HPO API MCP MCP server

An MCP server provided by Pipeworx that exposes the Human Phenotype Ontology (HPO) API. It allows AI agents to look up phenotype terms, disease-phenotype associations, and gene-disease relationships for clinical genomics through seven specific tools including term lookup, search, and hierarchy navigation.

Endpoint and access

No sign-in: your client connects and lists tools immediately, with no account or key.

No sign-inEndpoint checked 2026-10-05Operated by Pipeworx

MCP endpoint (Streamable HTTP)

https://gateway.pipeworx.io/hpo-api/mcp

Vendor documentation

What you can do with it

Look up HPO terms by ID
Search for phenotype terms using text
Retrieve direct children or parents of a term
Find diseases associated with a specific gene

Tools advertised by the last live check:

ask_pipeworx
ask_pipeworx_beta
ask_pipeworx_grounded
search_within
deep_research
discover_tools
resolve_entity
compare_entities
subscribe
unsubscribe
list_subscriptions
recent_alerts
entity_profile
recent_changes
validate_claim
company_facts
scan_dependency
bet_research
polymarket_arbitrage
polymarket_edges
polymarket_kalshi_spread
polymarket_fill_risk
polymarket_edge_tracker
kalshi_weather_edge
resolution_audit
resolution_diff
release_calendar_markets
pipeworx_trending
suggest_questions
generate_llms_txt
ai_visibility_check
scan_competitor_ai_presence
pipeworx_feedback
remember
recall
forget
term
search
term_children
term_parents
term_descendants
gene_diseases
disease_phenotypes

Connect from your client

Each snippet registers the same endpoint; pick the client you use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Claude Code

Run this once in a terminal. It registers a Streamable HTTP server. Use --scope project to write .mcp.json for the repo.

Claude Code configuration

claude mcp add --transport http hpo-api-mcp https://gateway.pipeworx.io/hpo-api/mcp

Codex

Run this once. Codex stores MCP servers in ~/.codex/config.toml (or .codex/config.toml in a trusted project).

Codex configuration

codex mcp add hpo-api-mcp --url https://gateway.pipeworx.io/hpo-api/mcp

Cursor

Merge this server into .cursor/mcp.json in your project, then enable hpo-api-mcp in your MCP settings.

Cursor configuration

{
  "mcpServers": {
    "hpo-api-mcp": {
      "url": "https://gateway.pipeworx.io/hpo-api/mcp"
    }
  }
}

Cline

Merge this into cline_mcp_settings.json (Cline → MCP Servers → Configure). The type must be streamableHttp for a remote HTTP server.

Cline configuration

{
  "mcpServers": {
    "hpo-api-mcp": {
      "type": "streamableHttp",
      "url": "https://gateway.pipeworx.io/hpo-api/mcp",
      "disabled": false
    }
  }
}

VS Code

Merge this server into .vscode/mcp.json. Use MCP: List Servers to start hpo-api-mcp and inspect its tools.

VS Code configuration

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

Gemini CLI

Run this once. It writes .gemini/settings.json in the current project; pass --scope user for ~/.gemini/settings.json.

Gemini CLI configuration

gemini mcp add --transport http hpo-api-mcp https://gateway.pipeworx.io/hpo-api/mcp

Claude Desktop

Merge this into claude_desktop_config.json (macOS: ~/Library/Application Support/Claude/, Windows: %APPDATA%\Claude\), then restart Claude Desktop.

Claude Desktop configuration

{
  "mcpServers": {
    "hpo-api-mcp": {
      "url": "https://gateway.pipeworx.io/hpo-api/mcp"
    }
  }
}

Windsurf

Merge this into ~/.codeium/windsurf/mcp_config.json, then refresh MCP in Cascade. Windsurf remote servers use serverUrl, not url.

Windsurf configuration

{
  "mcpServers": {
    "hpo-api-mcp": {
      "serverUrl": "https://gateway.pipeworx.io/hpo-api/mcp"
    }
  }
}

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