cxg-census-mcp server

by MaxMLang·io.github.MaxMLang/cxg-census-mcp·v0.1.2

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

A92/100grade A

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Safety scan

A92/100

full report

Adoption

Growing

0 stars19 downloads/wk

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If you have run it, two minutes of your experience saves the next person an afternoon.

cxg-census-mcp tools (13)

write = sends, deletes, buys or posts

Read from the package source without running it. The installed server may list more.

aggregate_expression
Per-gene expression stats by group; caps → export_snippet if over.
census_summary
Pinned Census summary: cells, schema, build date.
count_cells
Count cells (filters + optional group_by); tier 0.
expand_term
Expand a CURIE to descendants/ancestors filtered to Census presence.
export_snippet
Runnable Python for a stored plan; pass call_id from a prior response.
gene_coverage
Report whether a list of Ensembl gene IDs is present in Census var.
get_census_versions
List available Census versions visible to this server.
get_server_limits
Report cap configuration so clients can size their requests.
list_available_values
Distinct values for an obs column (discovery before resolve_term).
list_datasets
List datasets matching a structured filter, sorted by cell count.
preview_obs
Small obs slice + column cardinality (before a big scan).
resolve_term
Resolve text or CURIE to one term; typed refusal if ambiguous.
term_definition
Return label, definition, synonyms, IRI for a CURIE.

Public scan report

scanner v0.1.9 · 2026-09-27 · same rubric, same numbers if you re-run it

no findings

Code scan79 source files scanned25/25
–Live reliabilityno gateway calls yet and no remote to proben/a
–Tool poisoningtools not inspected (local package is not executed); not countedn/a
Auth qualitylocal package, no credentials required12/15
Maintenancelast push 6 days ago15/15
Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10

Overall 92/100. Components that don't apply are left out of the denominator. Any critical finding is an F.Rubric Appeal a finding JSON

How cxg-census-mcp compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score: 92/100; higher than 95% of 48,255 servers
Tools: 13; the typical server has 7
Tools that change things: 0%; typical: 0%. Fewer write tools means less an agent can break
Downloads a week: 19; more than 6% of 12,191 servers with a package

What its tools let an agent do: 13 read

Install cxg-census-mcp in Claude Code, Cursor or VS Code

claude mcp add cxg-census-mcp -- uvx cxg-census-mcp

Add to Cursor

What the publisher says

From the cxg-census-mcp repository's README, as published. We do not edit it. Read it 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 diseasemultivalue_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

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

cxg-census-mcp: common questions

Is cxg-census-mcp server safe?: Yes, by our scan: it is graded A (92/100). Read the cxg-census-mcp safety report
How do I install cxg-census-mcp?: It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does cxg-census-mcp need an API key?: Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is cxg-census-mcp maintained?: The last commit was 43 days ago (2026-09-22). The latest release is v0.1.2.
How does cxg-census-mcp compare with other MCP servers?: safety score 92/100 (higher than 95% of 48,255 servers); tools 13 (the typical server has 7); tools that change things 0% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.