TogoMCP: MCP Server for the RDF Portal

An MCP (Model Context Protocol) server that gives AI assistants (Claude, etc.) access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).

Quick Start: Remote Server (No Installation)

You can use the hosted TogoMCP server directly — no local setup needed.
See https://togomcp.rdfportal.org/ for connection instructions.

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Local Installation

Prerequisites

• Python >= 3.11
• uv package manager

1. Install uv

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

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

2. Clone and install

git clone https://github.com/dbcls/togo-mcp.git
cd togo-mcp
uv sync

3. Set NCBI API Key (required for NCBI tools)

Obtain your NCBI API key and export it:

export NCBI_API_KEY="your-key-here"

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Configuration

Claude Desktop

Edit your Claude Desktop config file:

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

{
    "mcpServers": {
        "togomcp": {
            "command": "/path/to/uv",
            "args": [
                "--directory",
                "/path/to/togo-mcp",
                "run",
                "togo-mcp-local"
            ],
            "env": {
                "NCBI_API_KEY": "your-key-here"
            }
        }
    }
}

Tip: Run which uv (macOS/Linux) or where uv (Windows) to find the full path to uv.

Admin Mode

Replace togo-mcp-local with togo-mcp-admin to also enable tools for generating new MIE (Metadata-Interoperability-Exchange) files — useful for contributors adding new database support.

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Docker

A Dockerfile is provided for containerized deployment:

docker build -t togo-mcp .
docker run -e NCBI_API_KEY="your-key-here" -p 8000:8000 togo-mcp

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Available Databases & Tools

TogoMCP exposes tools for querying the following (via SPARQL or REST APIs):

Category	Resources
Genomics / Sequences	UniProt, NCBI (Gene, PubMed, Taxonomy)
Chemistry	ChEMBL, PubChem, Rhea
Structure	PDB
Pathways	Reactome
Ontologies	MeSH, GO, ChEBI
General RDF	RDF Portal databases via SPARQL

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Example Prompts

Once connected, you can ask your AI assistant things like:

• "Find all human proteins associated with Alzheimer's disease in UniProt."
• "Run a SPARQL query on the ChEMBL database to find compounds targeting EGFR."
• "Search PubMed for recent papers on CRISPR base editing."
• "What pathways involve the TP53 gene in Reactome?"

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Directory Structure

togo-mcp/
├── togo_mcp/               # Main Python package
│   ├── server.py           # MCP server entry point
│   ├── main.py             # Core logic and tool registration
│   ├── admin.py            # Admin-mode tools (MIE generation)
│   ├── api_tools.py        # REST API integrations (ChEMBL, PDB, Reactome, etc.)
│   ├── ncbi_tools.py       # NCBI E-utilities tools
│   ├── rdf_portal.py       # RDF Portal / SPARQL tools
│   └── togoid.py           # TogoID identifier conversion tools
├── mie/                    # Metadata-Interoperability-Exchange (MIE) files (YAML)
│   ├── uniprot.yaml        # (one per supported database)
│   └── ...
├── sparql-examples/        # Example SPARQL queries per database
├── shex/                   # ShEx schemas for RDF validation
├── docs/                   # Developer documentation
│   ├── MIE_file_specs.md   # Spec for writing MIE files
│   └── ...
├── benchmark/              # Benchmarking scripts and results
├── scripts/                # Utility/maintenance scripts
├── resources/              # Static resources
├── Dockerfile              # Docker build configuration
├── pyproject.toml          # Python project metadata and entry points
└── uv.lock                 # Locked dependency versions (uv)

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Contributing

Contributions are welcome! To add support for a new database, see the mie/ directory and the admin-mode tools for generating MIE files. Please open an issue or pull request on GitHub.

License

This project is licensed under the MIT License.