delocalizer/gen3-mcp

Gen3 MCP Server

A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.

Install and Configure

These instructions are for using the server in a chat client. For development, see .

# Clone the repository
git clone <repository-url>

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

Create Gen3 credentials file

Create a file credentials.json containing your Gen3 API key:

{
  "api_key": "xxxx",
  "key_id": "xxxx"
}

Configure chat client

Example for Claude Desktop ~/.config/Claude/claude_desktop_config.json:

{
  "mcpServers": {
    "gen3-mcp-server": {
      "command": "uvx",
      "args": [
        "--from", "/path/to/gen3-mcp",
        "gen3-mcp"
      ],
      "env": {
        "GEN3_CREDENTIALS_FILE": "/path/to/credentials.json",
        "GEN3_BASE_URL": "https://gen3.datacommons.io/",
        "GEN3_LOG_LEVEL": "INFO"
      }
    }
  }
}

Example Usage in chat client

Available Tools

The MCP server provides the following tools:

Schema Discovery Tools

• get_schema_summary() - Get annotated overview of all entities and their relationships
• get_schema_entity(entity) - Get detailed schema info about a specific entity including all fields

Query Building Tools

• generate_query_template(entity_name, include_relationships=True, max_fields=20) - Generate safe query templates with validated fields
• validate_query(query) - Validate GraphQL query syntax and field names against schema

Query Execution Tool

• execute_graphql(query) - Execute validated GraphQL queries against the Gen3 data commons

Acknowledgments

Built with MCP (Model Context Protocol) and designed for Gen3 Data Commons.