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

Set your API keys as environment variables:

export CEDAR_API_KEY="your-cedar-key"
export BIOPORTAL_API_KEY="your-bioportal-key"

Option 1: Using UVX (Recommended)

Run directly without installation using uvx:

uvx cedar-mcp

Option 2: Using pip

Install from PyPI and run:

pip install cedar-mcp
cedar-mcp

Note: The --cedar-api-key and --bioportal-api-key CLI flags are deprecated and will be removed in a future release. Use environment variables instead.

Transport Options

By default, the server uses stdio transport. You can also run it as an HTTP server using SSE or streamable-http transports:

# SSE transport on default host/port (127.0.0.1:8000)
cedar-mcp --transport sse

# Streamable HTTP on custom host/port
cedar-mcp --transport streamable-http --host 0.0.0.0 --port 9000

Using with Claude Code

Add the CEDAR MCP server to Claude Code:

claude mcp add cedar-mcp --uvx -e CEDAR_API_KEY=your-cedar-key -e 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": [
        "cedar-mcp"
      ],
      "env": {
        "CEDAR_API_KEY": "your-cedar-key",
        "BIOPORTAL_API_KEY": "your-bioportal-key",
        "CEDAR_MCP_CACHE_TTL_SECONDS": "86400",
        "CEDAR_MCP_CACHE_DIR": "/path/to/custom/location"
      }
    }
  }
}

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",
        "CEDAR_MCP_CACHE_TTL_SECONDS": "86400",
        "CEDAR_MCP_CACHE_DIR": "/path/to/custom/location"
      }
    }
  }
}

The CEDAR_MCP_CACHE_TTL_SECONDS and CEDAR_MCP_CACHE_DIR environment variables are optional. When set under the "env" key, Claude Desktop injects them into the server process environment before it starts, so the cache picks them up automatically. If omitted, the defaults apply (24-hour TTL and a platform-specific cache directory — see Cache Configuration).

Available Tools

Here is the list of CEDAR tools with a short description

• get_cedar_template: Fetches a template from the CEDAR repository, using CEDAR's compact YAML rendering so it costs fewer tokens to read than the JSON-LD form. Pass expand_branches to list the values allowed by each ontology branch: "labels" for their labels alone, "terms" for labels with their IRIs, or the default "none" to report the branch itself and skip the lookups.
• get_instances_based_on_template: Gets template instances that belong to a specific template with pagination support.
• term_search_from_branch: Searches BioPortal for standardized ontology terms within a specific branch.
• term_search_from_ontology: Searches BioPortal for standardized ontology terms within an entire ontology.
• get_branch_children: Fetches all immediate children terms for a given branch in an ontology.
• get_ontology_class_tree: Fetches the hierarchical tree structure for a given class in an ontology.
• remove_stale_cache_entries: Removes expired entries from the BioPortal search cache.
• clear_bioportal_cache: Clears all entries from the BioPortal search cache.

Cache Configuration

BioPortal search results are cached locally using SQLite to reduce latency and API load. The cache persists across server restarts.

Default cache locations:

• macOS: ~/Library/Caches/cedar-mcp
• Linux: $XDG_CACHE_HOME/cedar-mcp or ~/.cache/cedar-mcp
• Windows: %LOCALAPPDATA%/cedar-mcp/cache

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

License

This project is licensed under the MIT License — see the LICENSE file for details.