotation_property (nullable).
set_ontology_iri	Set or update the ontology IRI and optional version IRI. Pass iri: null to clear. Params: owl_file_path, iri (nullable), version_iri (nullable).

Quality Checks

Tool	Purpose
test_pitfalls	Scan for common modeling pitfalls (31 OOPS!-inspired checks). Returns a JSON report listing detected issues, severity, and affected elements. Optionally filter by pitfall IDs. Params: owl_file_path, pitfalls (nullable, comma-separated IDs e.g. "P04,P08,P11").

Available pitfall checks: P02 (synonym classes), P03 ("is" relationship), P04 (unconnected elements), P05 (wrong inverses), P06 (class hierarchy cycles), P07 (merged concepts), P08 (missing annotations), P10 (missing disjointness), P11 (missing domain/range), P12 (undeclared equivalent properties), P13 (missing inverses), P19 (multiple domains/ranges), P20 (misused annotations), P21 (miscellaneous class), P22 (inconsistent naming), P24 (recursive definitions), P25 (self-inverse), P26 (inverse of symmetric), P27 (wrong equivalent properties), P28 (wrong symmetric), P29 (wrong transitive), P30 (undeclared equivalent classes), P31 (wrong equivalent classes), P32 (duplicate labels), P33 (single-property chain), P34 (untyped class), P35 (untyped property), P36 (URI file extension), P38 (no ontology declaration), P39 (ambiguous namespace), P41 (no license).

Usage Tips

1. Always use absolute paths: Pass the full absolute path in owl_file_path to ensure the MCP server can resolve the file regardless of working directory.
2. Finding content: Call find_axioms with a regex pattern; set include_labels: true for human-readable labels appended as ## comments. Use annotation_property to override the default rdfs:label (e.g. for skos:prefLabel).
3. Adding axioms: Use OWL functional syntax. Add one axiom per call with add_axiom, or batch with add_axioms. Ensure required prefixes exist (e.g. owl, rdf, rdfs, xsd); add custom ones with add_prefix.
4. Setting the ontology IRI: Use set_ontology_iri to establish the ontology IRI and version IRI before adding axioms to a new file. Always pass full IRIs (e.g. "http://example.org/ontology/my-ontology/"), never CURIEs (e.g. "ex:"). CURIEs in the Ontology(...) header produce files that ROBOT cannot parse.
5. Project workflow: After the user approves a draft (Step 5), use these tools to implement the change in the OWL file (Step 6), then run test_pitfalls as part of automated review (Step 7).
6. Imports: Add import axioms via add_axiom using full IRIs in angle brackets: Import(<http://purl.obolibrary.org/obo/bfo.owl>). Never use CURIEs in Import(...) (e.g. Import(obo:bfo.owl) is invalid and will cause ROBOT parsing failures).
7. Annotating the ontology itself: When the subject of an AnnotationAssertion is the ontology (e.g. for rdfs:label, rdfs:comment, dcterms:license), use the full ontology IRI as the subject, not a bare CURIE. Example: AnnotationAssertion(rdfs:label <http://example.org/ontology/my-ontology/> "My Ontology"@en).

Tool Requirements

This skill requires the following tools (proxied from the owl-mcp MCP server):

• add_axiom, add_axioms, remove_axiom, find_axioms, get_all_axioms
• add_prefix, ontology_metadata, get_labels_for_iri
• set_ontology_iri, test_pitfalls

After learning this skill, call setup_tools(skills: ["ontology-editor"]) to activate these tools, then use call_tool(name: "<tool_name>", data: {...}) to invoke them.