mcp-reactome

Reactome biological pathway database

Part of Pipeworx — an MCP gateway connecting AI agents to 250+ live data sources.

Tools

| Tool | Description | |------|-------------| | search | Search across all Reactome objects. | | pathway | Full pathway record by stable id (e.g. R-HSA-68886). | | participants | Entity participants of a pathway. | | pathways_for_entity | Pathways containing an entity, looked up by external resource id (e.g. UniProt accession). | | orthologous_events | Orthologous pathways/reactions in another species. |

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

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

Or connect to the full Pipeworx gateway for access to all 250+ data sources:

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

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Reactome data" })

The gateway picks the right tool and fills the arguments automatically.

More

• All tools and guides
• pipeworx.io

License

MIT