MCP server

Monarch Initiative

io.github.pipeworx-io/monarch-initiative

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Monarch Initiative MCP — biomedical knowledge graph.

From the maker's README Monarch Initiative MCP — biomedical knowledge graph linking diseases, phenotypes, genes, and variants across species. Keyless. Source

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

47

Token cost

About 26,948 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http monarch-initiative https://gateway.pipeworx.io/monarch-initiative/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.monarch-initiative]
url = "https://gateway.pipeworx.io/monarch-initiative/mcp"

Gemini CLI

{"mcpServers":{"monarch-initiative":{"httpUrl":"https://gateway.pipeworx.io/monarch-initiative/mcp"}}}

Cursor

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

VS Code

{"servers":{"monarch-initiative":{"type":"http","url":"https://gateway.pipeworx.io/monarch-initiative/mcp"}}}

Antigravity

agy mcp add monarch-initiative https://gateway.pipeworx.io/monarch-initiative/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"monarch-initiative","server_url":"https://gateway.pipeworx.io/monarch-initiative/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"monarch-initiative","server_url":"https://gateway.pipeworx.io/monarch-initiative/mcp"}

Tools

• associations ~253 tokens
  Fetch biolink associations (edges) involving a Monarch entity by its CURIE ID (e.g. MONDO:0007947); filter by association category (e.g. biolink:DiseaseToPhenotypicFeatureAssociation), predicate, or direction (subject/object/both).
• entity ~65 tokens
  Single node by curie (e.g. "MONDO:0007947").
• gene_to_disease ~69 tokens
  Diseases associated with a gene (NCBIGene:… or HGNC:… id).
• phenotype_to_gene ~68 tokens
  Genes annotated to a phenotype (HP:… id).
• search ~190 tokens
  Full-text search across the Monarch biomedical knowledge graph for diseases, genes, phenotypes, and other biolink entities by query string; filter by category (e.g. biolink:Disease) and paginate with limit/offset.

Browse

• GitHub tools
• GitHub and code hosting
• Memory for agents

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Badge for your README

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