Cxg Census Mcp

Name: Cxg Census Mcp
Author: MaxMLang

by MaxMLangcommunityv0.1.2

An MCP server that lets LLM agents query the CZ CELLxGENE Discover Census single-cell atlas with ontology-aware filtering, cost limits, and provenance/attribution on responses. It supports use in MCP clients like Cursor, Claude Desktop, and Claude Code for natural-language questions about cell composition and gene expression.

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

GitHub Repository Website

Install & configure

Prerequisites

required
Install uv/uvx
Install Astral's uv so you can run the recommended PyPI-based MCP server via uvx.
https://docs.astral.sh/uv/
required
Install the package from PyPI with census support
Install the MCP server package with the optional [census] extra for real Census access. Without the extra, the server runs in mock mode.
```
$ uv tool install "cxg-census-mcp[census]"
```
https://pypi.org/project/cxg-census-mcp/

Install in your client

Paste into the AI you're chatting with — it will figure out the rest

Please install the `cxg-census-mcp` MCP server into my current AI client (that's you).

Required prerequisites (do these first if not already done):
- **Install uv/uvx** — Install Astral's uv so you can run the recommended PyPI-based MCP server via uvx. (https://docs.astral.sh/uv/)
- **Install the package from PyPI with census support** — Install the MCP server package with the optional [census] extra for real Census access. Without the extra, the server runs in mock mode. Run: `uv tool install "cxg-census-mcp[census]"` (https://pypi.org/project/cxg-census-mcp/)

Canonical MCP server config (stdio transport):
- command: `<absolute-path-to-uvx>`
- args: ["--from","cxg-census-mcp[census]","cxg-census-mcp"]
- optional environment variables:
  - `CXG_CENSUS_MCP_CENSUS_VERSION`: Census release to pin. (example: `<census-version>`)
  - `CXG_CENSUS_MCP_CACHE_DIR`: Disk cache root directory. (example: `<your-cache-directory>`)
  - `CXG_CENSUS_MCP_MOCK_MODE`: If set to 1, never opens a real Census handle and uses mock mode. (example: `<0-or-1>`)
  - `CXG_CENSUS_MCP_LOG_LEVEL`: Python stdlib log level. (example: `<log-level>`)

Note: Recommended portable config uses uvx with an absolute path because MCP clients may not inherit your shell PATH. The server speaks MCP over stdio. No API key is required. Installing without the [census] extra yields mock mode instead of real Census access.

Add this MCP server to my current client's config in the correct format for you. If you need secrets or credentials I haven't provided, ASK me — do not invent values or leave raw placeholders. After adding it, tell me how to verify the server is connected.

Note: Recommended portable config uses uvx with an absolute path because MCP clients may not inherit your shell PATH. The server speaks MCP over stdio. No API key is required. Installing without the [census] extra yields mock mode instead of real Census access.

Tools (13)

census_summary

Summarize the Census and available data context

get_census_versions

List or retrieve available Census versions

count_cells

Count cells matching a filter or query

list_datasets

List datasets matching criteria

gene_coverage

Check gene coverage in the Census

aggregate_expression

Aggregate gene expression over a query

preview_obs

Preview observation rows for a query

export_snippet

Export a data snippet for a query

get_server_limits

Return server limits and constraints

resolve_term

Resolve a free-text term to ontology concepts

expand_term

Expand an ontology term to related concepts

term_definition

Get the definition of a term

list_available_values

List available values for a field

Environment variables

CXG_CENSUS_MCP_CENSUS_VERSIONPins the Census release to use

CXG_CENSUS_MCP_CACHE_DIRRoot directory for disk cache

CXG_CENSUS_MCP_MOCK_MODEIf set to 1, runs without opening a real Census handle

CXG_CENSUS_MCP_LOG_LEVELStdlib log level for server logging

Packages

cxg-census-mcp

pypiv0.1.2transport: stdio

Details

Language: Python
License: NOASSERTION
Released: Apr 22, 2026
Last commit: Jul 6, 2026
Registry name: io.github.MaxMLang/cxg-census-mcp

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