RDFPortal MCP

IMPORTANT!!

This project has been superseded by TogoMCP at DBCLS.

RDFPortal-MCP

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.

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 RDFPortal-MCP server

# Clone the repository
git clone https://github.com/arkinjo/RDFPortal-MCP.git
cd RDFPortal-MCP

# Install dependencies
uv sync

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": {
        "rdfportal": {
            "command": "/Users/arkinjo/.local/bin/uv",
            "args":[
                "--directory",
                "/Users/arkinjo/work/GitHub/RDFPortal-MCP",
                "run",
                "src/server.py"
            ]
        },
        "api_tools": {
            "command": "/Users/arkinjo/.local/bin/uv",
            "args": [
                "--directory",
                "/Users/arkinjo/work/GitHub/RDFPortal-MCP",
                "run",
                "src/api_tools.py"
            ]
        }
    }
}

Here, "rdfportal" is the main MCP server for RDFPortal, whereas "api_tools" is an additional (optional) MCP server providing REST APIs.

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: arkinjo
• Source: arkinjo/RDFPortal-MCP
• License: MIT

Install and usage instructions live in the source repository linked above.