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 `qwen3-embedding:0.6b`, `nomic-embed-text`, `bge-m3`, 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

One-line install (macOS + Claude Desktop)

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/sweir1/obsidian-brain/main/scripts/install.sh)"

Installs Homebrew + Node 20+ if you don't already have them, adds the `/usr/local/bin` symlinks that Claude Desktop needs, merges obsidian-brain into your `claude_desktop_config.json`, opens the Full Disk Access pane for you to toggle Claude on, and relaunches Claude. You'll be asked for your macOS password once (for Homebrew + the symlinks) and your vault path once. Everything else is automatic. Audit what it does: `scripts/install.sh`.

Manual install

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

18 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`, `index_status`

→ Arguments, examples, and response shapes: Tool reference

How it works

flowchart LR
    Client["MCP ClientClaude Desktop · Claude CodeCursor · Jan · Windsurf · ..."]

    subgraph OB ["obsidian-brain (Node process)"]
        direction TB
        SQL["SQLite indexnodes · edgesFTS5 · vec0 embeddings"]
        Vault["Vault on diskyour .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 v1.7.x pairs with plugin v1.7.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` (your client still shows the previous release after a publish) — 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

• v1.7.24 (2026-05-16) — embeddings.md BYOM callout + 5 devDep bumps
• v1.7.23 (2026-05-16) — BYOM Ollama auto-pull gate + logger sweep + SIGTERM unit test
• v1.7.22 (2026-05-15) — structured stderr (NDJSON) + Ollama preparing-state + dependabot security bumps + SIGTERM drain integration test
• v1.7.21 (2026-04-27) — install.sh vault-picker fix + auto `ollama pull` + docs/test polish
• v1.7.20 (2026-04-27) — Ollama prefix-lookup bug + 13 audit polish items

→ 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).

Related projects

• `apple-notes-brain` — sibling

MCP server for Apple Notes on macOS: read, write, and search with full

Markdown round-trip in both directions.

License

Apache License 2.0 — Copyright 2026 sweir1.