TogoMCP: MCP server for the RDF Portal databases

This MCP server executes SPARQL queries against various biological/biomedical RDF databases provided at the RDF Portal.

Additional functionalities are also provided that interact with a few REST APIs at various sites.

Remote MCP Server

You can use the remote TogoMCP server (no need for local installation). See https://togomcp.rdfportal.org/ for instructions.

Installation

• Python (>= 3.11)
• uv package manager

Install uv (if not yet installed)

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

# Windows
> powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Install TogoMCP server

# Clone the repository
git clone https://github.com/dbcls/togo-mcp.git
cd togo-mcp

# Install dependencies
uv sync

Set NCBI API KEY

Part of TogoMCP tools require NCBI API keys. Obtain your NCBI API KEY and set it as the NCBI_API_KEY environment variable.

export NCBI_API_KEY="your-key-here"

Configuration

Claude Desktop Configuration

Change the file paths as appropriate.

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: ~\AppData\Roaming\Claude\claude_desktop_config.json

{
    "mcpServers": {
        "togomcp": {
            "command": "{path to uv}/uv",
            "args":[
                "--directory",
                "{path to togo-mcp}/togo-mcp",
                "run",
                "togo-mcp-server"
            ]
        }
    }
}

"Admin" mode

In the above setting, you can also use togo-mcp-admin instead of togo-mcp-server, which includes additional MCP tools for generating new MIE files.