ROBOT Ontology MCP

MCP server wrapping the ROBOT command-line tool for OWL ontology editing.

Prerequisites

ROBOT must be installed and available on your PATH:

robot --version

See ROBOT installation for setup instructions.

Installation

With uvx (recommended)

uvx robot-tool-mcp

From source

git clone https://github.com/<owner>/robot-mcp.git
cd robot-mcp
uv run robot-mcp

Claude Desktop Configuration

Add to your Claude Desktop config (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "robot-mcp": {
      "command": "uvx",
      "args": ["robot-tool-mcp"]
    }
  }
}

Or for local development:

{
  "mcpServers": {
    "robot-mcp": {
      "command": "uv",
      "args": ["run", "--directory", "/path/to/robot-tool-mcp", "robot-mcp"]
    }
  }
}

Tools

Individual Command Tools (25 tools)

Each ROBOT command is exposed as a dedicated MCP tool with typed parameters:

Tool	Description
robot_annotate	Add metadata annotations to an ontology
robot_collapse	Simplify class hierarchies by removing intermediates
robot_convert	Transform ontology between formats (OWL, OBO, TTL, etc.)
robot_diff	Compare two ontologies semantically
robot_expand	Convert shortcut annotations into OWL axioms
robot_explain	Debug inferred statements with minimal explanations
robot_export	Generate tabular output (CSV, TSV, JSON, HTML, XLSX)
robot_extract	Create a subset module (STAR, BOT, TOP, MIREOT)
robot_filter	Selectively copy axioms (inverse of remove)
robot_materialize	Assert inferred superclass relationships
robot_measure	Compute ontology metrics and statistics
robot_merge	Combine multiple ontologies into one
robot_mirror	Cache imported ontologies locally
robot_query	Execute SPARQL queries (SELECT, ASK, CONSTRUCT, UPDATE)
robot_reason	Run OWL reasoner (ELK, HermiT, JFact, Whelk)
robot_reduce	Remove redundant subClassOf axioms
robot_relax	Convert equivalence axioms to subclass axioms
robot_remove	Eliminate selected axioms (inverse of filter)
robot_rename	Modify entity IRIs
robot_repair	Fix common ontology problems
robot_report	Run quality control checks with violation report
robot_template	Convert tabular data (CSV/TSV) into OWL
robot_unmerge	Remove axioms of one ontology from another
robot_validate_profile	Check OWL 2 profile conformance (EL/RL/QL/DL)
robot_verify	Check ontology against SPARQL rules

Chain Tool

The robot_chain tool pipelines multiple commands in a single ROBOT process. Ontology objects pass in-memory between steps — no intermediate files needed.

{
  "steps": [
    {"command": "merge", "input": ["edit.owl", "base.owl"]},
    {"command": "reason", "reasoner": "ELK"},
    {"command": "annotate", "ontology_iri": "https://example.org/my.owl"},
    {"command": "convert", "format": "ofn", "output": "result.owl"}
  ]
}

This produces a single CLI call:

robot merge --input edit.owl --input base.owl \
      reason --reasoner ELK \
      annotate --ontology-iri https://example.org/my.owl \
      convert --format ofn --output result.owl

Argument mapping rules:

• Underscores become hyphens: ontology_iri → --ontology-iri
• Lists repeat the flag: {"input": ["a.owl", "b.owl"]} → --input a.owl --input b.owl
• Booleans become strings: true → "true"

Common Workflows

Build a release:

{
  "steps": [
    {"command": "merge", "input": ["edit.owl"]},
    {"command": "reason", "reasoner": "ELK"},
    {"command": "relax"},
    {"command": "reduce", "reasoner": "ELK"},
    {"command": "annotate", "ontology_iri": "https://example.org/release.owl",
     "version_iri": "https://example.org/2024-01-01/release.owl"},
    {"command": "convert", "output": "release.owl"}
  ]
}

Extract a module:

{
  "steps": [
    {"command": "merge", "input": ["full-ontology.owl"]},
    {"command": "extract", "method": "BOT", "term": ["GO:0005634", "GO:0005737"]},
    {"command": "annotate", "ontology_iri": "https://example.org/module.owl"},
    {"command": "convert", "output": "module.owl"}
  ]
}

Quality check:

{
  "steps": [
    {"command": "merge", "input": ["edit.owl"]},
    {"command": "report", "fail_on": "ERROR", "output": "report.tsv"}
  ]
}

Global Options

All tools support these global options:

Option	Description
catalog	XML catalog file for resolving imports
prefixes	JSON-LD prefix file
add_prefix	Add individual prefixes (list)
noprefixes	Disable default prefixes
verbose	Enable verbose logging
strict	Fail on unparsed triples
xml_entities	Use XML entities in RDF/XML output
working_directory	Working directory for file paths
extra_args	Escape hatch for rarely-used flags (list of strings)

How to Contribute

1. Fork the repository
2. Create a feature branch from main:

   git checkout -b feature/your-feature
   

3. Install dev dependencies:

   uv sync --dev
   

4. Make your changes and ensure code quality:

   uv run ruff format src/
   uv run ruff check src/
   

5. Commit your changes and push to your fork
6. Open a Pull Request against main

The main branch is protected — all changes must go through a PR.

License

BSD 2-Clause License