TogoMCP

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/togomcp.git
cd togomcp
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/togomcp",
                "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.

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Docker

A Dockerfile is provided for containerized deployment.

Recommended: docker compose

compose.yaml defines two services — togomcp-main (port 8000) and togomcp-test (port 8001) — so you can run production and staging endpoints side by side from the same image.

cp .env.example .env                                # then fill in NCBI_API_KEY
docker build -t localhost/togo-mcp:latest .         # build main image (tag in .env)
docker compose up -d togomcp-main                   # start main endpoint

Common operations:

docker compose logs -f togomcp-main                 # tail logs
docker compose down                                 # stop and remove all services
docker compose down togomcp-test                    # stop and remove just one
docker compose up -d togomcp-test                   # after rebuilding, recreates with new image

Override image tags and host ports via .env — see .env.example for the full list. Use docker compose up -d --force-recreate <svc> if compose doesn't pick up a rebuilt image, and docker image prune -f to clean up dangling layers.

Simple: docker run

For a single container without compose:

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

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Tool-Call Logging (Optional)

TogoMCP can record every MCP tool call as one JSON line per call (timestamp, tool name, arguments, status, elapsed_ms, session/request/client IDs, transport, client IP). SPARQL calls are enriched with endpoint URL, HTTP code, row/byte counts, and a SHA-256 of the query. Useful for benchmarking, MIE iteration, and reconstructing multi-tool sequences.

On/off is a single env var: TOGOMCP_QUERY_LOG. Unset/empty = disabled (zero-overhead default). Set to a writable file path to enable. Output uses RotatingFileHandler (50 MB × 10, ~500 MB cap).

Docker

compose.yaml bind-mounts ./logs (and ./logs-test) on the host to /var/log/togomcp inside each container and passes through TOGOMCP_QUERY_LOG / TOGOMCP_QUERY_LOG_TEST from .env. Opt in:

echo 'TOGOMCP_QUERY_LOG=/var/log/togomcp/togomcp.jsonl' >> .env
mkdir -p logs
docker compose up -d togomcp-main
tail -f logs/togomcp.jsonl

The path in the env var is the container-side path; the bind mount makes the same file visible at ./logs/togomcp.jsonl on your host. Leaving the var unset keeps logging off — no compose changes needed.

Claude Desktop (local stdio)

Add TOGOMCP_QUERY_LOG to the env block alongside NCBI_API_KEY. Use an absolute path (the spawned process's cwd is unpredictable) and ensure the parent directory exists:

"env": {
    "NCBI_API_KEY": "your-key-here",
    "TOGOMCP_QUERY_LOG": "/Users/you/togomcp-logs/togomcp.jsonl"
}

Then mkdir -p ~/togomcp-logs once and fully restart Claude Desktop.

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Available Databases & Tools

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

Category	Resources
Proteins / Proteomics	UniProt, PDB, jPOST
Genes / Genomics	NCBI Gene, Ensembl, HGNC, OMA, Bgee, HCO, MCO, DDBJ, MoG+, TogoVar
Chemistry	ChEMBL, PubChem, ChEBI, Rhea, BRENDA, MassBank
Pathways	Reactome
Disease / Clinical	ClinVar, MedGen, MONDO, NANDO
Literature	PubMed, PubTator
Microbiology	BacDive, MediaDive, AMR Portal, NBRC
Glycomics	GlyCosmos
Ontologies / Vocabulary	MeSH, GO, Ontology Graphs (HP, UBERON, CL, SO, ECO, EFO, PRO, FMA, …)
Taxonomy	NCBI Taxonomy
Materials Science	SuperCon

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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

togomcp/
├── togo_mcp/               # Main Python package
│   ├── server.py           # Root FastMCP instance + tool-call logging middleware
│   ├── main.py             # Assembles the server, mounts sub-servers, entry points
│   ├── rdf_portal.py       # RDF Portal / SPARQL, MIE, and endpoint tools
│   ├── api_tools.py        # REST search wrappers (UniProt, PDB, ChEMBL, Reactome, etc.)
│   ├── ncbi_tools.py       # NCBI E-utilities sub-server
│   ├── togoid.py           # TogoID identifier-conversion sub-server
│   ├── togovar.py          # TogoVar human-variation sub-server
│   ├── stats.py            # Tool-call usage-log analysis
│   └── data/               # Bundled data files (included in wheel)
│       ├── mie/            # MIE files (YAML, one per database)
│       ├── docs/           # Developer documentation (MIE spec, examples)
│       └── resources/      # Static resources (endpoints.csv, usage guide, etc.)
├── benchmark/              # Benchmark question set, scripts, and results
├── scripts/                # Utility/maintenance scripts (deploy, Docker, MIE keywords)
├── tests/                  # Pytest test suite
├── Dockerfile              # Docker build configuration
├── compose.yaml            # Docker Compose (main + test services)
├── 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, add an MIE file under togo_mcp/data/mie/ and a corresponding row in togo_mcp/data/resources/endpoints.csv (see the MIE spec in togo_mcp/data/docs/). Please open an issue or pull request on GitHub.

Reference

Kinjo, A. R., Yamamoto, Y., Bustamante-Larriet, S., Labra-Gayo, J.-E., & Fujisawa, T. (2026). TogoMCP: Natural Language Querying of Life-Science Knowledge Graphs via Schema-Guided LLMs and the Model Context Protocol. bioRxiv. https://doi.org/10.64898/2026.03.19.713030

License

This project is licensed under the MIT License.