A Terraforming MCP for Knowledge Graphs
Validate, classify, and govern AI-generated ontologies. Written in Rust. Ships as a single binary.
Quick Start · Studio · Benchmarks · Tools · Architecture · Docs
Open Ontologies is a Rust MCP server and desktop Studio for AI-native ontology engineering. It exposes 42 tools that let Claude build, validate, query, diff, lint, version, reason over, align, and persist RDF/OWL ontologies using an in-memory Oxigraph triple store — with Terraform-style lifecycle management, clinical crosswalks, semantic embeddings, and a full lineage audit trail.
The Studio wraps the engine in a visual desktop environment: 3D force-directed graph, AI chat panel, Protégé-style property inspector, and lineage viewer.
No JVM. No Protégé. No GUI required.
| Full UI | 3D Graph |
|---|---|
 |
 |
Forest ontology built entirely in natural language. Claude called onto_clear → onto_load → onto_reason → onto_save automatically.
Pre-built binaries:
# 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-ontologiesDocker:
docker pull ghcr.io/fabio-rovai/open-ontologies:latest
docker run -i ghcr.io/fabio-rovai/open-ontologies serveFrom source (Rust 1.85+):
git clone https://github.com/fabio-rovai/open-ontologies.git
cd open-ontologies && cargo build --release
./target/release/open-ontologies initClaude Code
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.
Claude Desktop
Add to ~/Library/Application Support/Claude/claude_desktop_config.json:
{
"mcpServers": {
"open-ontologies": {
"command": "/path/to/open-ontologies/target/release/open-ontologies",
"args": ["serve"]
}
}
}Cursor / Windsurf / any MCP-compatible IDE
Add to .cursor/mcp.json or equivalent:
{
"mcpServers": {
"open-ontologies": {
"command": "/path/to/open-ontologies/target/release/open-ontologies",
"args": ["serve"]
}
}
}Docker
{
"mcpServers": {
"open-ontologies": {
"command": "docker",
"args": ["run", "-i", "--rm", "ghcr.io/fabio-rovai/open-ontologies", "serve"]
}
}
}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 calls onto_validate → onto_load → onto_stats → onto_lint → onto_query automatically, fixing errors along the way.
The Studio lives in studio/ — a Tauri 2 desktop app that provides a visual interface on top of the same engine.
Prerequisites: Rust + Cargo · Node.js 18+
# 1. Build the engine binary (from repo root)
cargo build --release
# 2. Install JS dependencies
cd studio && npm install
# 3. Run
PATH=/opt/homebrew/bin:~/.cargo/bin:$PATH npm run tauri dev| Feature | Description |
|---|---|
| 3D Graph Canvas | Live force-directed OWL class hierarchy (Three.js / WebGL). Drag to orbit, scroll to zoom, click to inspect, right-click to add, Delete to remove. |
| AI Agent Chat | Natural language ontology engineering via Claude Sonnet 4.6 + Agent SDK. Type instructions — Claude calls the right tools automatically. |
| Property Inspector | Protégé-style inline triple editor. Click to edit, hover to delete, + Add for new triples. |
| Lineage Panel | Full audit trail from SQLite: plan · apply · enforce · drift · monitor · align, grouped by session. |
| Named Save | ⌘S to save as ~/.open-ontologies/<name>.ttl. Auto-saves to studio-live.ttl after every mutation. |
Keyboard shortcuts: ⌘J chat · ⌘I inspector · ⌘S save · Delete remove node
OntoAxiom tests axiom identification across 9 ontologies and 3,042 ground truth axioms.
| Approach | F1 | vs o1 (paper best) |
|---|---|---|
| o1 (paper's best) | 0.197 | — |
| Bare Claude Opus | 0.431 | +119% |
| MCP extraction | 0.717 | +264% |
One sentence input: "Build a Pizza ontology following the Manchester tutorial specification."
| Metric | Reference (Protégé, ~4 hours) | AI-Generated (~5 min) | Coverage |
|---|---|---|---|
| Classes | 99 | 95 | 96% |
| Properties | 8 | 8 | 100% |
| Toppings | 49 | 49 | 100% |
| Named Pizzas | 24 | 24 | 100% |
Dataset: UCI Mushroom Dataset — 8,124 specimens classified by mycology experts.
| Metric | Result |
|---|---|
| Accuracy | 98.33% |
| Recall (poisonous) | 100% — zero toxic mushrooms missed |
| False negatives | 0 |
| Classification rules | 6 OWL axioms |
LUBM Scaling (load + reason cycle)
| Axioms | Open Ontologies | HermiT | Speedup |
|---|---|---|---|
| 1,000 | 15ms | 112ms | 7.5× |
| 5,000 | 14ms | 410ms | 29× |
| 10,000 | 14ms | 1,200ms | 86× |
| 50,000 | 15ms | 24,490ms | 1,633× |
Full benchmark writeup: docs/benchmarks.md
42 tools organized by function — available as MCP tools (prefixed onto_) and CLI subcommands:
| 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 + Poincaré structural) |
| Reasoning | reason dl_explain dl_check |
Native OWL2-DL SHOIQ tableaux reasoner |
flowchart TD
subgraph Clients["Clients"]
Claude["Claude / LLM\nMCP stdio"]
CLI["CLI\nonto_* subcommands"]
Studio["Studio\nHTTP REST"]
end
subgraph Server["Open Ontologies Server"]
direction TB
subgraph Transport["Transport Layer"]
MCP_HTTP["MCP Streamable HTTP\n/mcp"]
REST["REST API\n/api/query · /api/update\n/api/save · /api/load · /api/lineage"]
end
subgraph ToolGroups["42 Tools"]
direction LR
Core["Core\nvalidate · load · save · clear\nstats · query · diff · lint\nconvert · status"]
DataPipe["Data Pipeline\nmap · ingest · shacl\nreason · extend · import-schema"]
Lifecycle["Lifecycle\nplan · apply · lock · drift\nenforce · monitor · lineage"]
Advanced["Alignment + Clinical\nalign · crosswalk · enrich\nenrich · embed · search · similarity\ndl_explain · dl_check"]
Version["Versioning\nversion · history · rollback"]
end
subgraph Core2["Core Engine"]
GraphStore["Oxigraph Triple Store\nRDF/OWL in-memory\nSPARQL 1.1"]
SQLite["SQLite\nlineage events\nversion snapshots\nlint/enforce feedback\nembedding vectors"]
Reasoner["OWL2-DL Reasoner\nSHOIQ tableaux\nRDFS · OWL-RL"]
Embedder["Embedding Engine\ntract-onnx (ONNX)\ntext + Poincaré structural"]
end
end
subgraph External["External Sources"]
PG["PostgreSQL\nschema import"]
SPARQL["Remote SPARQL\nendpoints"]
OWL["OWL URLs\nowl:imports chains"]
Parquet["Parquet / Arrow\nclinical crosswalks\nICD-10 · SNOMED · MeSH"]
Files["Files\nCSV · JSON · XML\nYAML · XLSX · Parquet"]
end
Claude -->|"MCP stdio"| MCP_HTTP
CLI -->|"subcommands"| MCP_HTTP
Studio -->|"sessionless"| REST
MCP_HTTP --> ToolGroups
REST --> ToolGroups
ToolGroups --> GraphStore
ToolGroups --> SQLite
ToolGroups --> Reasoner
ToolGroups --> Embedder
Reasoner --> GraphStore
Embedder --> SQLite
DataPipe --> Files
Advanced --> Parquet
Core --> OWL
Core --> SPARQL
DataPipe --> PG
flowchart TD
subgraph UI["React UI (Vite + Tailwind CSS)"]
Graph["3D Graph Canvas\n3d-force-graph / Three.js"]
Chat["AI Chat Panel\nZustand store"]
Inspector["Property Inspector\nInline SPARQL edit"]
Lineage["Lineage Panel\nAudit trail"]
Save["Named Save\n⌘S → ~/.open-ontologies/"]
end
subgraph Tauri["Tauri 2 Shell (Rust)"]
IPC["Tauri IPC\ninvoke / event"]
ChatState["ChatState\nstdin/stdout pipe"]
end
subgraph Engine["Engine Sidecar (Rust / Axum)"]
MCP["/mcp — MCP Streamable HTTP\n42 onto_* tools"]
REST2["/api/query · /api/update\n/api/save · /api/load-turtle\n/api/stats · /api/lineage"]
Store["Arc<GraphStore>\nOxigraph"]
DB["SQLite"]
end
subgraph Agent["Agent Sidecar (Node.js)"]
SDK["Claude Sonnet 4.6\nAgent SDK"]
Proto["stdin/stdout JSON protocol"]
end
Graph -->|"SPARQL SELECT · REST"| REST2
Inspector -->|"SPARQL UPDATE · REST"| REST2
Lineage -->|"GET /api/lineage"| REST2
Save -->|"POST /api/save"| REST2
Chat -->|"invoke send_chat_message"| IPC
IPC --> ChatState
ChatState -->|"stdin { type: chat }"| Proto
Proto --> SDK
SDK -->|"MCP tools/call"| MCP
SDK -->|"stdout { type: text/tool_call/done }"| Proto
Proto -->|"Tauri emit agent-message"| Chat
MCP --> Store
REST2 --> Store
Store --> DB
| Decision | Reason |
|---|---|
| UI reads use sessionless REST | No MCP session management needed for SPARQL queries or stats |
UI writes use REST /api/update + /api/save |
Avoids session lifecycle issues in the Tauri WebKit webview |
Agent writes go through MCP tools/call |
The Agent SDK manages its own MCP session; Claude needs the full tool set |
Shared Arc<GraphStore> |
All MCP sessions and REST handlers share the same in-memory triple store |
| Agent sidecar over stdin/stdout | Keeps Node.js isolated; Tauri manages the full lifecycle |
| Layer | Tech |
|---|---|
| Engine language | Rust (edition 2024) — single binary, no JVM |
| Triple store | Oxigraph 0.4 — pure Rust RDF/SPARQL 1.1 engine |
| MCP protocol | rmcp — Streamable HTTP transport |
| State / lineage / feedback | SQLite (rusqlite) |
| Clinical crosswalks | Apache Arrow / Parquet |
| Embeddings runtime | tract-onnx — pure Rust ONNX (optional) |
| Desktop shell | Tauri 2 |
| Frontend | React 19, Vite 7, TypeScript 5.8, Tailwind CSS 4 |
| 3D graph | 3d-force-graph 1.79 (Three.js / WebGL) |
| UI state | Zustand 5 |
| AI agent | Claude Sonnet 4.6 via Agent SDK (Node.js sidecar) |
| 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 |
MIT