Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants
Config is the same across clients — only the file and path differ.
{
"mcpServers": {
"monarch-initiative": {
"url": "https://gateway.pipeworx.io/monarch-initiative/mcp"
}
}
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Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants
No automated test available for this server. Check the GitHub README for setup instructions.
Five weighted categories — click any category to see the underlying evidence.
No known CVEs.
No package registry to scan.
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Monarch Initiative MCP — biomedical knowledge graph.
Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.
| 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). |
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"
}
}
}
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.
MIT