`pubtator_relations`

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

List the relations PubTator 3 has extracted for a gene, disease, chemical or variant — which drugs treat a disease, which genes a disease is associated with, which chemicals inhibit a gene — ranked by supporting-publication count, each labelled machine-extracted, and the top relations carrying their supporting passages (the actual sentences, with PMIDs). Filter by relation type (treat, cause, associate, interact, inhibit, stimulate, prevent, positive/negative_correlate, cotreat, drug_interact, compare) and/or by a second entity. Accepts a PubTator id (@GENE_BRCA1) or a plain name. Sourced from the PubTator 3 relation-extraction model at NCBI/NLM — predictions from text, not curated. Keyless.

Parameters

Name	Type	Required	Description
`entity`	string	yes	The entity to list relations for: a PubTator id (“@GENE_BRCA1”, “@CHEMICAL_Doxorubicin”) or a plain name (“BRCA1”, “doxorubicin”) — a name is resolved via autocomplete and reported in resolved_from.
`type`	string	no	Restrict to one relation type. Omit for all types.
`target`	string	no	Optional second entity to restrict to (id or plain name), e.g. “@DISEASE_Breast_Neoplasms”.
`limit`	number	no	Max relations to return, 1-50 (default 20).
`evidence_for`	number	no	How many of the top relations get supporting passages attached (one search each), 0-5 (default 3). Each attaches up to 3 passages with PMIDs.

Example call

Arguments

{
  "entity": "@CHEMICAL_Doxorubicin",
  "type": "treat",
  "limit": 10,
  "evidence_for": 2
}

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_relations","arguments":{"entity":"@CHEMICAL_Doxorubicin","type":"treat","limit":10,"evidence_for":2}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('pubtator_relations', {
  "entity": "@CHEMICAL_Doxorubicin",
  "type": "treat",
  "limit": 10,
  "evidence_for": 2
});

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_relations