Ontology Assistant

A chat assistant inside Protégé that reads and edits your live ontology — conversationally, with no external client to configure.

Table of contents

1. What it is
2. Prerequisites
3. Using it
   1. Attachments and long pastes
4. Privacy & cost
5. Settings (Settings ▸ Ontology Assistant)
6. Troubleshooting

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What it is

The Ontology Assistant (introduced in 0.3.0) is a chat tab and view built into the plugin. Instead of calling a model API directly, it drives a coding-agent CLI you already have installed — Claude Code (claude) or OpenAI Codex (codex) — and points that CLI back at this plugin’s own MCP server.

So the assistant reads and edits through exactly the same tools an external MCP client uses:

• Changes appear in the Protégé GUI immediately and join the Edit ▸ Undo stack.
• The read-only and confirm-each-write gates still apply — the chat cannot escalate past them.
• No API key is stored by Protégé. Each CLI uses your existing login (Claude subscription/keychain; codex login).

Prerequisites

• Install and log in to at least one CLI:
  • Claude Code — https://docs.claude.com/en/docs/claude-code (then claude works in your terminal), or
  • Codex — https://github.com/openai/codex (codex login).
• The MCP server must be running. The chat starts it automatically on your first message.

Only CLIs that are actually detected on your system are offered as providers.

Using it

1. Open the Ontology Assistant tab (a top-level tab), or add the Ontology Assistant view to any tab via Window ▸ Views.
2. Pick a provider — Use Claude / Use Codex (only installed CLIs appear) — and optionally a model (blank uses the CLI’s own default).
3. Type a request and press Enter (Shift+Enter inserts a newline). Start with a read, then an edit:
   • “What classes are in this ontology?”
   • “Create a class FooBar under Thing with label ‘Foo Bar’.”
4. Watch the reply stream in. Stop cancels mid-turn. Edit ▸ Undo reverts any edit it made.

Attachments and long pastes

The chat input accepts more than plain text (added in 0.3.1):

• Long pasted text is compacted in the input as [Pasted content #N: … chars], while the full body still reaches the assistant. Large bodies are buffered to a temp file and referenced by path, so a paste can never overflow the command line.
• Files and images — via the Attach button, drag-and-drop, or clipboard paste — become placeholders such as [Image #1] or [File #2: name]. Codex receives images natively (--image); Claude is granted read access to the file (--add-dir).
• Deleting the placeholder before sending removes the attachment (backspace next to a placeholder deletes the whole token); a placeholder edited away before Send is reported and not sent.

Privacy & cost

The chat sends your prompts, any attachments/pasted content, and the ontology content the assistant reads to your model provider via the CLI. A one-time banner discloses this before the first send.

• Each attached file or image is copied into its own private temp folder, and only that single-file copy is exposed to the CLI — never the rest of its containing folder. The temp copies are deleted when the turn finishes.
• Cost and rate limits are governed by your CLI’s own subscription/account, not by Protégé.
• Edits obey the MCP preferences (read-only, confirm-each-write). A Confirm each edit checkbox in the panel toggles confirmation live.

Settings (Settings ▸ Ontology Assistant)

• CLI path overrides — if Protégé was launched from the macOS Dock/Finder, it may not inherit your shell PATH, so a CLI can fail to resolve. Set an explicit path to the claude / codex executable here. The panel shows what was detected.
• Reset egress consent — re-arm the one-time disclosure banner.
• Show thinking — optionally include the model’s reasoning in the transcript.

Troubleshooting

• No providers offered — no CLI was detected. Install one, or set its explicit path in Settings ▸ Ontology Assistant (common when Protégé is launched from the Dock/Finder without your shell PATH).
• “Not logged in” / auth errors — log in in your terminal first (claude, or codex login). The plugin spawns the CLI through a login shell so it can pick up your environment.
• Edits don’t apply — check read-only mode and any pending confirm-each-write dialog (Settings ▸ MCP), and the Confirm each edit checkbox in the panel.