`search`

Pack: reactome · 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/search for the schema, then POST the same URL with its arguments for the data.

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 — 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 reactome pack

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

See Getting Started for client-specific install steps.

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