`pubtator_find_entity`

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

Resolve a gene, disease, chemical/drug, variant, species or cell-line name to its normalized PubTator 3 entity id (e.g. “BRCA1” -> @GENE_BRCA1, NCBI Gene 672; “breast cancer” -> @DISEASE_Breast_Neoplasms, MeSH D001943). Use the id with pubtator_search and pubtator_relations. Sourced from the PubTator 3 autocomplete index at NCBI/NLM, which normalizes to NCBI Gene, MeSH, LitVar/dbSNP and NCBI Taxonomy. Keyless.

Parameters

Name	Type	Required	Description
`query`	string	yes	Name or synonym to look up, e.g. “BRCA1”, “metformin”, “breast cancer”, “V600E”.
`concept`	string	no	Restrict to one entity type. Omit to search all six. gene, disease, chemical and variant are densely covered; species and cellline autocomplete is sparse.
`limit`	number	no	Max matches to return, 1-25 (default 10).

Example call

Arguments

{
  "query": "BRCA1",
  "concept": "gene",
  "limit": 5
}

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_find_entity","arguments":{"query":"BRCA1","concept":"gene","limit":5}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('pubtator_find_entity', {
  "query": "BRCA1",
  "concept": "gene",
  "limit": 5
});

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_find_entity