# Human Phenotype Ontology (HPO) Scraper (`ninhothedev/hpo-phenotype-scraper`) Actor

$0.5/1K 🔥 HPO Phenotypes! Search human phenotype terms with gene & disease links. No key. JSON, CSV, Excel or API in seconds. Support rare-disease and clinical genetics ⚡

- **URL**: https://apify.com/ninhothedev/hpo-phenotype-scraper.md
- **Developed by:** [ninhothedev](https://apify.com/ninhothedev) (community)
- **Categories:** Developer tools, Automation, AI
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $0.50 / 1,000 results

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.

Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event

## What's an Apify Actor?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.
Actors are written with capital "A".

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

## Human Phenotype Ontology (HPO) Scraper

Turn the **Human Phenotype Ontology** into clean, structured JSON: phenotype
terms with definitions, synonyms, cross-references, parent/child terms, and
their **gene** and **disease** associations. No API key, no login — HPO is a
free and open resource.

Built on the official Monarch/JAX ontology API (`ontology.jax.org`). Great for
rare-disease diagnosis, clinical genetics, phenotype-driven gene prioritisation,
and biomedical NLP pipelines.

### Modes

| Mode | Input used | What you get |
|------|-----------|--------------|
| `search` | `queries` (free text) | Phenotype terms matching each query |
| `terms`  | `hpoIds` (e.g. `HP:0001250`) | Full detail for explicit HP ids |
| `genes`  | `queries` (gene symbols, e.g. `SCN1A`) | Phenotypes associated with a gene |

### Input

```json
{
  "mode": "search",
  "queries": ["seizure", "intellectual disability"],
  "hpoIds": ["HP:0001250"],
  "includeAssociations": true,
  "maxItems": 200
}
```

- **mode** — `search` (default), `terms`, or `genes`.
- **queries** — phenotype queries (search) or gene symbols (genes).
- **hpoIds** — explicit HP ids for `terms` mode.
- **includeAssociations** — fetch gene + disease links per term (default `true`).
  When off, association fields are `null`.
- **maxItems** — cap on output records (default `200`, max `3000`).

### Output

Each record:

```json
{
  "type": "phenotype",
  "hpo_id": "HP:0001250",
  "name": "Seizure",
  "definition": "A seizure is an intermittent abnormality of nervous system physiology...",
  "comment": "The term epilepsy is not used to describe recurrent febrile seizures.",
  "synonyms": ["Epileptic seizure", "Seizures", "Epilepsy"],
  "xrefs": ["SNOMEDCT_US:128613002", "UMLS:C0014544"],
  "parent_count": 1,
  "parents": [{"id": "HP:0012638", "name": "Abnormal nervous system physiology"}],
  "child_count": 30,
  "children": [{"id": "HP:0002069", "name": "Bilateral tonic-clonic seizure"}],
  "descendant_count": 346,
  "gene_count": 2127,
  "associated_genes": ["SCN1A", "ADAM22", "..."],
  "disease_count": 3129,
  "associated_diseases": [{"id": "OMIM:607208", "name": "Dravet syndrome"}],
  "url": "https://hpo.jax.org/browse/term/HP:0001250",
  "source": "hpo",
  "scraped_at": "2026-08-11T00:00:00+00:00"
}
```

Cross-refs (`xrefs`) surface UMLS / SNOMED / MeSH mappings. `associated_genes`
and `associated_diseases` are enrichment fields — capped (50 genes, 30 diseases)
and only populated when `includeAssociations` is on.

### Use cases

- **Rare disease diagnosis** — map a patient's phenotypes to candidate diseases.
- **Clinical genetics** — link phenotypes to causative genes.
- **Phenotype-driven gene prioritisation** — rank genes by phenotype overlap.
- **Biomedical NLP** — normalise clinical text to HPO terms + cross-refs.

### Pricing

Lightweight and cheap to run — roughly **~$0.50 per 1,000 phenotype records**
depending on association enrichment. HPO data itself is free and open.

### Related actors

- [Clinical Trials Scraper](https://apify.com/ninhothedev/clinical-trials-scraper)
- [NCBI E-utilities Scraper](https://apify.com/ninhothedev/ncbi-eutils-scraper)
- [Reactome Pathways Scraper](https://apify.com/ninhothedev/reactome-pathways-scraper)
- [Cellosaurus Scraper](https://apify.com/ninhothedev/cellosaurus-scraper)

### Development

```bash
python3 tests/test_mapping.py   # offline smoke tests, stdlib only
```

Data © the Human Phenotype Ontology / Jackson Laboratory, used under their open
terms. This actor is an independent tool and is not affiliated with HPO/JAX.

# Actor input Schema

## `mode` (type: `string`):

What to scrape: 'search' queries phenotype terms by free text (uses Queries); 'terms' resolves explicit HP ids (uses HPO IDs); 'genes' returns phenotypes associated with a gene symbol (uses Queries as gene symbols).

## `queries` (type: `array`):

Free-text phenotype queries for 'search' mode, or gene symbols (e.g. SCN1A) for 'genes' mode. Ignored in 'terms' mode.

## `hpoIds` (type: `array`):

Explicit HPO term ids (e.g. HP:0001250) to resolve in 'terms' mode. Ignored in other modes.

## `includeAssociations` (type: `boolean`):

Fetch associated genes and diseases for each phenotype term (one extra request per term). When off, association fields are left null.

## `maxItems` (type: `integer`):

Maximum number of phenotype records to output.

## Actor input object example

```json
{
  "mode": "search",
  "queries": [
    "seizure",
    "intellectual disability"
  ],
  "hpoIds": [
    "HP:0001250"
  ],
  "includeAssociations": true,
  "maxItems": 200
}
```

# Actor output Schema

## `results` (type: `string`):

No description

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "queries": [
        "seizure",
        "intellectual disability"
    ],
    "hpoIds": [
        "HP:0001250"
    ]
};

// Run the Actor and wait for it to finish
const run = await client.actor("ninhothedev/hpo-phenotype-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = {
    "queries": [
        "seizure",
        "intellectual disability",
    ],
    "hpoIds": ["HP:0001250"],
}

# Run the Actor and wait for it to finish
run = client.actor("ninhothedev/hpo-phenotype-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print(f"💾 Check your data here: https://console.apify.com/storage/datasets/{run.default_dataset_id}")
for item in client.dataset(run.default_dataset_id).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "queries": [
    "seizure",
    "intellectual disability"
  ],
  "hpoIds": [
    "HP:0001250"
  ]
}' |
apify call ninhothedev/hpo-phenotype-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "type": "http",
            "url": "https://mcp.apify.com/?tools=fetch-actor-details,ninhothedev/hpo-phenotype-scraper"
        }
    }
}

```

The hosted server signs you in with OAuth on first connect, so no API token belongs in this config. Clients without OAuth support can send an `Authorization: Bearer <APIFY_API_TOKEN>` header instead, using a token from API & Integrations in Apify Console (https://console.apify.com/settings/integrations).

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/2vAyKb3PFu6f3zaWc/builds/0Dq0Vk01Psziuulfs/openapi.json