Summary
Connects Claude to the Monarch Initiative's biomedical knowledge graph, letting you search across diseases, phenotypes, genes, and variants without leaving your editor. You get five focused tools: full-text search across nodes, entity lookup by curie identifiers like MONDO:0007947, association queries between entities, phenotype-to-gene mapping for HP terms, and gene-to-disease linking for NCBIGene or HGNC identifiers. Runs through Pipeworx's gateway over streamable HTTP, so no local setup. Useful when you're prototyping healthcare tools, exploring rare disease relationships, or need to validate gene-phenotype connections during research workflows.
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mcp-monarch-initiative
Monarch Initiative MCP — biomedical knowledge graph.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ 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 673+ 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
License
MIT
Featured
Keep your Mac awake while Claude Code and 40+ AI agents run. Sleeps when they're idle.
One time payment $9 →Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →On Capafy, your Skill runs online 24/7 as an agent product, and you get paid every time someone uses it.
Start earning →
