Obsidian Semantic Search MCP

Your Obsidian vault is useful only if your agent can find the right note.

Keyword search misses context. Full write-capable Obsidian MCP servers expose more power than a retrieval agent needs. Obsidian plugins are great inside Obsidian, but they are not always the right boundary for Codex, Claude Desktop, Cursor, or any other MCP client.

This project is the narrow version:

local Obsidian vault -> read-only scanner -> local SQLite index -> MCP search/read tools

No note writes. No cloud embeddings. No Obsidian plugin runtime. No sync service.

Status: 0.2.1 early preview. The server is usable today, but ranking behavior and tool schemas may change before 1.0.

What You Get

Example result shape:

{
  "path": "02_Projects/RealtimeAPI/05_Interview_QA.md",
  "title": "Interview Q&A",
  "score": 0.7431,
  "matched_sections": [
    {
      "heading": "Level 4 > Redis Lua atomicity",
      "lines": [266, 305],
      "reason": "semantic=1, keyword=0.5565, metadata=0.6"
    }
  ]
}

Related MCP server: second-brain-mcp

Quick Start

Requirements:

• Node.js >= 24

• Ollama

• An Obsidian vault

• An MCP client such as Codex, Claude Desktop, Cursor, or another stdio MCP client

Install the embedding model:

ollama pull bge-m3
curl http://localhost:11434/api/tags

Print setup guidance:

npx -y --package @dalecb/obsidian-semantic-mcp obsidian-semantic-mcp-setup

Codex Setup

Add this to ~/.codex/config.toml:

[mcp_servers.obsidian_semantic]
command = "npx"
args = ["-y", "@dalecb/obsidian-semantic-mcp"]

[mcp_servers.obsidian_semantic.env]
OBSIDIAN_VAULT_ROOT = "/path/to/your/Obsidian Vault"
OBSIDIAN_SEMANTIC_MCP_HOME = "/Users/you/.obsidian-semantic-mcp"
OBSIDIAN_EMBED_MODEL = "bge-m3"
OBSIDIAN_SEMANTIC_STARTUP_INDEX = "false"

Restart Codex, then run:

obsidian_semantic.index_status
obsidian_semantic.index_vault { "mode": "incremental" }
obsidian_semantic.search_notes { "query": "Redis Lua atomicity", "limit": 5 }

JSON MCP Clients

Claude Desktop, Cursor, and other JSON-style MCP clients can use:

{
  "mcpServers": {
    "obsidian_semantic": {
      "command": "npx",
      "args": ["-y", "@dalecb/obsidian-semantic-mcp"],
      "env": {
        "OBSIDIAN_VAULT_ROOT": "/path/to/your/Obsidian Vault",
        "OBSIDIAN_SEMANTIC_MCP_HOME": "/Users/you/.obsidian-semantic-mcp",
        "OBSIDIAN_EMBED_MODEL": "bge-m3",
        "OBSIDIAN_SEMANTIC_STARTUP_INDEX": "false"
      }
    }
  }
}

Why This Exists

This isn't aiming to be the most powerful Obsidian automation server. It aims to be the safest retrieval tool you can hand an agent.

Here's how it stacks up against the two tools it usually comes down to — a full-permission Obsidian MCP server (Local REST API based) and GBrain (a broader knowledge-compilation platform):

That trade is on purpose: give up writing, editing, and running inside Obsidian, and you get fewer moving parts and a smaller blast radius in return.

Use this if your agent should answer:

• "Which note explains this project decision?"

• "Find the file where I wrote about idempotency payload mismatch."

• "Show me the career notes related to this interview topic."

• "Search my vault, but do not mutate it."

Do not use this if you want an Obsidian UI plugin, automatic note generation, or write-capable vault automation.

Tools

index_status

Returns index metadata and safety settings.

index_vault

Builds or updates the external SQLite index.

{ "mode": "incremental" }

Specific files:

{
  "mode": "incremental",
  "paths": ["02_Projects/My Note.md"]
}

search_notes

Searches notes with hybrid semantic and keyword ranking.

{
  "query": "live coding notes",
  "limit": 8,
  "mode": "hybrid"
}

Modes:

• hybrid: semantic vector + SQLite FTS5 + metadata boosts

• semantic: vector-first search

• keyword: FTS5 keyword search without embedding the query

read_note

Reads a note or line range by vault-relative path.

{
  "path": "02_Projects/My Note.md",
  "start_line": 10,
  "end_line": 40
}

How It Works

index_vault
  -> scan Markdown files under OBSIDIAN_VAULT_ROOT
  -> block denied paths and symlink escapes
  -> split notes by Markdown headings
  -> create one summary chunk per file
  -> embed chunks with Ollama bge-m3
  -> store notes, chunks, FTS rows, and vectors in SQLite

search_notes
  -> embed the query with Ollama
  -> score vector similarity
  -> score SQLite FTS5 keyword matches
  -> apply title/path/heading metadata boosts
  -> regroup chunk matches into file-level results

Default storage:

~/.obsidian-semantic-mcp/
  data/semantic.sqlite
  logs/
  cache/

The vault remains the source of truth. The SQLite database is a derived index and can be deleted/rebuilt.

Safety Model

The server reads your vault and never writes to it. Three layers decide what an agent can see.

1. Always denied (system / tooling). Never indexed, no override:

• .obsidian/, .smart-env/, .claude/, .codex-*/

• any hidden folder (name starts with .)

• node_modules, cache, logs

2. Sensitive — denied by default, unlockable. Stays blocked even when a tool call passes include_sensitive: true, unless the server is started with OBSIDIAN_SEMANTIC_ALLOW_SENSITIVE=true. Defaults to 08_PersonalInfo/. Override the list with OBSIDIAN_SEMANTIC_SENSITIVE_PATHS (comma- or newline-separated folders):

OBSIDIAN_SEMANTIC_SENSITIVE_PATHS = "08_PersonalInfo, 09_Finance"

3. Your own excludes — always denied. Folders you never want indexed, searched, or read. No unlock flag:

OBSIDIAN_SEMANTIC_EXCLUDE = "03_Journal, Private, Clients/Acme"

Which one do you want?

• "Don't index this at all" → OBSIDIAN_SEMANTIC_EXCLUDE

• "Keep it locked, but I can unlock it with a flag when I need to" → OBSIDIAN_SEMANTIC_SENSITIVE_PATHS + OBSIDIAN_SEMANTIC_ALLOW_SENSITIVE

Additional guards:

• All paths are resolved through realpath.

• Path traversal and URL-encoded traversal are blocked.

• Symlinks that escape the vault root are blocked.

Changing these lists only affects new indexing. Already-indexed notes keep their stored state until you reindex. After tightening EXCLUDE or SENSITIVE, run index_vault { "mode": "full" } so search_notes cannot surface stale hits. (read_note always enforces the live config.) You can confirm the active lists with index_status.

The local index stores snippets and embedding vectors. Treat it as a derived copy of your vault. See PRIVACY.md.

Indexing Strategy

The server does not watch your vault in real time.

After editing notes, run:

{ "mode": "incremental" }

This keeps the first public version predictable and avoids background watcher risks. You can opt into startup indexing with:

OBSIDIAN_SEMANTIC_STARTUP_INDEX = "true"

Development

npm test
npm run pack:check

Before publishing:

npm pack --dry-run

Confirm the package does not include data/, *.sqlite, or private vault files.

License

MIT