STRING MCP Server

Exposes STRING database functionality as an MCP (Model Context Protocol) server.
This server wraps STRING API endpoints and makes them available as MCP tools for use with AI agents or other MCP-compatible clients.

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Features

• Resolve protein identifiers to STRING metadata
• Retrieve interaction networks
• Perform homology lookups across species
• Access evidence links for protein–protein interactions
• Run functional enrichment analysis (including enrichment plots)
• Get curated functional annotations for proteins
• Query proteins by functional terms (GO, KEGG, Reactome, etc.)

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Requirements

• Python ≥ 3.10
• Dependencies (see requirements.txt):
  • fastmcp==2.10.6
  • httpx==0.28.1
  • pydantic==2.11.7

Note: If the server crashes on startup, it’s very likely due to an incompatible FastMCP version.

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Configuration

The server reads settings from config/server.config (JSON). Example:

{
  "base_url": "https://string-db.org",
  "server_port": 57416,
  "verbosity": "low"
}

Installation

git clone [email protected]:meringlab/string-mcp.git
cd string-mcp
pip install -r requirements.txt

Running

python server.py

License / Citation

The STRING MCP server is released under the CC-BY-4.0 license.
You are free to share and adapt the code with attribution. If you use this code in your work, please also cite the latest STRING manuscript.