Obsidian RAG Assistant

A local-first retrieval system that semantically searches an Obsidian Markdown vault from the command line or through read-only MCP tools for Claude.

Features

• Recursively scans Markdown notes while ignoring .obsidian, .git, .trash, and hidden folders.

• Parses headings, YAML front matter, tags, and Obsidian wiki-links.

• Uses heading-aware structural chunking with an 800-character body limit and paragraph boundaries.

• Generates local 384-dimensional embeddings with Ollama and all-minilm:22m.

• Stores text, vectors, and source metadata in persistent local ChromaDB.

• Performs dense semantic vector search with file and heading citations.

• Incrementally synchronizes new, changed, and deleted notes without creating duplicates.

• Exposes read-only search_notes, read_note, and vault_status MCP tools.

Current retrieval is dense semantic search only. BM25, hybrid search, overlap, semantic chunking, and reranking are not implemented yet.

Related MCP server: obsidian_mcp

Architecture

flowchart LR
    subgraph Indexing
        A[Obsidian vault] --> B[Recursive scanner]
        B --> C[Markdown parser]
        C --> D[Heading-aware chunks]
        D --> E[Ollama MiniLM embeddings]
        E --> F[(Persistent ChromaDB)]
    end

    subgraph Retrieval
        G[Natural-language question] --> H[Query embedding]
        H --> I[Vector similarity search]
        F --> I
        I --> J[Top-k cited passages]
    end

    subgraph Generation
        J --> K[MCP]
        K --> L[Claude]
    end

MCP does not perform RAG. It exposes the already-working retrieval functions to Claude, which uses the returned evidence to generate an answer.

Requirements

• Python 3.11 or newer

• uv

• Ollama

• The all-minilm:22m Ollama model

Quick start

git clone https://github.com/Amanaakash/Obsidian-RAG-with-Claude-mcp.git
cd Obsidian-RAG-with-Claude-mcp
uv sync --locked
ollama pull all-minilm:22m

Ollama normally starts with its desktop application. If it is not running, start it with ollama serve. Do not start a second server if port 11434 is already in use.

Index and search the included sample notes:

uv run obsidian-rag index --vault sample_vault
uv run obsidian-rag search "What is reciprocal rank fusion?"

Every result includes its relative source path, heading hierarchy, vector distance, and retrieved text. Distance is a relative ranking signal, not a confidence percentage.

Use a real Obsidian vault

Choose a separate database directory for each vault:

uv run obsidian-rag index --vault "/absolute/path/to/ObsidianVault" --db ".rag_data/my_vault"
uv run obsidian-rag search "How do I evaluate retrieval quality?" --db ".rag_data/my_vault"

Re-run index after changing the vault. Unchanged notes are skipped, changed notes are replaced, new notes are added, and deleted notes are removed from the index.

Changing the embedding model changes the vector dimensions and semantic space. Use a new database directory or rebuild the existing generated index after switching models.

Claude through MCP

The MCP server reads configuration exclusively from environment variables:

Claude Desktop

Merge an obsidian-rag entry into Claude Desktop's MCP configuration. Keep any existing server entries.

{
  "mcpServers": {
    "obsidian-rag": {
      "command": "uv",
      "args": [
        "--directory",
        "/absolute/path/to/Obsidian-RAG-with-Claude-mcp",
        "run",
        "obsidian-rag-mcp"
      ],
      "env": {
        "OBSIDIAN_RAG_VAULT": "/absolute/path/to/ObsidianVault",
        "OBSIDIAN_RAG_DB": "/absolute/path/to/Obsidian-RAG-with-Claude-mcp/.rag_data/my_vault",
        "OBSIDIAN_RAG_MODEL": "all-minilm:22m",
        "OBSIDIAN_RAG_COLLECTION": "obsidian_notes"
      }
    }
  }
}

On Windows, Claude Desktop stores this file at %APPDATA%\Claude\claude_desktop_config.json. Completely quit and reopen Claude Desktop after changing it.

Claude Code

Register the same stdio server in user scope:

claude mcp add --scope user obsidian-rag -e "OBSIDIAN_RAG_VAULT=/absolute/path/to/ObsidianVault" -e "OBSIDIAN_RAG_DB=/absolute/path/to/Obsidian-RAG-with-Claude-mcp/.rag_data/my_vault" -e "OBSIDIAN_RAG_MODEL=all-minilm:22m" -e "OBSIDIAN_RAG_COLLECTION=obsidian_notes" -- uv --directory /absolute/path/to/Obsidian-RAG-with-Claude-mcp run obsidian-rag-mcp

Each MCP process starts a non-blocking incremental refresh. A cross-process file lock prevents Claude Desktop and Claude Code from writing to Chroma at the same time.

Privacy and safety

• Vault scanning, embeddings, and Chroma storage run locally.

• The MCP server is read-only and cannot create, edit, or delete notes.

• read_note rejects absolute paths, traversal, hidden directories, non-Markdown files, and symlink escapes.

• Passages returned by search_notes or read_note are sent to Claude when Claude invokes those tools.

• Do not commit .env, .mcp.json, real vault notes, or .rag_data indexes.

• Review third-party MCP server permissions before granting access to a private vault.

Limitations

• Dense semantic retrieval only; no BM25, hybrid fusion, or reranker.

• Chunk limits are character-based rather than tokenizer-based.

• No chunk overlap is currently used.

• Heading-aware structural chunking is not LLM-based semantic chunking.

• Tags and links are stored as metadata but do not affect ranking.

• Only Markdown is indexed; PDFs, images, Canvas files, and attachments are ignored.

• Retrieval distance is not a calibrated relevance or correctness probability.

Development

uv sync --locked --all-groups
uv run pytest -q
uv build
uv run obsidian-rag --help

Automated tests use fake embedders and do not require Ollama, Claude, or a real vault. See CONTRIBUTING.md before opening a pull request.

Security and license

Report security issues privately as described in SECURITY.md. This project is available under the MIT License.