biomedical-mcp

Biomedical MCP Servers

Building Model Context Protocol servers that give AI agents structured, tested access to biomedical databases. Covers MCP server design, the GDC REST API behind TCGA, tool design for search and retrieval, pagination and caching, and the data-shape traps that make a naive wrapper wrong. Part 1 covers TCGA/GDC, Part 2 adds GEO, and Part 3 aggregates the CIViC, OncoKB and ClinVar biomarker databases.

When to Use This Skill

Activate when the user requests:

• An MCP server exposing TCGA, GDC, GEO, or a variant database to an agent
• Programmatic TCGA data access from Python (not R)
• Tools named like search_cancer_type, get_mutations, get_clinical
• Wrapping a bioinformatics REST API for use by Claude, Cursor, or another agent
• Deciding between TCGAbiolinks (R) and the GDC REST API (Python)
• Pagination, caching, or rate-limit handling for a genomics API
• GEO dataset search, Series Matrix retrieval, or probe-to-gene mapping
• Handling NCBI E-utilities rate limits and API keys
• Aggregating CIViC, OncoKB, or ClinVar for variant clinical significance
• Reconciling variant nomenclature or evidence levels across databases

Inputs

Input	Form	Source
Cancer type / project	TCGA-LUAD, primary site	GDC projects endpoint
Case or sample filter	GDC filter JSON	built by the tool
Gene / variant	symbol, Ensembl ID, genomic change	GDC ssms endpoint
Auth token	file, only for controlled-access data	GDC, most data is open

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Environment

Versions verified 2026-08.

pip install "mcp[cli]"        # 2.0.0 - the official Model Context Protocol SDK
pip install httpx             # HTTP client for the API calls

mcp 2.0.0 is a MAJOR version and the API changed. The server class is
MCPServer, imported from mcp.server. Tutorials and older code use
`from mcp.server.fastmcp import FastMCP`; that path is from the 1.x line.
Verify against the installed version before copying an example.

  1.x:  from mcp.server.fastmcp import FastMCP ; mcp = FastMCP("name")
  2.0:  from mcp.server import MCPServer        ; mcp = MCPServer("name")

The tool decorator and the type-hints-are-the-schema model are the same in
both, so most tool bodies port unchanged; the import and constructor do not.