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CEDAR MCP Server

by BACH-AI-Tools
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Python
Remote
MIT License

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/

Prerequisites

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

CEDAR API Key

BioPortal 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
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