ncbi-datasets-mcp

NOTE: This is not affiliated with NCBI or NCBI Datasets, this is a user provided tool.

An MCP server that gives Claude access to NCBI Datasets v2 — discover what data NCBI Datasets offers, search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.

Tools

Discovering available data

Not sure what NCBI Datasets offers? Ask "what kind of data can I get from datasets?" and the server's list_data_types tool returns a readable catalog of every data report type — genes, genome assemblies, genome sequences, taxonomy, viruses, and more — along with which tools retrieve each one. Pass a specific type (e.g. genome-assembly) for its full field list and schema documentation link.

Installation

Option 1 — Desktop Extension (recommended for Claude Desktop users)

1. Download ncbi-datasets.mcpb from the Releases page.
2. Double-click the file and click Install in Claude Desktop.
3. Optionally enter your NCBI API key and download directory.

The NCBI CLI tools are downloaded automatically on first use (NCBI_AUTO_INSTALL=true is set by default in the extension).

Option 2 — JSON config (Claude Desktop / Claude Code)

Add to claude_desktop_config.json (macOS: ~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "ncbi-datasets": {
      "command": "uvx",
      "args": ["ncbi-datasets-mcp"],
      "env": {
        "NCBI_API_KEY": "your_key_here",
        "NCBI_DOWNLOAD_DIR": "/path/to/downloads",
        "NCBI_AUTO_INSTALL": "true"
      }
    }
  }
}

Requires uv (curl -LsSf https://astral.sh/uv/install.sh | sh).

Configuration

Development

# Install with dev extras
pip install -e ".[dev]"

# Run unit tests
pytest

# Run all tests including live network calls
pytest -m integration

# Regenerate enums from the current NCBI OpenAPI spec
python scripts/gen_enums.py

# Run the server locally (stdio transport)
ncbi-datasets-mcp

Architecture

src/ncbi_datasets_mcp/
  server.py           FastMCP app — tool registrations only
  config.py           Pydantic-settings env config
  cli/
    locator.py        Find datasets/dataformat (config → PATH → cache)
    installer.py      Download binaries from NCBI FTP
    runner.py         Async subprocess wrapper
  rest/
    client.py         httpx client for metadata/summary endpoints
  domains/
    _generated_enums.py  Vendored enums from OpenAPI spec
    common.py         Shared utilities (output dir, filename sanitising)
    genome.py         Genome CLI arg builders + response shaping
    taxonomy.py       Taxonomy CLI arg builders
  models/
    responses.py      Shared DownloadResult dataclass

Summary tools (no file I/O) → REST API.
Download and format-conversion tools → NCBI CLI binaries.

Cite

If you use NCBI Datasets in your research, please cite:

NCBI Datasets. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/datasets/

License

MIT