HPO Phenotype Ontology Scraper

HPO Phenotype Ontology Scraper

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

The Human Phenotype Ontology (HPO) is the standard vocabulary for describing phenotypic abnormalities in human disease, but its official API and website are built for browsing, not bulk analysis. This Actor reads the public HPO term pages directly, filtered by search query, and returns each matching term in one fixed schema. It is the fastest way to build a local dataset of phenotype terms for bioinformatics pipelines, rare disease research, or clinical NLP training.

Who uses it	What they scrape HPO Phenotype Ontology for
Bioinformaticians	Building a local copy of HPO terms for variant annotation pipelines
Rare disease researchers	Compiling phenotype profiles for a cohort of patients
Clinical NLP engineers	Creating a training corpus of phenotype terms and synonyms
Ontology curators	Auditing term definitions and cross-references at scale

What it does

This Actor collects HPO phenotype terms by search query and returns each one as a flat row with its ID, definition, synonyms, and disease associations.

• 🔍 Search query: pass any free-text term like 'seizure' or 'abnormal heart morphology' and get matching HPO terms.
• 📊 Bulk collection: set maxItems up to 1,000,000 to pull the full ontology or a large subset in one run.
• 🧬 Disease associations: each term row includes linked diseases and genes where available, ready for downstream analysis.
• 💾 Multiple export formats: download results as CSV, JSON, Excel, or XML directly from the Apify dataset.

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

What you can do with HPO Phenotype Ontology data

🧬 Build a phenotype annotation pipeline.

A bioinformatician runs the Actor with no query and maxItems 1,000,000 to download the entire HPO, then loads the JSON export into a local database for variant prioritization.

📋 Compile cohort phenotype profiles.

A rare disease researcher searches for terms like 'intellectual disability' and 'seizure', collects all matching HPO terms, and maps them to patient records for a case series.

🤖 Train clinical NLP models.

An NLP engineer scrapes HPO terms and their synonyms to build a gazetteer for named entity recognition in electronic health records.

🔎 Audit ontology coverage.

An ontology curator runs weekly scrapes of specific branches to check for missing definitions or outdated cross-references.

Why choose this scraper

	What you get
No API key or registration	Start scraping immediately without signing up for HPO API access
Flat, analysis-ready rows	Every term is returned as a single record with consistent fields
Scales to the full ontology	Collect up to a million terms per run for complete coverage
Built for automation	Schedule runs or integrate with Apify's API for recurring updates

How it compares

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

	HPO Phenotype Ontology Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When HPO 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 an optional search query and a maximum number of terms, and filters run as each term is read so only matches reach your dataset. The Input tab lists every parameter.

A first run with the defaults:

{
 "maxItems": 10
}

A larger pull:

{
 "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 Phenotype Ontology 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 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-phenotype-jax-scraper"

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

Troubleshooting

Why am I getting no results?

Your query may be too specific or misspelled. Try a broader term like 'seizure' instead of 'generalized tonic-clonic seizure'. Also ensure maxItems is at least 1.

The run is taking too long.

Large maxItems values will take longer because the Actor must paginate through many pages. Reduce maxItems or narrow your query to speed up the run.

Some fields are empty in the output.

Not all HPO terms have synonyms or disease associations. Empty fields are expected for terms without those annotations.

I get an error about the website structure.

The HPO website may have changed its layout. Try running the Actor again later, or contact support with the run ID so we can update the scraper.

FAQ

Question	Answer
What is the Human Phenotype Ontology?	The HPO is a standardized vocabulary of phenotypic abnormalities encountered in human disease, maintained by an international consortium. Each term has a unique ID, a definition, synonyms, and links to associated diseases and genes.
Do I need an API key to scrape HPO?	No. This Actor reads the public HPO term pages directly, so no registration or API key is required.
Can I scrape the entire HPO ontology?	Yes. Set maxItems to 1,000,000 and leave the query empty to collect all terms. The Actor will paginate through the ontology until it reaches the limit or exhausts the source.
What data does each term row include?	Each row includes the HPO term ID, name, definition, synonyms, and associated diseases and genes where available. The exact fields are shown in the sample output below.
How do I filter by a specific phenotype?	Use the query input to search for a term like 'seizure' or 'abnormal heart morphology'. The Actor will return only terms matching that query.
Can I export results to CSV or Excel?	Yes. After the run finishes, you can download the dataset as CSV, JSON, Excel, or XML from the Apify platform.
Is this Actor suitable for commercial use?	Yes, as long as you comply with the HPO license (CC BY 4.0) and Apify's terms of service. Attribution to the HPO project is appreciated.
How often is the HPO updated?	The HPO is updated regularly, typically several times a year. You can schedule this Actor to run weekly or monthly to keep your local copy current.
Can I run this Actor on a schedule?	Yes. Use Apify's scheduler to run the Actor at any interval, such as daily or weekly, and automatically store the latest ontology data.
What if I get no results for my query?	Check the spelling of your query and try a broader term. HPO uses specific medical terminology, so 'heart problem' may not match but 'abnormal heart morphology' will.

Related actors

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.