Installation

How to install Protégé MCP, the Java requirement it depends on, and how to confirm it loaded.

Table of contents

1. Requirements
2. Install the plugin
   1. Option A — Manual (drop-in jar)
   2. Option B — Check for plugins (auto-discovery + updates)
3. Verify it loaded
4. Next steps

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Requirements

Protégé must run on Java 17 or newer.

The MCP Java SDK and the embedded Jetty 12 host are Java 17 bytecode, and the bundle’s OSGi manifest declares Require-Capability: osgi.ee … JavaSE 17. On Java 11 the bundle will not resolve — there is no Java-11 build path, because every published MCP SDK version is Java 17 bytecode.

Protégé’s bundled launchers may ship a Java 11 runtime. If Protégé is on Java 11, the plugin silently fails to load (it never appears in the views/menus). Point Protégé at a 17+ JDK first.

Protégé’s run.sh / run.command launchers honour the PROTEGE_JAVA_HOME environment variable:

export PROTEGE_JAVA_HOME=/path/to/jdk-17
./run.sh        # or ./run.command

For the macOS .app / Windows .exe launchers, set the JVM in the launcher’s own configuration instead (e.g. the .app’s Info.plist / bundled jre, or the Windows launcher .l4j.ini).

Install the plugin

You can install manually (drop in a jar) or let Protégé discover and update the plugin for you.

Option A — Manual (drop-in jar)

1. Download protege-mcp-<version>.jar from the latest release.
2. Drop it into Protégé’s plugins directory:
   • macOS: ~/.Protege/plugins/ (per-user), or the in-bundle Protégé.app/Contents/Java/plugins/.
   • Windows / Linux: the plugins/ folder inside the Protégé install, e.g. C:\Program Files\Protege-5.6.x\plugins\ or <protege-install>/plugins/.
3. Restart Protégé on a Java 17+ JVM (see Requirements).

Keep exactly one protege-mcp-*.jar (or io.github.hakjuoh-*.jar) in the plugins folder. The bundle is a singleton; two versions side by side will conflict. Delete the old jar before adding a new one.

Option B — Check for plugins (auto-discovery + updates)

Protégé can discover the plugin and offer future updates from a self-hosted registry. See Install via Check for plugins for the full walk-through. In short:

1. Settings ▸ Plugins ▸ Plugin registry → https://raw.githubusercontent.com/hakjuoh/protege-mcp/main/protege-mcp.repository
2. File ▸ Check for plugins → tick Protege MCP Server → install → restart.

Verify it loaded

After restarting, you should see:

• A MCP Server view — add it from Window ▸ Views ▸ Miscellaneous views, or to any tab. It shows the server status, bound URL, and bearer token.
• A MCP settings tab under Settings ▸ MCP (port, autostart, read-only, confirm-writes).
• An Ontology Assistant top-level tab, and an Ontology Assistant settings tab under Settings ▸ Ontology Assistant.

The bundle id is io.github.hakjuoh (singleton).

Next steps

• Connect an external MCP client (Claude Code, Codex CLI, VS Code, Claude Desktop), or
• Open the Ontology Assistant and start chatting.

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Table of contents

• Install via Check for plugins