STRING Database MCP Server

Official STRING Database MCP Server

Exposes STRING database functionality as a Model Context Protocol (MCP) server.

This implementation allows AI agents and other MCP-compatible clients to access STRING data through a structured and self-describing interface.

It is built on top of the STRING API but adapted specifically for model-based use, with emphasis on conciseness and context efficiency. The server controls the amount and type of data so that responses stay within the reasoning limits of large language models. It also adapts the structure and adds metadata to support more consistent parsing and interpretation by agentic systems.

The server is also available as a hosted remote MCP endpoint at https://mcp.string-db.org.

For a live demonstration of MCP capabilities, see STRING Chat.

For reproducible workflows and large-scale integration, use the STRING API.

For agentic workflows, use the optional agent skill at skills/string-database/SKILL.md.

Features

• Resolve protein identifiers to STRING metadata
• Retrieve interaction networks
• Cluster and visualize 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 function or disease (GO, KEGG, Reactome, DISEASES etc.)

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Requirements

• Python ≥ 3.11 (with Python 3.10, optional parameter descriptions are misplaced in the tool schemas)
• Dependencies (see requirements.txt):
  • fastmcp==2.14.7
  • mcp==1.29.0
  • httpx>=0.28,<0.29
  • pydantic>=2.11,<3.0

Note: If the server crashes on startup, it is 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 https://github.com/meringlab/string-mcp.git
cd string-mcp
pip install -r requirements.txt

Running

python server.py

To serve over standard input/output instead of HTTP, for example when a local MCP client starts the server itself:

python server.py --stdio

The stdio mode also reads config/server.config for the STRING API endpoint.

Testing

curl -v -H "Accept: text/event-stream" http://localhost:[port]/mcp

You should see a 200 OK response with content-type: text/event-stream.

Note: HTTP requests sent with default headers will trigger anyio.ClosedResourceError and 406 Not Acceptable. This is expected behavior for the MCP streaming protocol and does not indicate a problem.

Docker

1. Ensure you have a config/server.config file (copy from config/server.config.example if needed):

   cp config/server.config.example config/server.config
   

2. Build the image:

   docker build -t string-mcp .
   

3. Run the container:

   Linux/macOS:

   docker run -p 57416:57416 -v $(pwd)/config:/app/config:ro string-mcp
   

   Windows PowerShell:

   docker run -p 57416:57416 -v ${PWD}/config:/app/config:ro string-mcp
   

   Windows Command Prompt:

   docker run -p 57416:57416 -v %cd%/config:/app/config:ro string-mcp
   

   To run in detached mode:

   # Linux/macOS
   docker run -d -p 57416:57416 -v $(pwd)/config:/app/config:ro --name string-mcp-server string-mcp
   
   # Windows PowerShell
   docker run -d -p 57416:57416 -v ${PWD}/config:/app/config:ro --name string-mcp-server string-mcp
   

   The -v flag mounts your local config directory so you can customize settings without rebuilding the image.

   Note: If you don't need to modify the config, you can omit the volume mount and the container will use the default config from the image.

4. Stop the container (if running in detached mode):

   docker stop string-mcp-server
   docker rm string-mcp-server
   

Note: The Docker container will use the configuration from config/server.config. If this file doesn't exist, the container will copy from server.config.example on first run.

Frozen STRING releases are available under versioned paths: /12.0/ (STRING v12.0) and /12.5/ (STRING v12.5).

License / Citation

The STRING MCP server source code is released under the MIT License.
Associated data and outputs are released under the CC BY 4.0 License.
You are free to use, share, and modify the code with proper attribution.

If you use this code or data in your work, please also cite the latest STRING manuscript.