`pubtator_search`

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_search for the schema, then POST the same URL with its arguments for the data.

Search PubMed/PMC literature by biomedical entity and get back, for each paper, the sentence that matched with its entity mentions decoded (gene, disease, chemical, variant, species, cell line — each normalized to an id). Query by plain text (“metformin alzheimer”), by PubTator entity ids combined with AND/OR (“@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms”), or by a relation (“relations:treat|@CHEMICAL_Doxorubicin|@DISEASE_Breast_Neoplasms”). 10 results per page; total count and page count returned. Sourced from the PubTator 3 search index at NCBI/NLM (~36M PubMed abstracts + PMC open-access full text). Keyless.

Parameters

Name	Type	Required	Description
`query`	string	yes	Free text, or PubTator entity ids joined with AND / OR (e.g. “@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms”), or a relation query “relations:\|\|”. Get ids from pubtator_find_entity.
`page`	number	no	Result page, 1-based (default 1). 10 results per page.

Example call

Arguments

{
  "query": "@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms",
  "page": 1
}

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_search","arguments":{"query":"@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms","page":1}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('pubtator_search', {
  "query": "@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms",
  "page": 1
});

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_search