`pubtator_annotations`

Pack: pubtator · Connect: https://pipeworx.io/mcp (see Connect below for a single-pack URL)

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

Entity annotations for specific PubMed articles: every gene, disease, chemical, variant, species and cell-line mention in the title and abstract (or PMC full text), each normalized to NCBI Gene / MeSH / dbSNP / Taxonomy ids with its character offsets, plus any relations PubTator 3 extracted within the article. Up to 20 PMIDs per call. Sourced from the PubTator 3 BioC JSON export at NCBI/NLM; all annotations are machine-extracted. Keyless.

Parameters

Name	Type	Required	Description
`pmids`	array	yes	PubMed ids, 1-20, e.g. [“31022191”, “25616998”].
`items`	string	no
`full_text`	boolean	no	Return PMC open-access full-text passages when available (default false: title + abstract only). Full text can be 100+ passages; each passage is truncated to 1,500 characters.

Example call

Arguments

{
  "pmids": [
    "31022191",
    "25616998"
  ]
}

curl

curl -X POST https://gateway.pipeworx.io/pubtator/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"pubtator_annotations","arguments":{"pmids":["31022191","25616998"]}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('pubtator_annotations', {
  "pmids": [
    "31022191",
    "25616998"
  ]
});

Connect

Add this to your MCP client config — every tool in the catalog, including this one — or use one-click install buttons:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://pipeworx.io/mcp"
    }
  }
}

Connect to just the pubtator pack

{
  "mcpServers": {
    "pubtator": {
      "url": "https://gateway.pipeworx.io/pubtator/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

pubtator_annotations