NCBI Datasets

liveBiologyScience

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.

3tools
0msauth
free tier50 calls/day

Tools

ncbi_genome_reports

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

No parameters required.

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ncbi_gene_by_symbol

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

No parameters required.

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ncbi_taxonomy

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

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/ncbi-datasets/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/ncbi-datasets/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"ncbi_genome_reports","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("ncbi_genome_reports", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("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");