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CEDAR MCP Server

by BACH-AI-Tools
GitHub
Python
MIT License
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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
Deploy Server
-
security - not tested
A
license - permissive license
-
quality - not tested

How are these scores calculated?

remote-capable server

The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.

Tools

Enables interaction with the CEDAR (Center for Expanded Data Annotation and Retrieval) metadata repository to fetch templates and retrieve template instances. Supports querying structured metadata and biomedical data annotations through the CEDAR platform.

  1. 🚀 快速启动（推荐）
    1. 使用 UVX 一键启动
    2. 在 Cursor/Cherry Studio 中配置
  2. Prerequisites
    1. CEDAR API Key
    2. BioPortal API Key
  3. Running the CEDAR MCP Server
    1. Option 1: Using UVX from PyPI (Recommended)
    2. Option 2: Install from PyPI
    3. Option 3: Using Environment Variables
    4. Option 4: Local Development
  4. Using with Claude Code
    1. Using with Claude Desktop
      1. Available Tools
        1. Development
          1. Install Development Dependencies
          2. Running Tests
        2. Contributing

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