<!-- mcp-name: io.github.fabio-rovai/open-ontologies -->

A Terraforming MCP for Knowledge Graphs: validate, classify, and govern AI-generated ontologies.

Open Ontologies is a standalone MCP server and CLI for AI-native ontology engineering. It exposes 42 tools and 5 workflow prompts that let Claude validate, query, diff, lint, version, and persist RDF/OWL ontologies using an in-memory Oxigraph triple store — plus plan changes, detect drift, enforce design patterns, monitor health, align ontologies, track lineage, and learn from user feedback.

Written in Rust, ships as a single binary. No JVM, no Protege, no GUI.

Quick Start

1. Install

Pre-built binaries

Download from GitHub Releases:

# macOS (Apple Silicon)
curl -LO https://github.com/fabio-rovai/open-ontologies/releases/latest/download/open-ontologies-aarch64-apple-darwin
chmod +x open-ontologies-aarch64-apple-darwin && mv open-ontologies-aarch64-apple-darwin /usr/local/bin/open-ontologies

# macOS (Intel)
curl -LO https://github.com/fabio-rovai/open-ontologies/releases/latest/download/open-ontologies-x86_64-apple-darwin
chmod +x open-ontologies-x86_64-apple-darwin && mv open-ontologies-x86_64-apple-darwin /usr/local/bin/open-ontologies

# Linux (x86_64)
curl -LO https://github.com/fabio-rovai/open-ontologies/releases/latest/download/open-ontologies-x86_64-unknown-linux-gnu
chmod +x open-ontologies-x86_64-unknown-linux-gnu && mv open-ontologies-x86_64-unknown-linux-gnu /usr/local/bin/open-ontologies

Docker

docker pull ghcr.io/fabio-rovai/open-ontologies:latest
docker run -i ghcr.io/fabio-rovai/open-ontologies serve

From source (Rust 1.85+)

git clone https://github.com/fabio-rovai/open-ontologies.git
cd open-ontologies
cargo build --release
./target/release/open-ontologies init

2. Connect to your MCP client

<details> <summary><strong>Claude Code</strong></summary>

Add to ~/.claude/settings.json:

{
  "mcpServers": {
    "open-ontologies": {
      "command": "/path/to/open-ontologies/target/release/open-ontologies",
      "args": ["serve"]
    }
  }
}

Restart Claude Code. The onto_* tools are now available. </details>

<details> <summary><strong>Claude Desktop</strong></summary>

Add to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "open-ontologies": {
      "command": "/path/to/open-ontologies/target/release/open-ontologies",
      "args": ["serve"]
    }
  }
}

</details>

<details> <summary><strong>Cursor / Windsurf / any MCP-compatible IDE</strong></summary>

Add to your MCP settings (usually .cursor/mcp.json or equivalent):

{
  "mcpServers": {
    "open-ontologies": {
      "command": "/path/to/open-ontologies/target/release/open-ontologies",
      "args": ["serve"]
    }
  }
}

</details>

<details> <summary><strong>Docker</strong></summary>

{
  "mcpServers": {
    "open-ontologies": {
      "command": "docker",
      "args": ["run", "-i", "--rm", "ghcr.io/fabio-rovai/open-ontologies", "serve"]
    }
  }
}

</details>

3. Build your first ontology

Build me a Pizza ontology following the Manchester University tutorial.
Include all 49 toppings, 22 named pizzas, spiciness value partition,
and defined classes (VegetarianPizza, MeatyPizza, SpicyPizza).
Validate it, load it, and show me the stats.

Claude generates Turtle, then automatically calls onto_validate → onto_load → onto_stats → onto_lint → onto_query, fixing errors along the way.

Why This Exists

Single-shot LLM ontology generation has real problems: no validation, no verification, no iteration, no persistence, no scale, no integration. Open Ontologies solves all of these with a proper RDF/SPARQL engine (Oxigraph) exposed as MCP tools that Claude calls automatically.

Tools

42 tools organized by function:

Category	Tools	Purpose
Core	validate, load, save, clear, stats, query, diff, lint, convert, status	RDF/OWL validation, querying, and management
Remote	pull, push, import-owl	Fetch/push ontologies, resolve owl:imports
Schema	import-schema	PostgreSQL → OWL conversion
Data	map, ingest, shacl, reason, extend	Structured data → RDF pipeline
Versioning	version, history, rollback	Named snapshots and rollback
Lifecycle	plan, apply, lock, drift, enforce, monitor, monitor-clear, lineage	Terraform-style change management
Alignment	align, align-feedback	Cross-ontology class matching with self-calibrating confidence
Clinical	crosswalk, enrich, validate-clinical	ICD-10 / SNOMED / MeSH crosswalks
Feedback	lint-feedback, enforce-feedback	Self-calibrating suppression
Embeddings	embed, search, similarity	Dual-space semantic search (text + Poincare structural)
Reasoning	reason, dl_explain, dl_check	Native OWL2-DL SHOIQ tableaux reasoner

All tools are available both as MCP tools (prefixed onto_) and as CLI subcommands.

Architecture

flowchart TD
    Claude["Claude / LLM"]
    MCP["Open Ontologies MCP Server"]

    subgraph Core["Core Engine"]
        GraphStore["Oxigraph Triple Store"]
        StateDb["SQLite State"]
    end

    subgraph Tools["42 Tools + 5 Prompts"]
        direction LR
        Ontology["validate · load · query\nsave · diff · lint · convert"]
        Data["map · ingest · shacl\nreason · extend"]
        Lifecycle["plan · apply · lock\nenforce · monitor · drift"]
        Advanced["align · crosswalk · enrich\nlineage · embed · search"]
    end

    Claude -->|"MCP stdio"| MCP
    MCP --> Tools
    Tools --> Core

Documentation

Topic	Link
Quickstart	docs/quickstart.md
Data Pipeline	docs/data-pipeline.md
Ontology Lifecycle	docs/lifecycle.md
Schema Alignment	docs/alignment.md
OWL2-DL Reasoning	docs/reasoning.md
Semantic Embeddings	docs/embeddings.md
Clinical Crosswalks	docs/clinical.md
Benchmarks	docs/benchmarks.md
Contributing	CONTRIBUTING.md
Changelog	CHANGELOG.md

Stack

• Rust (edition 2024) — single binary, no JVM
• Oxigraph 0.4 — pure Rust RDF/SPARQL engine
• rmcp — MCP protocol implementation
• SQLite (rusqlite) — state, versions, lineage, feedback, embeddings
• Apache Arrow/Parquet — clinical crosswalk file format
• tract-onnx — pure Rust ONNX runtime for text embeddings (optional)
• tokenizers — HuggingFace tokenizer (optional)

License

MIT

<a href="https://glama.ai/mcp/servers/fabio-rovai/open-ontologies"><img width="380" height="200" src="https://glama.ai/mcp/servers/fabio-rovai/open-ontologies/badge" /></a>