Protégé MCP

Give AI tools live, gated access to the ontology you have open in Protégé Desktop — and chat with an assistant that edits it for you, without ever leaving Protégé.

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What is Protégé MCP?

Protégé MCP is a plugin for Protégé Desktop that runs a local MCP (Model Context Protocol) server inside Protégé. It exposes the live, active ontology — the one you have open in the editor — to any MCP-compatible AI client, so the client can explore it and make edits for you through 55 structured tools and 6 guided prompts.

Two ways to use it:

1. As an MCP server for an external client. Point Claude Code, Codex CLI, VS Code, or Claude Desktop at http://127.0.0.1:8123/mcp and it can read and edit your ontology.

2. As an in-app assistant. The built-in Ontology Assistant chat tab drives a coding-agent CLI you already have (Claude Code or Codex) back into the same MCP server — so you get a conversational editor inside Protégé, with no separate client to run.

Everything an AI client does flows through Protégé’s own model manager, so:

Edits appear in the GUI immediately and join the shared Edit ▸ Undo stack.
Safety gates apply to every write — a read-only mode and a confirm-each-write prompt you control from Settings ▸ MCP.
The server is local and authorized — it binds to 127.0.0.1 only and requires an OAuth authorization or a bearer token on every request.

Why use it?

Author faster in natural language. “Create a class Centrifuge under Equipment with a definition and label,” or “find every class with no definition and propose fixes” — the assistant turns that into concrete, previewable axiom changes.
Stay in control. Preview edits before they apply, gate or confirm every write, and undo anything with one keystroke. The AI can never escalate past the gates you set.
Reason and query. Run the reasoner, explain entailments, find unsatisfiable classes, and run SPARQL 1.1 over the active ontology and its imports — all through tools.
Govern your project. Audit modelling quality and project-governance policy (OWL 2 profile conformance, IRI policy, required annotations, module ownership / import layering).
No API key stored by Protégé. The Ontology Assistant reuses your existing CLI login; nothing is kept in the plugin.

Quick start

Install the plugin (drop the jar into Protégé’s plugins/ folder, or use File ▸ Check for plugins). Protégé must run on Java 17+.
Open the MCP Server view, start the server, and note the URL (http://127.0.0.1:8123/mcp).
Either connect an external client or open the Ontology Assistant tab and type a request.

Documentation map

Section	What’s inside
Installation	Requirements (Java 17+), manual install, and Check for plugins.
Connecting a client	The server model (ports, OAuth vs. bearer token) and per-environment recipes for Claude Code, Codex CLI, VS Code, and Claude Desktop.
Ontology Assistant	The in-Protégé chat: what it is, how it works, attachments, privacy, and settings.
Tools	All 55 tools by category, each with arguments and returns, plus the axiom-type catalog and guided prompts.
Contributing	Build from source, run the tests, project layout, and how to add a tool.
Versioning & releases	The SemVer + Keep-a-Changelog scheme and how releases are cut.
Changelog	Release notes for every version.

Protégé MCP is licensed under the BSD 2-Clause License.