Building a Local Obsidian RAG with DuckDB and MotherDuck

ArticleSimon SpätiTutorial

Simon Späti details an architecture for exploring personal Obsidian vaults using vector search and graph backlinks. The system runs locally using DuckDB and syncs to MotherDuck, serving search queries directly in the browser via WebAssembly.

Key points

  1. Local-first vector search powered by DuckDB's Vector Similarity Search (VSS) extension with an HNSW index.
  2. Markdown-aware chunking (approx. 512 characters) prepends note titles and section headings as semantic anchors while indexing Wikilinks up to two hops away.
  3. Support for all-MiniLM-L6-v2 (384 dimensions) for rapid testing and BAAI/bge-m3 (1024 dimensions) for production retrieval.
  4. A Next.js front end connects to MotherDuck directly in the client using the DuckDB-WASM driver, removing the need for a custom database backend.
  5. A dedicated FastAPI service hosted on Railway serves the BGE-M3 embedding model to circumvent Hugging Face API rate limits and timeouts.
  6. Retrieval-only design: The setup surfaces relevant notes, snippets, and hidden connections without piping output through a generative LLM.

Why it matters

Users with sensitive knowledge bases often avoid uploading raw notes to hosted AI platforms. This implementation illustrates how data engineering tooling, local vector storage, and in-browser WASM engines can provide private, cost-effective RAG capabilities over personal Markdown archives.

Analysis

By focusing strictly on the retrieval phase rather than text generation, the setup avoids LLM hallucinations while surfacing forgotten or non-obvious cross-links across thousands of notes. Architecturally, pairing DuckDB for local ingestion with MotherDuck and DuckDB-WASM for client-side querying demonstrates a highly efficient, serverless design for personal knowledge graphs.

Summary generated by AI (Gemini 3.8 Flash, 27 September 2026). It may contain errors – the original source is authoritative.

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