MCP server for the CZ CELLxGENE Census. Single-cell, ontology-aware. Community, unaffiliated.
Config is the same across clients — only the file and path differ.
{
"mcpServers": {
"io-github-maxmlang-cxg-census-mcp": {
"command": "<see-readme>",
"args": []
}
}
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MCP server for the CZ CELLxGENE Census. Single-cell, ontology-aware. Community, unaffiliated.
No automated test available for this server. Check the GitHub README for setup instructions.
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An MCP server that lets LLM agents query the CZ CELLxGENE Discover Census single-cell atlas without lying about it — ontology-aware filters, cost caps, full provenance + attribution on every response. Drop it into Cursor / Claude Desktop / Claude Code and ask questions like "compare immune cell composition of healthy vs COVID-19 human lung" in plain English.
Independent / unaffiliated. Not affiliated with, endorsed by, or sponsored by the Chan Zuckerberg Initiative (CZI), EMBL-EBI, the U.S. Census Bureau, or anyone else. "CELLxGENE" is a CZI mark; references here are descriptive (nominative) use only.
No warranty. MIT-licensed source, "as is". Research/exploration tool — not a clinical or diagnostic instrument. Always verify results before publication. See LICENSE for the full trademark and content attribution notice, and SECURITY.md for the threat model and known-issues policy.
Alpha (v0.1.2).
CHANGELOG.md
Healthy vs COVID-19 lung, side-by-side. Two parallel queries, the
disease_multi_value_v7 schema-drift rewrite kicks in for the COVID
cohort, attribution from both contributing dataset sets surfaces in the
same chat turn.
https://github.com/user-attachments/assets/c836f225-5075-4643-87aa-70d311bc5fd2
Cell-type composition of human lung in one query. Free-text "lung"
resolved to UBERON:0002048, routed through tissue_general, every CURIE
labeled, all in a single Tier-0 call.
https://github.com/user-attachments/assets/b0e10ca7-e46b-4e5f-ae63-11949d328c4d
(Videos render on GitHub. On PyPI they appear as bare URLs — head to the GitHub README to watch.)
More prompts in docs/example-questions.md.
┌──────────────────────────────────────────────┐
MCP client │ tools/ thin MCP wrappers, no logic │
(Claude, ─► │ │ │
Cursor, │ ▼ │
Code, …) │ planner/ FilterSpec → QueryPlan, │
│ │
... [View full README on GitHub](https://github.com/MaxMLang/cxg-census-mcp#readme)