graph-query-mcp
Surgical queries against an Obsidian / vault knowledge graph. Loads a graph.json (NetworkX node-link format) once at startup and answers targeted questions without making Claude read a 50K-line graph report.
Designed to pair with graphify (the graph-building skill in ai-brain-starter), but the server accepts any graph in NetworkX node-link JSON. Supports up to two scopes (primary + secondary, e.g. personal + team).
Why use this
If you've already run graphify on a vault, you've got a graph.json and a GRAPH_REPORT.md. Reading the full report into Claude burns thousands of tokens for every question. This MCP loads the graph once at startup, answers in <50ms, and never spills the whole graph into context.
| Tool | What it does |
|---|
search_nodes(query, scope, limit) | Fuzzy match against node names. Returns node IDs ranked by exact / starts-with / contains. |
get_neighbors(node_id, scope, max_hops, limit) | Connected nodes within N hops, sorted by degree. |
find_path(source, target, scope) | Shortest path between two concepts. Auto-fuzzy-matches both ends. |
get_top_nodes(scope, n) | Highest-degree nodes (the "god nodes"). |
query_subgraph(concepts, scope, max_hops, limit) | Subgraph around a list of concepts; reports node + edge counts. |
get_node_info(node_id, scope) | Full metadata + top neighbors for one node. |
get_community_members(node_id, scope, limit) | All nodes in the same community-detection cluster. |
Scope defaults to personal; pass scope="onde" (or whatever secondary scope name you've configured) for the second graph.
Configuration
Two env vars, both optional:
| Env var | Default | Use for |
|---|
GRAPH_JSON_PATH | ~/Documents/Vault/Meta/graphify-out/graph.json | Primary graph (the personal scope) |
SECONDARY_GRAPH_JSON_PATH | ~/Documents/Vault/Team/Meta/graphify-out/graph.json | Secondary graph (the onde scope, historical name) |
ONDE_GRAPH_JSON_PATH is also accepted as a backward-compat alias for SECONDARY_GRAPH_JSON_PATH.
If a path doesn't exist at startup, the server logs a warning and the tools return a friendly error when that scope is queried. The server still starts — a missing secondary graph never blocks the primary.
Install
Open Claude Code, paste:
/plugin marketplace add adelaidasofia/graph-query-mcp
/plugin install graph-query-mcp@graph-query-mcp
Legacy install
git clone https://github.com/adelaidasofia/graph-query-mcp.git ~/.claude/graph-query-mcp
cd ~/.claude/graph-query-mcp
pip3 install --break-system-packages -r requirements.txt
Register in your project .mcp.json:
{
"mcpServers": {
"graph-query": {
"type": "stdio",
"command": "fastmcp",
"args": ["run", "/Users/YOU/.claude/graph-query-mcp/server.py"],
"env": {
"GRAPH_JSON_PATH": "/path/to/your/vault/Meta/graphify-out/graph.json"
}
}
}
}
Restart Claude Code, then claude mcp list should show graph-query connected.
Generating the graph
This MCP doesn't build the graph; it queries one. Use graphify (a skill in ai-brain-starter) to produce a graph.json from your vault, or any other NetworkX-compatible builder. The expected format is the output of networkx.node_link_data(G).
Verification
python3 tests/integration/test_smoke.py
Architecture
FastMCP, stdio transport, Python 3.10+. Graphs are loaded once at startup and cached in memory. No daemons, no listeners, no external services. NetworkX in-memory for query primitives.
Same author, same architecture pattern (FastMCP, draft+confirm on writes where applicable, vault auto-export, MIT):
Telemetry
This plugin sends a single anonymous install signal to myceliumai.co the first time it loads in a Claude Code session on a given machine.
What is sent:
- Plugin name (e.g.
slack-mcp)
- Plugin version (e.g.
0.1.0)
What is NOT sent:
- No user identifiers, names, emails, tokens, or API keys
- No file paths, message content, or anything from your work
- No IP address is stored after dedup processing
Why: Helps the maintainer know which plugins people actually install, so attention goes to the ones that get used.
Opt out: Set the environment variable MYCELIUM_NO_PING=1 before launching Claude Code. The hook will skip the network call entirely. Already-pinged installs leave a sentinel at ~/.mycelium/onboarded-<plugin> — delete it if you want to reset state.
License
MIT. See LICENSE.