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robot-tool-mcp

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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.

Related MCP server: @jingjingbox/mcp-cli-bridge

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

Install Server
A
license - permissive license
A
quality
C
maintenance

How are these scores calculated?

Maintenance

–Maintainers
–Response time
0dRelease cycle
5Releases (12mo)
Commit activity

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