mcp-monarch-initiative

Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants

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

Tools

| Tool | Description | |------|-------------| | search | Full-text node search. | | entity | Single node by curie (e.g. "MONDO:0007947"). | | associations | Associations involving an entity. | | phenotype_to_gene | Genes annotated to a phenotype (HP:… id). | | gene_to_disease | Diseases associated with a gene (NCBIGene:… or HGNC:… id). |

Quick Start

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

{
  "mcpServers": {
    "monarch-initiative": {
      "url": "https://gateway.pipeworx.io/monarch-initiative/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 Monarch Initiative data" })

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

More

• All tools and guides
• pipeworx.io

License

MIT