{
  "markdown": "# STRING MCP Server\n\nExposes [STRING database](https://string-db.org) functionality as a **Model Context Protocol (MCP)** server.  \n\nThis implementation allows AI agents and other MCP-compatible clients to access STRING data through a structured and self-describing interface.\n\nIt 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.\n\nThe server is also available as a hosted remote MCP endpoint at [https://mcp.string-db.org](https://mcp.string-db.org).\n\nFor a live demonstration of MCP capabilities, see [STRING Chat](https://string-db.org/cgi/chat).\n\nFor reproducible workflows and large-scale integration, use the [STRING API](https://string-db.org/cgi/help?subpage=api).\n\nFor agentic workflows, use the optional agent skill at [skills/string-database/SKILL.md](skills/string-database/SKILL.md).\n\n## Features\n\n- Resolve protein identifiers to STRING metadata\n- Retrieve interaction networks\n- Cluster and visualize interaction networks\n- Perform homology lookups across species\n- Access evidence links for protein–protein interactions\n- Run functional enrichment analysis (including enrichment plots)\n- Get curated functional annotations for proteins\n- Query proteins by function or disease (GO, KEGG, Reactome, DISEASES etc.)\n\n---\n\n## Requirements\n\n- **Python** ≥ 3.10  \n- Dependencies (see `requirements.txt`):\n  - `fastmcp==2.10.6`\n  - `httpx==0.28.1`\n  - `pydantic==2.11.7`\n\n> **Note:** If the server crashes on startup, it is very likely due to an incompatible **FastMCP** version.\n\n---\n\n## Configuration\n\nThe server reads settings from `config/server.config` (JSON). Example:\n\n```json\n{\n  \"base_url\": \"https://string-db.org\",\n  \"server_port\": 57416,\n  \"verbosity\": \"low\"\n}\n```\n\n## Installation\n\n```bash\ngit clone https://github.com/meringlab/string-mcp.git\ncd string-mcp\npip install -r requirements.txt\n```\n\n## Running \n\n```\npython server.py\n```\n\n## Testing\n\n   ```bash\n   curl -v -H \"Accept: text/event-stream\" http://localhost:[port]/mcp\n   ```\n\nYou should see a `200 OK` response with `content-type: text/event-stream`. \n\n**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.\n\n## Docker\n\n1. Ensure you have a `config/server.config` file (copy from `config/server.config.example` if needed):\n   ```bash\n   cp config/server.config.example config/server.config\n   ```\n\n2. Build the image:\n   ```bash\n   docker build -t string-mcp .\n   ```\n\n3. Run the container:\n   \n   **Linux/macOS:**\n   ```bash\n   docker run -p 57416:57416 -v $(pwd)/config:/app/config:ro string-mcp\n   ```\n   \n   **Windows PowerShell:**\n   ```powershell\n   docker run -p 57416:57416 -v ${PWD}/config:/app/config:ro string-mcp\n   ```\n   \n   **Windows Command Prompt:**\n   ```cmd\n   docker run -p 57416:57416 -v %cd%/config:/app/config:ro string-mcp\n   ```\n\n   To run in detached mode:\n   ```bash\n   # Linux/macOS\n   docker run -d -p 57416:57416 -v $(pwd)/config:/app/config:ro --name string-mcp-server string-mcp\n   \n   # Windows PowerShell\n   docker run -d -p 57416:57416 -v ${PWD}/config:/app/config:ro --name string-mcp-server string-mcp\n   ```\n\n   The `-v` flag mounts your local config directory so you can customize settings without rebuilding the image.\n   \n   **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.\n\n4. Stop the container (if running in detached mode):\n   ```bash\n   docker stop string-mcp-server\n   docker rm string-mcp-server\n   ```\n\n**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.\n\n\nSTRING v12.0 is the frozen network release, available under the `/v12.0/` path.\n\n\n## License / Citation\n\nThe STRING MCP server source code is released under the [MIT License](https://opensource.org/licenses/MIT).  \nAssociated data and outputs are released under the [CC BY 4.0 License](https://creativecommons.org/licenses/by/4.0/).  \nYou are free to use, share, and modify the code with proper attribution.\n\nIf you use this code or data in your work, please also cite the latest [STRING manuscript](https://string-db.org/cgi/about?footer_active_subpage=references).\n",
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