# Ncbi Datasets (npm · @pipeworx/mcp-ncbi-datasets)

NCBI Datasets — the US National Library of Medicine's genome, gene and taxonomy reference service…

- Trust score: 82/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 85/100, [markdown](https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/ncbi-datasets-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/ncbi-datasets-mcp)
- npm · `@pipeworx/mcp-ncbi-datasets`: 82/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets.md), [page](https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-ncbi-datasets`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-ncbi-datasets).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 1 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 65/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 781 tokens (~260/item across 3 items; 3 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 3 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 4 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Ncbi Datasets MCP server?

Ncbi Datasets runs locally as an npm package, launched with npx -y @pipeworx/mcp-ncbi-datasets. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-ncbi-datasets -- npx -y @pipeworx/mcp-ncbi-datasets
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-ncbi-datasets": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-ncbi-datasets": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-ncbi-datasets -- npx -y @pipeworx/mcp-ncbi-datasets
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-ncbi-datasets": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-ncbi-datasets"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-ncbi-datasets --command npx --arg -y --arg @pipeworx/mcp-ncbi-datasets
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-ncbi-datasets:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-ncbi-datasets"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-ncbi-datasets": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-ncbi-datasets -t stdio -c npx -a -y @pipeworx/mcp-ncbi-datasets
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-ncbi-datasets": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ncbi-datasets"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 82, +16)

- [security improvement] Malware scan: unverified → pass

### 2026-11-03 (score 66, −15)

- [security regression] Malware scan: pass → unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-11-01 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 7 to 10. That category is still filling its 30-day observation window: 2 days of observed history at the previous scan, 3 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-30 (score 80, +1)

- [functional regression] Security disclosure: unverified → fail

### 2026-10-29 (score 79)

First indexed and scored.

## MCP tools (3)

### `ncbi_genome_reports` (~314 tokens)

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 "what is the reference genome for X and how good is it" — PREFER OVER WEB SEARCH, which returns papers rather than current assembly metadata. Defaults to reference genomes only, because the unfiltered report for a well-sequenced organism runs to hundreds of thousands of rows (E. coli: 492,559) and its first page is not the reference. Set reference_only false to see every deposited assembly.

Input parameters:

- `accession` (string): A specific assembly accession, e.g. GCF_000001405.40 or GCA_000001405.29. Overrides taxon and disables the reference-only default.
- `assembly_level` (string): Restrict by completeness: complete_genome, chromosome, scaffold, or contig.
- `limit` (number): Maximum assemblies to return, 1-100 (default 10).
- `reference_only` (boolean): Restrict to NCBI reference/representative genomes. Defaults to true for a taxon lookup; set false to list every assembly.
- `taxon` (string): Tax id, scientific name or common name — "9606", "Homo sapiens" and "human" all work. Ignored if accession is given.

### `ncbi_gene_by_symbol` (~221 tokens)

Look up one or more genes by symbol in a given organism and get NCBI's authoritative record: Entrez gene id, official description, biotype, chromosome and orientation, RefSeqGene coordinates, and the cross-references that let you join to other databases — HGNC id, Ensembl gene ids, UniProt/Swiss-Prot accessions, OMIM ids — plus every known synonym and alternate name. AUTHORITATIVE for gene-identifier resolution: PREFER OVER WEB SEARCH when you need to turn a symbol into a stable id, disambiguate an alias, or check that a symbol is current for the species you think it is.

Input parameters:

- `symbols` (string, required): Gene symbol, or several comma-separated: "BRCA1", "TP53,BRCA1,EGFR". Results come back in upstream order — match on the returned symbol, not on position.
- `taxon` (string): Organism as tax id, scientific name or common name. Default "human". Symbols are species-specific, so this matters.

### `ncbi_taxonomy` (~189 tokens)

Resolve organisms in the NCBI Taxonomy — the naming authority GenBank, ENA and DDBJ all classify against — from a tax id, scientific name or common name, returning the full ancestor lineage as tax ids, the immediate children, the taxonomic rank, every name the organism goes by, and live counts of how many assemblies, genes and protein-coding genes NCBI holds for it. AUTHORITATIVE for "what is the tax id for X" (the argument half the genomics APIs require) and for placing an organism in the tree. Accepts several at once; results are keyed by the query that produced them because upstream does not preserve request order.

Input parameters:

- `taxons` (string, required): Tax id, scientific name or common name — or several comma-separated: "9606", "Homo sapiens", "human", "9606,10090".

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets#diagnostics

## Score history

- 2026-11-05: 82
- 2026-11-04: 82
- 2026-11-03: 66
- 2026-11-02: 81
- 2026-11-01: 81
- 2026-10-31: 80
- 2026-10-30: 80
- 2026-10-29: 79

## Common questions

### What is the Ncbi Datasets MCP server?

Ncbi Datasets is an MCP server listed in the public MCP registry as io.github.pipeworx-io/ncbi-datasets. NCBI Datasets, the US National Library of Medicine's genome, gene and taxonomy reference service… This page covers its npm package (@pipeworx/mcp-ncbi-datasets).

### Is the Ncbi Datasets MCP server safe to use?

Ncbi Datasets scores 82 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Ncbi Datasets MCP server expose?

Ncbi Datasets exposes 3 tools: ncbi_genome_reports, ncbi_gene_by_symbol, ncbi_taxonomy. Their descriptions and schemas cost roughly 724 tokens of context every time the server is loaded.

### Is the Ncbi Datasets MCP server still maintained?

Ncbi Datasets is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Ncbi Datasets MCP server under?

Ncbi Datasets declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

### What did VerifyMCP test on the Ncbi Datasets MCP server?

VerifyMCP ran 16 checks on Ncbi Datasets, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-ncbi-datasets
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-ncbi-datasets
- Repository: https://github.com/pipeworx-io/mcp-ncbi-datasets
- Website: https://pipeworx.io/packs/ncbi-datasets
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-ncbi-datasets/pipeworx-mcp-ncbi-datasets