F
license-
qualityD
maintenanceAn MCP server that provides access to Monarch Initiative's biomedical data through the Biolink API, enabling agents to query biological entities, associations, and knowledge graphs using natural language.
ncbi-datasets-mcp
by syntheticgio
This server provides access to NCBI Datasets v2, enabling genomic and taxonomic data discovery, metadata retrieval, and file downloads.
Install CLI tools: Automatically check, download, and install the required NCBI
datasetsanddataformatbinaries needed for downloads and format conversion.Discover data types: Browse all available NCBI Datasets report types (genes, genome assemblies, sequences, taxonomy, viruses, etc.), including which tools retrieve each type and full field/schema details for a specific type.
Search genome assemblies by taxon: Query genome assembly metadata by organism name or tax ID, with filters for assembly level, source (GenBank/RefSeq), reference status, and annotation status.
Fetch genome metadata by accession: Retrieve detailed assembly metadata for one or more known RefSeq or GenBank accessions.
Download genome packages: Download genome data (sequences, RNA, proteins, GFF3, etc.) by taxon or accession, with support for dehydrated packages.
Rehydrate genome packages: Fetch the full sequence files for a previously downloaded dehydrated package.
Convert genome reports to TSV: Transform genome JSONL data reports into TSV format, with optional field selection.
Explore taxonomy: Get lineage, rank, scientific/common names, and child taxa for any taxon by name or tax ID.
Download taxonomy packages: Retrieve a complete taxonomy data package for a given taxon.
The server is configurable via environment variables or a Claude Desktop JSON config, supporting settings like an NCBI API key (for higher rate limits), default download directory, auto-installation of CLI tools, and maximum results for summary tools.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@ncbi-datasets-mcpsearch genome assemblies for Escherichia coli"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
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
Tool | Transport | Description |
| — | Install the NCBI CLI tools (run once, or set |
| — | Describe what kinds of data NCBI Datasets provides; optional per-type detail |
| REST | Search genome assemblies by organism name or tax ID |
| REST | Fetch assembly metadata for known accessions |
| CLI | Download a genome package by taxon |
| CLI | Download a genome package by accession |
| CLI | Fetch sequence files for a dehydrated package |
| CLI | Convert a genome JSONL data report to TSV |
| REST | Get lineage, rank, and names for a taxon |
| CLI | Download a taxonomy package |
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.
Related MCP server: mcp-pubmed
Installation
Option 1 — Desktop Extension (recommended for Claude Desktop users)
Download
ncbi-datasets.mcpbfrom the Releases page.Double-click the file and click Install in Claude Desktop.
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
Variable | Default | Description |
| (none) | NCBI API key — raises rate limit to 10 req/s |
|
| Default download location |
|
| Auto-install CLI tools on startup |
|
| Cap for summary tool result counts |
|
| Seconds before a download times out |
| (auto) | Override path to |
| (auto) | Override path to |
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-mcpArchitecture
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 dataclassSummary 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
Maintenance
–Maintainers
–Response time
1dRelease cycle
3Releases (12mo)
Commit activity
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