`search`

Pack: reactome · Endpoint: https://gateway.pipeworx.io/reactome/mcp

Search the Reactome biological pathway database by keyword across all object types (Pathway, Reaction, Protein, Complex, etc.); returns stable IDs and display names grouped by type.

Parameters

Name	Type	Required	Description
`query`	string	yes
`types`	string	no	Comma-sep: Pathway,Reaction,Protein,Complex,…
`cluster`	boolean	no	Group results by type (default true).

Example call

Arguments

{
  "query": "apoptosis"
}

curl

curl -X POST https://gateway.pipeworx.io/reactome/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"search","arguments":{"query":"apoptosis"}}}'

TypeScript (@pipeworx/sdk)

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

const result = await pipeworx.call('search', {
  "query": "apoptosis"
});

More examples

{
  "query": "TP53",
  "types": "Protein,Pathway",
  "cluster": true
}

Response shape

Field	Type	Description
`results`	array	List of matching objects
`entries`	number	Total number of results

Full JSON Schema

{
  "type": "object",
  "description": "Search results from Reactome, optionally clustered by type",
  "properties": {
    "results": {
      "type": "array",
      "description": "List of matching objects",
      "items": {
        "type": "object",
        "properties": {
          "dbId": {
            "type": "number",
            "description": "Internal database ID"
          },
          "displayName": {
            "type": "string",
            "description": "Display name of the object"
          },
          "className": {
            "type": "string",
            "description": "Type of object (Pathway, Reaction, Protein, etc.)"
          },
          "stableId": {
            "type": "string",
            "description": "Stable identifier for the object"
          },
          "species": {
            "type": "object",
            "properties": {
              "dbId": {
                "type": "number"
              },
              "displayName": {
                "type": "string"
              }
            }
          }
        }
      }
    },
    "entries": {
      "type": "number",
      "description": "Total number of results"
    }
  }
}

Connect

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

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

See Getting Started for client-specific install steps.

search