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Hpo Api

Queries HPO terms, hierarchies, gene-disease links, and disease-phenotype annotations through MCP.

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Install Hpo Api

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "hpo-api": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-hpo-api"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

Automated check passed— started and listed 7 tools correctly (15d ago).

Overview

Hpo Api MCP server exposes Human Phenotype Ontology terms and gene or disease annotations through MCP tools. It reads from the newer HPO REST API and falls back to the older HPO endpoint when needed. Use it to search clinical phenotype concepts, traverse HPO hierarchies, or connect genes and diseases to phenotype data. It supports a hosted gateway endpoint, direct HTTP calls, and a local keyless stdio package.

Use cases

  • Search HPO terms from clinical phenotype descriptions
  • Traverse parent, child, and descendant relationships
  • Find diseases associated with an NCBIGene identifier
  • Retrieve phenotypes annotated to an OMIM, ORPHA, or MONDO disease
  • Call HPO lookups from an MCP client or HTTP workflow

Key features

  • HPO term lookup by HP identifier
  • Paginated text search across HPO terms
  • Parent, child, and descendant traversal
  • Gene-to-disease association queries
  • Disease-to-phenotype annotation queries
  • Hosted gateway and local stdio modes

Tools7

What Hpo Api lets your agent do. Expand a tool for its parameters.

Verified live~637 tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 2d ago

Recent health check succeeded.

7/7 checks healthy over the last 46d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 14d ago via OSV.dev · @pipeworx/mcp-hpo-api (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

npm downloads473Package downloads in the last 30 days.
Last commit26d agoMost recent push to the default branch.
Availability100%Our rolling endpoint + install checks that succeeded.
Install checkPassedOur sandbox started it and listed its tools.
Tools exposed7Callable tools this server registers over MCP.
Directory activity4 viewsConfig copies, upvotes, and views on AllMCPs.

How Hpo Api works

What Hpo Api MCP server does

Hpo Api MCP server provides agent access to Human Phenotype Ontology data. Its tools cover individual HPO term retrieval, text search, parent and child relationships, complete descendant subtrees, gene-to-disease associations, and disease-to-phenotype annotations.

The service accepts HPO identifiers such as HP:0001250 for term and hierarchy operations. Gene lookups use NCBIGene identifiers, while disease phenotype queries accept OMIM, ORPHA, or MONDO identifiers. The package is keyless, so the supplied connection examples do not require an API credential.

How it works

The implementation uses the HPO REST service at https://ontology.jax.org/api/hp/ and can fall back to https://hpo.jax.org/api/hpo/. MCP clients can connect to the hosted pack endpoint at https://gateway.pipeworx.io/hpo-api/mcp. That endpoint lists the HPO tools together with shared Pipeworx meta-tools, including routing and discovery functions.

A full gateway connection at https://gateway.pipeworx.io/mcp exposes the broader Pipeworx catalog directly. Both hosted URLs use the same gateway, while the pack endpoint lists the HPO pack as its direct scope. The standalone package instead communicates over stdin and stdout and exposes only the HPO pack tools.

Setup and configuration

For a hosted connection, add the pack URL to an MCP client configuration. The README specifically names Claude Desktop, Cursor, and Windsurf as compatible clients. No account is needed for the initial HTTP calls described in the documentation.

For local use, run npx -y @pipeworx/mcp-hpo-api or configure that command as an MCP server with no arguments. This route avoids a Pipeworx account and gateway round trip. It uses the same source and capabilities as the hosted pack, without the gateway’s shared meta-tools.

The tools can also be called over HTTP. For example, send a JSON POST containing an HPO identifier to /v1/tools/term; tool inspection is available through the corresponding GET endpoint.

Tools and capabilities

  • term(id) retrieves one HPO term by identifier.
  • search(query, limit?, page?) searches HPO terms by text with optional pagination controls.
  • term_children(id) returns a term’s direct children.
  • term_parents(id) returns a term’s direct parents.
  • term_descendants(id) returns the full descendant subtree with pagination.
  • gene_diseases(id) finds diseases associated with an NCBIGene identifier.
  • disease_phenotypes(id) returns HPO terms annotated to an OMIM, ORPHA, or MONDO disease identifier.

Limitations and notes

The Hpo Api MCP server is focused on HPO terms and the listed gene or disease annotation relationships. The hosted pack endpoint also includes shared Pipeworx tools, so its reported tool count is larger than the seven HPO-specific tools above. The local stdio mode does not provide those shared tools or cross-catalog ask_pipeworx routing.

Descendant results are paginated, and text search accepts optional limit and page values.

Read the full README View source on GitHub

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Frequently Asked Questions about Hpo Api

Hpo Api is an MCP server that connects AI agents to Human Phenotype Ontology REST data and provides tools for HPO term lookup, text search, hierarchy traversal, gene-disease associations, and disease-phenotype annotations. It supports gateway or local stdio use and requires no API key.

Install it locally with `npx -y @pipeworx/mcp-hpo-api` or add the hosted MCP URL `https://gateway.pipeworx.io/hpo-api/mcp` to your client configuration. The local option runs over stdin/stdout and does not require a Pipeworx account.

Yes, Hpo Api works with Cursor through the hosted MCP endpoint. Add `https://gateway.pipeworx.io/hpo-api/mcp` as the server URL in Cursor’s MCP configuration.

Call the gateway’s `/v1/tools/` endpoints with JSON over HTTP, such as posting `{"id":"HP:0000118"}` to `/v1/tools/term`.

Hpo Api accepts HP identifiers for term and hierarchy tools, NCBIGene identifiers for gene-disease queries, and OMIM, ORPHA, or MONDO identifiers for disease phenotype queries.

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