UniProt MCP Server

mcp-name: io.github.josefdc/uniprot-mcp

The UniProt MCP server exposes curated UniProtKB data as Model Context Protocol (MCP) resources, tools, and prompts. It allows MCP-compatible agents to fetch protein entries, sequences, Gene Ontology annotations, and identifier mappings from the UniProt REST API through a consistent, typed interface.

Features

• Protocols: Supports both stdio (development) and streamable HTTP (remote deployments with proper CORS headers).
• Resources: uniprot://uniprotkb/{accession} provides raw entry JSON; uniprot://help/search documents query syntax.
• Tools: Structured outputs for fetch_entry, get_sequence, search_uniprot, and map_ids (with progress notifications).
• Prompts: Built-in prompt for summarising a UniProt accession.
• Retries & resilience: Tenacity-based retries for 429/5xx responses, progress reporting for long-running mapping tasks, and defensive parsing of UniProt payloads.

Installation

pip install uniprot-mcp

Quickstart

Stdio server (development / MCP Inspector)

uniprot-mcp

This launches the stdio transport (the same entry point MCP Inspector uses).

Streamable HTTP server

uniprot-mcp-http --host 0.0.0.0 --port 8000

The server exposes a health check at /healthz and the MCP endpoint at /mcp. Browser clients can read the Mcp-Session-Id response header because the server is configured with permissive CORS defaults. If prometheus-client is installed (included by default), metrics are served at /metrics.

Available MCP primitives

Resources

• uniprot://uniprotkb/{accession} – returns raw UniProtKB entry JSON.
• uniprot://help/search – simple usage guide for search_uniprot.

Tools

Prompts

• Summarize Protein – prompts an agent to summarise a UniProt accession, optionally including organism, GO annotations, and notable features.

Environment variables and CLI flags

Every HTTP response includes X-Request-Id. Forward this header in client requests to correlate logs across transports.

Development

The project is managed with uv.

# Install dependencies
uv sync --group dev

# Lint & format check
uv tool run ruff check .
uv tool run ruff format --check .

# Type check
uv tool run mypy src

# Run tests (with coverage)
uv run pytest --maxfail=1 --cov=uniprot_mcp --cov-report=term-missing

# Launch stdio server for local inspection
uv run uniprot-mcp

# Launch HTTP server with auto-reload
uv run python -m uvicorn uniprot_mcp.http_app:app --reload

Publishing & MCP Registry

1. Build artifacts: uv build
2. Publish to PyPI: uv publish --token $PYPI_TOKEN
3. Prepare/validate server.json (see docs/registry.md for the schema link).
4. Use mcp-publisher to publish the server metadata, optionally linking a remote HTTP deployment.

Support & Compatibility

• Python 3.11 and 3.12 are tested in CI.
• External dependencies are pinned via uv.lock.
• Issues and feature requests: GitHub Issues

License

Distributed under the MIT License. See LICENSE for details.