bach-cedar-mcp 1.0.0

A Model Context Protocol server for interacting with CEDAR metadata repository

CEDAR MCP Server

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

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 (Recommended)

Run directly without installation using uvx:

uvx --from git+https://github.com/musen-lab/cedar-mcp.git cedar-mcp \
  --cedar-api-key "your-cedar-key" \
  --bioportal-api-key "your-bioportal-key"

Option 2: Local Installation with UV

Clone and run using uv:

# Clone the repository
git clone https://github.com/musen-lab/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"

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 --from git+https://github.com/musen-lab/cedar-mcp.git cedar-mcp

# Or run locally
uv run python -m cedar_mcp.server

Using with Claude Code

Add the CEDAR MCP server to Claude Code:

# Add using uvx (from Git repository)
claude mcp add cedar-mcp --uvx --from git+https://github.com/musen-lab/cedar-mcp.git \
  --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": [
        "--from", 
        "git+https://github.com/musen-lab/cedar-mcp.git",
        "cedar-mcp"
      ],
      "env": {
        "CEDAR_API_KEY": "your-cedar-key",
        "BIOPORTAL_API_KEY": "your-bioportal-key"
      }
    }
  }
}

Or if you have it installed locally:

{
  "mcpServers": {
    "cedar-mcp": {
      "command": "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