Cxg Census Mcp
Query CZ CELLxGENE Census single-cell datasets and ontology metadata from your coding agent without hand-writing Census API calls.
Overview
cxg-census-mcp is an MCP server for the Idea phase that lets your agent query the CZ CELLxGENE Census with ontology-aware single-cell data access.
What is this MCP server?
- stdio MCP server installable via uvx from PyPI package cxg-census-mcp[census]
- Connects agents to CZ CELLxGENE Census for ontology-aware single-cell queries
- Community-maintained, unaffiliated with Chan Zuckerberg Initiative
- Version 0.1.2 with positional runtime argument cxg-census-mcp
- MCP integration for genomics research workflows, not a bundled analysis notebook
- Server version 0.1.2 on PyPI package cxg-census-mcp
- Transport: stdio
- Runtime hint: uvx with --from cxg-census-mcp[census]
What problem does it solve?
You need census-backed single-cell answers in the agent loop but do not want to manually navigate CELLxGENE APIs and ontologies every time.
Who is it for?
Indie bioinformatics or health-AI builders validating cell-type or expression questions against the public CELLxGENE Census from an MCP-capable agent.
Skip if: Builders with no genomics use case, or teams that need regulated clinical pipelines without a separate validation layer.
What do I get? / Deliverables
Your agent can pull ontology-aware Census context during research so downstream plans and prototypes align with real reference data.
- Registered stdio MCP server entry pointing at cxg-census-mcp via uvx
- Agent-callable access to CZ CELLxGENE Census-backed research queries
- Reusable census query workflow during idea and validation research
Recommended MCP Servers
Journey fit
Researchers and bioinformatics builders discover and validate hypotheses against reference single-cell atlases before committing to pipelines or product features. Research subphase is where external reference data and ontology-aware exploration happen prior to prototype or backend implementation.
How it compares
MCP integration to CELLxGENE Census, not a standalone scRNA-seq analysis skill or notebook product.
Common Questions / FAQ
Who is Cxg Census Mcp for?
Developers and researchers building agent-assisted genomics workflows who already use MCP clients such as Claude Code or Cursor.
When should I use Cxg Census Mcp?
Use it in the research phase when you need ontology-aware single-cell census queries while scoping a bioinformatics feature or dataset-backed prototype.
How do I add Cxg Census Mcp to my agent?
Register the stdio server in your MCP config with uvx, --from Cxg Census Mcp[census], and the positional command Cxg Census Mcp per the published server manifest.