io.github.MaxMLang/cxg-census-mcp

Official

by MaxMLang · Python

cxg-census-mcp

MCP server for the CZ CELLxGENE Census. Single-cell, ontology-aware. Community, unaffiliated.

Query single-cell genomics data from CZ CELLxGENE Census.

Topics

agentsai-agentsbioinformaticscellxgenecellxgene-censuscomputational-biologymcpmodel-context-protocolsingle-cellsingle-cell-rna-seqpython

README.md12 KBView on GitHub

cxg-census-mcp

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 "Visualize the cell-type composition of the 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

Demos

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.

Architecture at a glance

code

                 ┌──────────────────────────────────────────────┐
   MCP client    │   tools/        thin MCP wrappers, no logic  │
   (Claude,  ─►  │     │                                        │
    Cursor,      │     ▼                                        │
    Code, …)     │   planner/      FilterSpec → QueryPlan,      │
                 │     │           cost estimate, tier routing  │
                 │     ▼                                        │
                 │   ontology/     OLS4 + hint overlay,         │
                 │     │           CL/UBERON/MONDO expansion    │
                 │     ▼                                        │
                 │   execution/    Tier 0  facet counts         │
                 │     │           Tier 1  chunked obs scan     │
                 │     │           Tier 2  expression aggregate │
                 │     │           Tier 9  refuse → snippet     │
                 │     ▼                                        │
                 │   clients/      OLS4 (HTTPS) + Census/SOMA   │
                 │                                              │
                 │   caches/       OLS, facet, plan, filter LRU │
                 │   models/       Response envelope w/         │
                 │                 attribution + provenance     │
                 └──────────────────────────────────────────────┘
                                    │
                                    ▼
                       ┌────────────────────────┐
                       │ EBI OLS4 (ontology)    │
                       │ CZ CELLxGENE Census    │
                       │ (CC BY 4.0 data)       │
                       └────────────────────────┘

Full architecture notes: docs/architecture.md. Tool reference: docs/tool-reference.md. Example questions: docs/example-questions.md.

Install

From PyPI (recommended):

bash

uv tool install "cxg-census-mcp[census]"
cxg-census-mcp                       # speaks MCP over stdio

Or with pip:

bash

pip install "cxg-census-mcp[census]"

Without the [census] extra you get mock mode (deterministic fixtures) — handy for offline demos and verifying your MCP client config without pulling tiledbsoma's ~1 GB of native deps.

From source (for development):

bash

git clone https://github.com/MaxMLang/cxg-census-mcp
cd cxg-census-mcp
uv sync --extra dev --extra census
uv run cxg-census-mcp

MCP client config

Cursor (~/.cursor/mcp.json) and Claude Desktop (~/Library/Application Support/Claude/claude_desktop_config.json on macOS) both expect the same shape. Cleanest is uvx once installed from PyPI:

json

{
  "mcpServers": {
    "cxg-census": {
      "command": "/absolute/path/to/uvx",
      "args": ["--from", "cxg-census-mcp[census]", "cxg-census-mcp"]
    }
  }
}

Use the absolute path to uvx (which uvx from your shell). MCP clients spawn the server in a non-interactive subprocess that doesn't source your shell rc, so a bare "uvx" will fail with No such file or directory.

If you cloned from source instead, point at the checkout:

json

{
  "mcpServers": {
    "cxg-census": {
      "command": "/absolute/path/to/uv",
      "args": ["--directory", "/path/to/cxg-census-mcp", "run", "cxg-census-mcp"]
    }
  }
}

Claude Code:

bash

claude mcp add cxg-census -- /absolute/path/to/uvx --from "cxg-census-mcp[census]" cxg-census-mcp

Quit + relaunch your client (⌘Q on macOS — closing the window isn't enough) and the server should show up in the MCP panel with 13 tools.

Tools (13 total)

Workflow: census_summary, get_census_versions, count_cells, list_datasets, gene_coverage, aggregate_expression, preview_obs, export_snippet, get_server_limits.

Inspection: resolve_term, expand_term, term_definition, list_available_values.

Plus MCP resources (markdown docs at cxg-census-mcp://docs/{slug}), prompts (census_workflow, disambiguation), and cooperative progress / cancellation notifications. Details in docs/tool-reference.md.

Configuration

All env vars use the CXG_CENSUS_MCP_ prefix. Most useful:

Variable	Default	Purpose
`CXG_CENSUS_MCP_CENSUS_VERSION`	`stable`	Census release to pin
`CXG_CENSUS_MCP_CACHE_DIR`	platformdirs default	Disk cache root
`CXG_CENSUS_MCP_MOCK_MODE`	`0`	If `1`, never opens a real Census handle
`CXG_CENSUS_MCP_LOG_LEVEL`	`WARNING`	stdlib log level

Full list and validation: src/cxg_census_mcp/config.py.

Development & operations

Quick loop:

bash

make install-all                 # uv sync --extra dev --extra census
make lint typecheck test         # ruff + mypy + pytest (mock mode)
make cov                         # tests + coverage HTML in ./htmlcov
make audit                       # pip-audit on locked production deps

Operational tasks (cache pre-warm, schema diff, container build, metrics dump, plan-cache vacuum, weekly hint/facet refresh) live in the Makefile and are documented in docs/operational-playbook.md.

Documentation index

Topic	Where
System architecture	`docs/architecture.md`
Tool reference	`docs/tool-reference.md`
Example agent questions	`docs/example-questions.md`
Ontology resolution	`docs/ontology-resolution.md`
Schema-drift handling	`docs/schema-drift-format.md`
Census version pinning	`docs/version-pinning.md`
Progress / cancellation	`docs/progress-and-cancellation.md`
Error model	`docs/error-model.md`
Known limitations	`docs/limitations.md`
Ops runbook	`docs/operational-playbook.md`
Changelog	`CHANGELOG.md`

License & attribution

Source code: MIT. The MIT license covers only the code in this repository, not the upstream data, ontologies, or third-party trademarks.

Data. Tool responses are derived (filtered/aggregated) from the CZ CELLxGENE Discover Census, distributed by the Chan Zuckerberg Initiative under CC BY 4.0. Every response carries an attribution field; downstream users must preserve attribution and indicate that changes were made.
Ontologies are fetched via EBI Ontology Lookup Service (OLS4) from CL, UBERON, MONDO, EFO, HANCESTRO, and others; each carries its own license.
Trademarks ("CELLxGENE", "Cursor", "Claude", "Anthropic", "Model Context Protocol", …) belong to their respective owners. Use here is descriptive only and does not imply affiliation.

This project is a client of the CZ CELLxGENE Discover Census; it does not host, mirror, or redistribute Census data.

Full notice in LICENSE.

Install

Configuration

Arguments

--fromdefault cxg-census-mcp[census]

claude_desktop_config.json

{
  "mcpServers": {
    "cxg-census-mcp": {
      "command": "uvx",
      "args": [
        "cxg-census-mcp"
      ]
    }
  }
}