mcp-ncbi-datasetsSAFE
NCBI Datasets — the US National Library of Medicine's genome, gene and taxonomy reference service: which assemblies exist for an organism and how good they are, where a gene sits on the genome and what it is called everywhere else, and the NCBI taxonomy tree with per-node assembly and gene counts.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
NCBI Datasets (US National Library of Medicine) — which genome assemblies exist for an organism and how good they are, where a gene sits and what it is called in every other database, and the NCBI taxonomy tree with per-node assembly and gene counts.
Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.
Tools
ncbi_genome_reports(taxon?, accession?, reference_only?, assembly_level?, limit?)
— assemblies with level, length, contig/scaffold N50, GC%, submitter, BioProject and the paired RefSeq/GenBank accession.
ncbi_gene_by_symbol(symbols, taxon?)— Entrez gene id, biotype, chromosome,
RefSeqGene coordinates, plus HGNC / Ensembl / UniProt / OMIM cross-references and every synonym.
ncbi_taxonomy(taxons)— resolve a tax id, scientific name or common name to
the full lineage, children, rank and live assembly/gene counts.
Auth
Keyless. NCBI rate-limits anonymous callers by IP at roughly 5 requests/second across api.ncbi.nlm.nih.gov; the pack sends an identifying User-Agent, does not retry, and surfaces a 429 with that explanation rather than looping.
Not the same service as ncbi-eutils
E-utilities is a generic search/fetch layer over ~40 Entrez databases that hands back records you must parse. Datasets answers structured questions about genomes, genes and taxonomy with structured rows. Use this pack for those three; use ncbi-eutils for PubMed, dbSNP and the rest of Entrez.
Data sources
Things that cost time to rediscover (measured 2026-09-17)
- Without filters, a genome report is every assembly ever deposited. Taxon
562 (E. co
f85f235ed94eOBSERVED · 2026-10-11Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add mcp-ncbi-datasets -- npx -y @pipeworx/[email protected]
{
"mcpServers": {
"mcp-ncbi-datasets": {
"command": "npx",
"args": [
"-y",
"@pipeworx/[email protected]"
]
}
}
}Exposed tools (2)
2 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
ncbi_gene_by_symbol | read | Look up one or more genes by symbol in a given organism and get NCBI\ |
ncbi_genome_reports | read | List the genome assemblies NCBI holds for an organism (or fetch one by accession), with assembly level, total length, contig and scaffold N50, GC percent, submitter, release date, BioProject, and the paired RefSeq/GenBank accession. AUTHORITATIVE for |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (1 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (1)
@modelcontextprotocol/sdk, tsx, typescript, @cloudflare/workers-types
Gates applied: no_behavioural_pass.
f85f235ed94efull audit observations/trust-audit/mcp-server/pipeworx-io__mcp-ncbi-datasets.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-11 | f85f235ed94e | SAFE | B | 89 | first audit |
Questions
What is the mcp-ncbi-datasets MCP server?
NCBI Datasets — the US National Library of Medicine's genome, gene and taxonomy reference service: which assemblies exist for an organism and how good they are, where a gene sits on the genome and what it is called everywhere else, and the NCBI taxonomy tree with per-node assembly and gene counts.
What tools does mcp-ncbi-datasets expose?
2 in total: 2 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is mcp-ncbi-datasets safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does mcp-ncbi-datasets need?
No credential environment variables were found in its source, so it appears to need none.
How does mcp-ncbi-datasets run?
It speaks stdio and streamable-http, so it runs as a local process your client starts. It is published on npm as @pipeworx/mcp-ncbi-datasets at 0.1.1.
How current is this page?
The grade is for one exact copy of the source (f85f235ed94e), read on 2026-10-11. The repository is watched and re-audited when it changes.