`ncbi_taxonomy`

Pack: ncbi-datasets · Endpoint: https://gateway.pipeworx.io/ncbi-datasets/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/ncbi_taxonomy for the schema, then POST the same URL with its arguments for the data.

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.

Parameters

Name	Type	Required	Description
`taxons`	string	yes	Tax id, scientific name or common name — or several comma-separated: “9606”, “Homo sapiens”, “human”, “9606,10090”.

Example call

Arguments

{
  "taxons": "9606,10090"
}

curl

curl -X POST https://gateway.pipeworx.io/ncbi-datasets/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"ncbi_taxonomy","arguments":{"taxons":"9606,10090"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('ncbi_taxonomy', {
  "taxons": "9606,10090"
});

More examples

{
  "taxons": "Bos taurus"
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "ncbi-datasets": {
      "url": "https://gateway.pipeworx.io/ncbi-datasets/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

ncbi_taxonomy