graphthulhu

Knowledge graph MCP server for Logseq and Obsidian. 37 tools for reading, writing, searching, and analyzing your second brain.

MCP server that gives you full access to a Logseq or Obsidian knowledge graph. 37 tools across 9 categories: navigate, search, analyze, write, decisions, journals, flashcards, whiteboards, and health.

Install

Download the binary for your platform from GitHub Releases and put it on your PATH.

Or: go install github.com/skridlevsky/graphthulhu@latest

Configure

Obsidian

Add to your MCP settings:

json

{
  "mcpServers": {
    "graphthulhu": {
      "command": "graphthulhu",
      "args": ["--backend", "obsidian", "--vault", "/path/to/your/vault"]
    }
  }
}

No plugins required. Reads .md files directly. Full read-write support.

Logseq

Enable the HTTP API server in Logseq (Settings > Features > HTTP APIs server), start it, and create a token.

json

{
  "mcpServers": {
    "graphthulhu": {
      "command": "graphthulhu",
      "env": {
        "LOGSEQ_API_URL": "http://127.0.0.1:12315",
        "LOGSEQ_API_TOKEN": "your-token-here"
      }
    }
  }
}

What you can do

• Navigate — get pages with full block trees, traverse the link graph, list pages by namespace/tag/property
• Search — full-text search with context, property queries, tag hierarchy search, raw Datalog (Logseq)
• Analyze — graph overview, find connections between pages, detect knowledge gaps and orphans, discover topic clusters
• Write — create pages, append/upsert blocks with nested children, update/delete/move blocks, link pages bidirectionally, rename pages with link updates, bulk update properties
• Decisions — create decisions with deadlines, check status, resolve or defer with tracking
• Journals — read entries by date range, search within journals
• Flashcards — SRS stats, due cards, create new cards (Logseq)
• Whiteboards — list and inspect spatial canvases (Logseq)

Links

• GitHub
• Full tool reference