HPO Phenotypes Scraper

HPO Phenotypes Scraper

Scrape phenotype terms from the Human Phenotype Ontology, with disease and gene associations, up to a million per run. Each term comes with its ID, definition, synonyms, and computed enrichment data. No API key or registration. Export to CSV, JSON, Excel, or XML.

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities in human disease, but its official API requires technical setup and returns nested JSON that is hard to flatten. This Actor reads the public HPO search and term pages directly, so you can search by keyword or HPO ID and get each phenotype as a clean, flat row with optional disease and gene associations. It is ideal for bioinformaticians, clinical researchers, and anyone building phenotype-driven datasets.

Who uses it	What they scrape HPO Human Phenotype Ontology for
Bioinformaticians	Build a local dataset of phenotype terms for variant annotation pipelines
Clinical researchers	Map patient symptoms to standardized HPO terms for cohort analysis
Rare disease advocates	Compile lists of associated genes and diseases for a specific phenotype
Data scientists	Create training data for phenotype normalization or NLP models

What it does

This Actor collects HPO phenotype terms by search keyword or HPO ID, and returns each term as a flat row with its ID, name, definition, synonyms, and optional associated diseases and genes.

• 🔍 Search by keyword or ID: enter a term like 'seizure' or an ID like HP:0001250 to fetch matching phenotypes.
• 📊 Disease and gene associations: optionally enrich each term with its linked diseases and genes, at the cost of speed.
• ⚙️ Flexible limits: set a maximum number of phenotypes from 1 to 1,000,000 per run.
• 📦 Flat output: every phenotype is returned as a single row, ready for CSV, JSON, Excel, or XML export.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

What you can do with HPO Human Phenotype Ontology data

🧬 Build a phenotype reference set.

A bioinformatician runs the Actor with searchTerm 'seizure' and maxItems 500 to collect all seizure-related HPO terms and their definitions for a variant annotation pipeline.

🩺 Map patient symptoms to HPO.

A clinical researcher enters a list of symptom keywords one by one to retrieve matching HPO IDs, then uses the flat output to standardize electronic health records.

🔗 Link phenotypes to genes.

A rare disease advocate searches for 'short stature' with includeAssociations true to get all associated genes and diseases, then exports the list for a patient registry.

🤖 Train an NLP model.

A data scientist collects thousands of phenotype terms and their synonyms to create a training set for a phenotype normalization model.

Why choose this scraper

	What you get
No API key	Access public HPO data without registration or rate limits
Flat schema	Each phenotype is one row, no nested JSON to parse
Enrichment option	Add disease and gene associations with a single checkbox
Scalable	Collect up to a million phenotypes per run

How it compares

No other Store actor targets HPO Human Phenotype Ontology the same way, so the honest comparison is with the alternatives teams actually weigh.

	HPO Phenotypes Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When HPO Human Phenotype Ontology changes	Maintained for you	You fix it	You re-learn the page
Proxies, retries, anti-bot	Built in	Your problem	Browser only
Output	Fixed JSON schema, CSV/Excel export	Whatever you build	Copy-paste
Cost	Pay per result	Engineering time	Analyst hours

Configure the run

Drive the Actor with a search term or HPO ID, set a maximum number of phenotypes, and optionally include disease and gene associations for each term. The Input tab lists every parameter.

A first run with the defaults:

{
 "searchTerm": "seizure",
 "maxItems": 10
}

A larger pull:

{
 "searchTerm": "seizure",
 "maxItems": 200
}

Pricing

Pay-per-result: $0.0085 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$0.85
1,000 results	$8.50
10,000 results	$85.00

New Apify accounts start with $5 in free credit.

Free users

Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the HPO Phenotypes Scraper.
3. Set your inputs and any filters, then click Start.
4. Export the results as CSV, Excel, JSON, or XML from the Dataset tab.

Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.

Use with AI agents (MCP)

Give an AI agent live access to HPO Human Phenotype Ontology through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

claude mcp add --transport http apify "https://mcp.apify.com?tools=parseforge/hpo-phenotypes-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results?

Check that your searchTerm is spelled correctly or that the HPO ID is valid. Try a broader keyword like 'seizure' instead of a very specific phrase.

The run is slow when includeAssociations is on.

Fetching associations requires an extra request per phenotype. Reduce maxItems or disable includeAssociations if you only need the core term data.

Some fields are empty in the output.

Not all HPO terms have synonyms or associations. Empty fields are normal for terms without that data.

I get an error about maxItems.

maxItems must be between 1 and 1,000,000. Set a value within that range.

FAQ

Question	Answer
What is the Human Phenotype Ontology?	The Human Phenotype Ontology (HPO) is a standardized vocabulary of phenotypic abnormalities encountered in human disease. It provides terms, definitions, and relationships for describing patient phenotypes.
Do I need an API key to use this Actor?	No. This Actor scrapes the public HPO website directly, so no API key or registration is required.
Can I search by HPO ID instead of a keyword?	Yes. Enter an HPO ID such as HP:0001250 in the searchTerm field to fetch that specific term and its details.
What does includeAssociations do?	When enabled, the Actor fetches the diseases and genes associated with each phenotype term. This adds extra fields to the output but makes the run slower.
How many phenotypes can I collect in one run?	You can set maxItems from 1 to 1,000,000. The Actor will stop after reaching that number of matching terms.
What output formats are supported?	You can export the results as CSV, JSON, Excel, or XML from the Apify dataset.
Is the data up to date?	The Actor reads the live HPO website, so you get the current terms and associations as of the run time.
Can I run this on a schedule?	Yes, you can set up a scheduled run in Apify to refresh your phenotype dataset periodically.

Related actors

• google-scholar-scraper: Use this to find academic papers citing specific HPO terms.

Browse the full ParseForge collection for more scrapers.

🆘 Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by The Human Phenotype Ontology Project. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.