OWL MCP

A high-performance Model Context Protocol (MCP) server and CLI for OWL ontology management, written in Rust.

Built as a drop-in replacement for ai4curation/owl-mcp, designed to eliminate the crashes and timeouts inherent to the Python implementation. Axioms are expressed in OWL Functional Syntax.

Features

• 16 MCP tools — add, remove, search, and inspect axioms; add structured assertions (data/annotation/object property, class) with the literal value as a separate field; manage prefixes, labels, and ontology IRIs; scan for modeling pitfalls; evaluate ontology quality; run SPARQL queries
• CLI mode — every tool is also available as a direct CLI subcommand (owl-mcp find-axioms ...)
• 2 transport modes — stdio (default, for Cursor/Claude Desktop) and http (Streamable HTTP + SSE)
• Live file watching — automatically reloads ontology files modified externally
• OFN and RDF/XML support — reads and writes both formats; format is auto-detected from file extension and content
• Never crashes — errors are returned as MCP tool failures, not panics

Installation

via npx (recommended)

npx owl-mcp serve

via npm (global install)

npm install -g owl-mcp
owl-mcp --help

Build from source

Requires Rust 1.75+.

git clone https://github.com/Minitour/owl-mcp
cd owl-mcp
cargo build --release
./target/release/owl-mcp --help

Usage

owl-mcp has two modes: serve (MCP server) and CLI (direct commands).

MCP server mode

owl-mcp serve [OPTIONS]

Options:
  --transport <stdio|http>   Transport to use [default: stdio]
  --host <HOST>              Host to bind (HTTP only) [default: 127.0.0.1]
  --port <PORT>              Port to bind (HTTP only) [default: 8080]
  --sse-support              Enable legacy SSE endpoint [default: true]

CLI mode

Every MCP tool is available as a subcommand:

owl-mcp add-axiom --file ontology.owl --axiom "SubClassOf(:Dog :Animal)"
owl-mcp add-data-property-assertion --file ontology.owl --property :metaprops --subject :Plan1 --value-file ./long-value.txt
owl-mcp add-axioms --file ontology.owl --axioms-file ./axioms.json
owl-mcp find-axioms --file ontology.owl --pattern "Dog" --limit 50
owl-mcp get-all-axioms --file ontology.owl --include-labels
owl-mcp test-pitfalls --file ontology.owl
owl-mcp test-quality --file ontology.owl
owl-mcp sparql --file ontology.owl --query "SELECT ?c WHERE { ?c a owl:Class }"
owl-mcp sparql --file schema.owl --file data.owl --query "ASK { ?i a :Plan }"

Run owl-mcp --help for a full list of commands, or owl-mcp <command> --help for details on a specific command.

Cursor / Claude Desktop integration

Add the server to your MCP client configuration.

Cursor (~/.cursor/mcp.json or .cursor/mcp.json in your project):

{
  "mcpServers": {
    "owl-mcp": {
      "command": "npx",
      "args": ["-y", "owl-mcp", "serve"]
    }
  }
}

HTTP transport (useful for remote/shared setups):

{
  "mcpServers": {
    "owl-mcp": {
      "url": "http://localhost:8080/mcp"
    }
  }
}

Start the server with:

owl-mcp serve --transport http --port 8080

Tools

All tools operate on OWL files by absolute path. The manager lazily loads files on first access and caches them for subsequent calls.

Axiom operations

Tool	Description
add_axiom	Add a single axiom in OWL Functional Syntax
add_axioms	Add multiple axioms in one call
add_data_property_assertion	Assert a data property value (value passed as a separate field — no escaping)
add_annotation_assertion	Assert an annotation value (value passed as a separate field — no escaping)
add_object_property_assertion	Link two individuals via an object property
add_class_assertion	Assert that an individual is an instance of a class
remove_axiom	Remove an axiom
find_axioms	Search axioms with a regex pattern
get_all_axioms	List all axioms (up to a limit)

For long or special-character literal values (containing ;, =, /, ,, quotes, or newlines), prefer the structured assertion tools over hand-writing a quoted add_axiom string: they take the value as a separate field and build the axiom server-side, so no escaping is needed. In CLI mode, add-axioms also accepts --axioms-file <path> (a JSON array of strings, or NUL/newline-delimited; - for stdin), and the structured commands accept --value-file <path>, both of which bypass shell quoting entirely. add_axiom/add_axioms now return a hard error (instead of a silent warning) when an input parses to no axiom.

Metadata and labels

Tool	Description
add_prefix	Add a prefix mapping (ex: → http://example.org/)
ontology_metadata	Return ontology-level annotation axioms
get_labels_for_iri	Look up rdfs:label (or custom property) values for an IRI
set_ontology_iri	Set or update the ontology IRI and version IRI

Quality checks

Tool	Description
test_pitfalls	Scan for 31 common modeling pitfalls (inspired by OOPS!)
test_quality	Evaluate ontology quality using the OQuaRE framework (ISO/IEC 25000 SQuaRE)

find_axioms and get_all_axioms accept include_labels: true to annotate each axiom with human-readable labels appended as ## <IRI> # label comments.

test_quality uses the whelk OWL EL reasoner to compute inferred class hierarchy and returns a JSON report containing 19 raw and scaled metrics (ANOnto, AROnto, CBOOnto, CROnto, DITOnto, INROnto, LCOMOnto, NACOnto, NOCOnto, NOMOnto, RFCOnto, RROnto, TMOnto, WMCOnto, and variants), 22 subcharacteristics, 7 quality characteristics (Structural, Functional Adequacy, Maintainability, Operability, Reliability, Transferability, Compatibility), and an overall OQuaRE score on a 1–5 scale.

Querying

Tool	Description
sparql_query	Run a SPARQL query over one or more OWL files

sparql_query takes owl_file_paths (one or more absolute paths) and a query string. Each file is serialized to RDF and loaded together into an in-memory oxigraph store, so passing several paths merges a schema with its ABox or imports before the query runs. SELECT and ASK return the standard SPARQL 1.1 JSON results format; CONSTRUCT and DESCRIBE return a list of N-Triples. Queries run over asserted triples (no reasoning is applied).

Development

# Run tests
cargo test

# Check formatting and lints
cargo fmt --check
cargo clippy --all-targets -- -D warnings

# Build release binary
cargo build --release

License

MIT