🧠 HPO Phenotypes Scraper

🚀 Export Human Phenotype Ontology terms in seconds. HPO ID, name, definition, synonyms, parents, children, associated diseases, and genes.

🕒 Last updated: 2026-06-05 · 📊 10 fields per record · Jackson Lab HPO API · 17,000+ phenotype terms · Real-time

The HPO Phenotypes Scraper turns the public Jackson Laboratory HPO API into a flat dataset of phenotype terms. Search by keyword or HPO ID, and optionally enrich each term with its associated diseases and causal genes.

The Human Phenotype Ontology is the standard vocabulary of phenotypic abnormalities used in clinical genetics worldwide.

🎯 Target Audience	💡 Primary Use Cases
🧬 Clinical geneticists	Map patient phenotypes to candidate genes
🔬 Rare disease researchers	Build phenotype profiles for cohorts
🩺 Diagnostic teams	Enrich HPO term picklists
🤖 Bioinformaticians	Mirror HPO into local pipelines
📊 Pharma R&D	Track phenotypes linked to drug targets
👩‍💻 Developers	Skip the OBO file parsing

📋 What the HPO Phenotypes Scraper does

• Searches the HPO term catalog by keyword or resolves a single HPO ID.
• For each term, returns name, definition, synonyms, parent and child terms.
• Optionally enriches with associated OMIM / Orphanet diseases and causal genes.
• Flattens nested arrays to delimited strings for spreadsheet imports.
• Returns clean error rows on empty searches.
• Exports to your preferred dataset format.

💡 Why it matters: Most HPO consumers download the entire OBO file, parse it themselves, and then build a search index. This actor lets you query HPO directly with one click.

🎬 Full Demo

🚧 Coming soon.

⚙️ Input

Field	Type	Required	Description
searchTerm	string	No	Keyword or HPO ID like HP:0001250.
maxItems	integer	No	Free 10, paid up to 1,000,000.
includeAssociations	boolean	No	Fetch associated diseases and genes per term.

Example 1, search for 'seizure'

{ "searchTerm": "seizure", "maxItems": 20, "includeAssociations": true }

Example 2, lookup a single HPO ID

{ "searchTerm": "HP:0001250" }

⚠️ Good to Know: Disease and gene enrichment adds one extra request per term. Disable it for fast catalog dumps.

📊 Output

Field	Type	Description
🆔 hpoId	string	HPO term identifier.
🧠 name	string	Term name.
📖 definition	string	Formal definition.
🔄 synonyms	string	Exact and related synonyms.
⬆️ parents	string	Parent term IDs.
⬇️ children	string	Child term IDs.
🩺 associatedDiseases	string	OMIM / Orphanet disease names.
🧬 genes	string	Associated gene symbols.
🕒 scrapedAt	string	Fetch timestamp.
❌ error	string	Error message if any.

{
  "hpoId": "HP:0001250",
  "name": "Seizure",
  "definition": "A seizure is an intermittent abnormality of nervous system physiology...",
  "synonyms": "Seizures; Epileptic seizure",
  "parents": "HP:0012638",
  "children": "HP:0002197; HP:0002353",
  "associatedDiseases": "Dravet syndrome; Tuberous sclerosis",
  "genes": "SCN1A, TSC1, TSC2",
  "scrapedAt": "2026-06-05T12:00:00.000Z",
  "error": null
}

✨ Why choose this Actor

| 🆓 | Public Jackson Lab API, no key required. | | 🧹 | Flat rows, no OBO parsing. | | 🎯 | Optional disease and gene enrichment per term. | | 🔌 | One actor, the full HPO. | | 💾 | Push to dataset, instant export. |

📈 How it compares to alternatives

Approach	Setup	Search	Enrichment
Download OBO and parse	Hours	Build your own index	Manual joins
HPO API + custom client	30 min	Yes	Manual
This Actor	5 sec	Built-in	Built-in

🚀 How to use

1. Click Try for free.
2. Type a phenotype keyword or HPO ID.
3. Toggle disease and gene enrichment.
4. Click Start.

💼 Business use cases

🧬 Phenotype-driven diagnosis. Pull HPO terms with the right disease links for clinical decision support.

📊 Cohort building. Build phenotype profiles for rare disease cohorts.

🤖 Curation tools. Mirror HPO into your internal annotation UI.

📈 Drug-target research. Map phenotypes to target genes.

🔌 Automating HPO Phenotypes Scraper

• Make / Zapier trigger and push to Sheets or a database.
• Cron scheduler via Apify.
• Webhooks on run completion.
• Pipe to BigQuery / Snowflake / Postgres via integrations.

🌟 Beyond business use cases

🎓 Teaching. Walk medical students through phenotype hierarchies.

🧪 Personal research. Build a phenotype tracker for a rare condition.

🤝 Open science. Public phenotype-disease maps.

🧰 Prototyping. Add HPO autocomplete to a new tool in minutes.

🤖 Ask an AI assistant about this scraper

Paste this README into your assistant and describe your phenotype workflow.

❓ Frequently Asked Questions

❓ Do I need an API key? No.

❓ Can I look up a single ID? Yes, paste it in searchTerm.

❓ How big is HPO? 17,000+ terms.

❓ What's the rate limit? Be reasonable, the API is public.

❓ Are arrays flattened? Yes, semicolon-joined.

❓ Can I skip the enrichment? Yes, toggle off.

❓ Can I schedule runs? Yes.

❓ Is this scraping? API only.

❓ Will the schema change? Core fields stable.

❓ Download format? Any format Apify supports.

🔌 Integrate with any app

Apify ships native integrations with Make, Zapier, Slack, Discord, Google Drive, Google Sheets, Gmail, Airbyte, Keboola, Telegram, GitHub, and any REST or webhook endpoint.

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💡 Pro Tip: browse the complete ParseForge collection for 900+ production-grade scrapers across business intelligence, real estate, e-commerce, sports, finance, and public records.

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Disclaimer: This actor scrapes only publicly available data. ParseForge is not affiliated with Jackson Laboratory or HPO. Users are responsible for complying with the target site's terms of service and applicable law. Create a free account w/ $5 credit.