Server data from the Official MCP Registry
Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants
About
Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants
Remote endpoints: streamable-http: https://gateway.pipeworx.io/monarch-initiative/mcp
Security Report
Valid MCP server (1 strong, 0 medium validity signals). No known CVEs in dependencies. Imported from the Official MCP Registry. Trust signals: trusted author (392/393 approved). 1 finding(s) downgraded by scanner intelligence.
16 tools verified · Open access · 1 issue found
Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.
Permissions Required
This plugin requests these system permissions. Most are normal for its category.
How to Connect
Remote Plugin
No local installation needed. Your AI client connects to the remote endpoint directly.
Add this to your MCP configuration to connect:
{
"mcpServers": {
"io-github-pipeworx-io-monarch-initiative": {
"url": "https://gateway.pipeworx.io/monarch-initiative/mcp"
}
}
}Documentation
View on GitHubFrom the project's GitHub README.
@pipeworx/monarch-initiative
Monarch Initiative MCP — biomedical knowledge graph linking diseases, phenotypes, genes, and variants across species. Keyless.
Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.
Tools
search(query, category?, limit?, offset?)— full-text node searchentity(id)— single node by curie (e.g.MONDO:0007947)associations(entity_id, category?, predicate?, direction?, limit?)— associations involving an entityphenotype_to_gene(phenotype_id)— gene candidates for a phenotype (HP:…)gene_to_disease(gene_id)— diseases associated with a gene
Data source
https://api.monarchinitiative.org/v3/api/
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 1394+ 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
Reviews
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