CEDAR MCP Server

A Model Context Protocol (MCP) server for interacting with the CEDAR (Center for Expanded Data Annotation and Retrieval) metadata repository.

🚀 快速启动（推荐）

使用 UVX 一键启动

uvx bach-cedar-mcp

在 Cursor/Cherry Studio 中配置

{
  "mcpServers": {
    "cedar-mcp": {
      "command": "uvx",
      "args": ["bach-cedar-mcp"],
      "env": {
        "CEDAR_API_KEY": "<YOUR_CEDAR_API_KEY>",
        "BIOPORTAL_API_KEY": "<YOUR_BIOPORTAL_API_KEY>"
      }
    }
  }
}

PyPI 包地址: https://pypi.org/project/bach-cedar-mcp/

Related MCP server: Entrez MCP Server

Prerequisites

Before using this MCP server, you'll need API keys from:

CEDAR API Key

• Go to cedar.metadatacenter.org

• Create an account or log in

• Navigate to: Profile → API Key

• Copy your API key

BioPortal API Key

• Go to bioportal.bioontology.org

• Create an account or log in

• Navigate to: Account Settings → API Key

• Copy your API key

Running the CEDAR MCP Server

Option 1: Using UVX from PyPI (Recommended)

Run directly without installation using uvx:

uvx bach-cedar-mcp \
  --cedar-api-key "your-cedar-key" \
  --bioportal-api-key "your-bioportal-key"

Option 2: Install from PyPI

Install using pip and run:

# Install from PyPI
pip install bach-cedar-mcp

# Run the server
bach-cedar-mcp \
  --cedar-api-key "your-cedar-key" \
  --bioportal-api-key "your-bioportal-key"

Option 3: Using Environment Variables

Set environment variables instead of command-line arguments:

# Set environment variables
export CEDAR_API_KEY="your-cedar-key"
export BIOPORTAL_API_KEY="your-bioportal-key"

# Run with uvx
uvx bach-cedar-mcp

# Or if installed with pip
bach-cedar-mcp

Option 4: Local Development

Clone and run from source:

# Clone the repository
git clone https://github.com/BACH-AI-Tools/cedar-mcp.git
cd cedar-mcp

# Install dependencies and run
uv run python -m cedar_mcp.server \
  --cedar-api-key "your-cedar-key" \
  --bioportal-api-key "your-bioportal-key"

Using with Claude Code

Add the CEDAR MCP server to Claude Code:

# Add using uvx (from PyPI)
claude mcp add cedar-mcp --uvx bach-cedar-mcp \
  --cedar-api-key "your-cedar-key" \
  --bioportal-api-key "your-bioportal-key"

Using with Claude Desktop

To use with Claude Desktop app:

1. Install the MCP server using one of the methods above

2. Add to Claude Desktop configuration in your claude_desktop_config.json:

{
  "mcpServers": {
    "cedar-mcp": {
      "command": "uvx",
      "args": ["bach-cedar-mcp"],
      "env": {
        "CEDAR_API_KEY": "your-cedar-key",
        "BIOPORTAL_API_KEY": "your-bioportal-key"
      }
    }
  }
}

Or if you have it installed with pip:

{
  "mcpServers": {
    "cedar-mcp": {
      "command": "bach-cedar-mcp",
      "env": {
        "CEDAR_API_KEY": "your-cedar-key", 
        "BIOPORTAL_API_KEY": "your-bioportal-key"
      }
    }
  }
}

Available Tools

Here is the list of CEDAR tools with a short description

• get_template: Fetches a template from the CEDAR repository.

• get_instances_based_on_template: Gets template instances that belong to a specific template with pagination support.

Development

Install Development Dependencies

pip install -r requirements-dev.txt

Running Tests

This project includes comprehensive integration tests that validate real API interactions with both CEDAR and BioPortal APIs.

For detailed testing information, see test/README.md.

Contributing

Contributions are welcome! Please ensure all tests pass before submitting a Pull Request:

python run_tests.py --integration