obsidian-brain

A standalone Node MCP server that gives Claude (and any other MCP client) semantic search + knowledge graph + vault editing over an Obsidian vault. Runs as one local stdio process — no plugin, no HTTP bridge, no API key, nothing hosted. Your vault content never leaves your machine.

📖 Full docs → sweir1.github.io/obsidian-brain Companion plugin → sweir1/obsidian-brain-plugin (optional — unlocks active_note, dataview_query, base_query)

Contents — Why · Quick start · What you get · How it works · Companion plugin · Troubleshooting · Recent releases

Why obsidian-brain?

• Works without Obsidian running — unlike Local REST API-based servers, obsidian-brain reads .md files directly from disk. Obsidian can be closed; your vault is just a folder.
• No Local REST API plugin required — nothing to install inside Obsidian for the core experience.
• Chunk-level semantic search with RRF hybrid retrieval — embeddings at markdown-heading granularity, fused with FTS5 BM25 via Reciprocal Rank Fusion. Finds the exact chunk, ranks on meaning.
• The only Obsidian MCP server with PageRank + Louvain + graph analytics — ask for your vault's most influential notes, bridging notes, theme clusters. Nobody else ships this.
• Ollama provider for high-quality local embeddings — switch to bge-m3, nomic-embed-text, qwen3-embedding-8b, etc. with one env var.
• All in one npx install — no clone, no build, no API key, no hosted endpoint. Vault content never leaves your machine.

Quick start

Requires Node 20+ and an Obsidian vault (or any folder of .md files — Obsidian itself is optional).

Wire obsidian-brain into your MCP client. Example for Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "obsidian-brain": {
      "command": "npx",
      "args": ["-y", "obsidian-brain@latest", "server"],
      "env": { "VAULT_PATH": "/absolute/path/to/your/vault" }
    }
  }
}

Quit Claude Desktop (⌘Q on macOS) and relaunch. That's it.

[!NOTE] On first boot the server auto-indexes your vault and downloads a ~34 MB embedding model. Tools may take 30–60 s to appear in the client. Subsequent boots are instant.

[!TIP] Not a developer? The macOS walkthrough covers Homebrew, Node, the GUI-app PATH fix, and Full Disk Access step-by-step.

For every other MCP client (Claude Code, Cursor, VS Code, Jan, Windsurf, Cline, Zed, LM Studio, JetBrains AI, Opencode, Codex CLI, Gemini CLI, Warp): see Install in your MCP client.

→ Full env-var reference: Configuration → Model / preset / Ollama details: Embedding model → Migrating from aaronsb's plugin: Migration guide

What you get

17 MCP tools grouped by intent:

• Find & read — search, list_notes, read_note
• Understand the graph — find_connections, find_path_between, detect_themes, rank_notes
• Write — create_note, edit_note, apply_edit_preview, link_notes, move_note, delete_note
• Live editor (requires companion plugin) — active_note, dataview_query, base_query
• Maintenance — reindex

→ Arguments, examples, and response shapes: Tool reference

How it works

flowchart LR
    Client["<b>MCP Client</b><br/>Claude Desktop · Claude Code<br/>Cursor · Jan · Windsurf · ..."]

    subgraph OB ["obsidian-brain (Node process)"]
        direction TB
        SQL["<b>SQLite index</b><br/>nodes · edges<br/>FTS5 · vec0 embeddings"]
        Vault["<b>Vault on disk</b><br/>your .md files"]
        Vault -->|"parse + embed"| SQL
        SQL -.->|"writes"| Vault
    end

    Client <-->|"stdio JSON-RPC"| OB

Retrieval and writes both go through a SQLite index: reads are microsecond-cheap, writes land on disk immediately and incrementally re-index the affected file. Embeddings are chunk-level (heading-aware recursive chunker preserving code + LaTeX blocks), and search's default hybrid mode fuses chunk-level semantic rank with FTS5 BM25 via Reciprocal Rank Fusion.

→ Deeper write-up — why stdio, why SQLite, why local embeddings: Architecture → Live watcher behaviour + debounces: Live updates → Scheduled reindex (macOS launchd / Linux systemd): Scheduled indexing (macOS) · (Linux)

Companion plugin (optional)

An optional Obsidian plugin at sweir1/obsidian-brain-plugin exposes live Obsidian runtime state — active editor, Dataview results, Bases rows — over a localhost HTTP endpoint. When installed and Obsidian is running, active_note, dataview_query, and base_query light up. Install via BRAT with repo ID sweir1/obsidian-brain-plugin.

Ship plugin and server at the same major.minor (server 1.6.x ↔ plugin 1.6.x). Patch-version drift is fine.

→ Security model, capability handshake, Dataview / Bases feature coverage: Companion plugin

Troubleshooting

Four most common:

• "Connector has no tools available" in Claude Desktop — usually the server crashed at startup. Check ~/Library/Logs/Claude/mcp-server-obsidian-brain.log. Fix: npm install -g obsidian-brain@latest, quit Claude (⌘Q), relaunch.
• ERR_DLOPEN_FAILED / NODE_MODULE_VERSION mismatch — better-sqlite3 built against a different Node ABI. Fix: PATH=/opt/homebrew/bin:$PATH npm rebuild -g better-sqlite3.
• Vault path not configured — VAULT_PATH is unset. Set it in the env block of your client config or shell.
• Old version loading via npx (e.g. v1.2 when npm shows v1.6) — stale npx cache. Fix: rm -rf ~/.npm/_npx, then restart your client. Keeping @latest in your config prevents this.

→ Full troubleshooting guide (watcher not firing, stale index, running multiple clients, timeouts, embedding-dim mismatch, log locations): docs/troubleshooting.md

Recent releases

• v1.6.5 — heading/anchor stub lifecycle (schema v4): [[X#Section]] and [[X^block]] now migrate to real notes like bare refs; new edges.target_fragment column.
• v1.6.4 — path-qualified wiki-link rewriting through move_note: [[notes/BMW]] now updates to [[cars/BMW & Audi]] on a cross-folder rename.
• v1.6.3 — new renameNode DB primitive; move_note preserves inbound edges, chunk embeddings, and graph membership across rename (no delete-then-upsert).
• v1.6.2 — move_note ghost-link fix: inbound edges targeting _stub/<name>.md are now rewritten through rename; watcher path migrates forward-reference stubs inline.

→ Full changelog: docs/CHANGELOG.md · Forward plan: docs/roadmap.md · Build from source: docs/development.md

Credits

Thanks to obra/knowledge-graph and aaronsb/obsidian-mcp-plugin for the ideas and code this project draws on. Also Xenova/transformers.js (local embeddings), graphology (graph analytics), and sqlite-vec (vector search in SQLite).

License

MIT — see LICENSE.