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⇱ HPO Human Phenotype Ontology Scraper · Apify

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HPO Human Phenotype Ontology Scraper

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HPO Human Phenotype Ontology Scraper

Search the Human Phenotype Ontology by keyword or HP ID and pull back terms with hpoId, name, definition, synonyms, parents, children, plus optional associated diseases and genes. Useful for rare disease research, clinical curation, and genomic variant annotation pipelines.

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from $7.50 / 1,000 results

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👁 ParseForge

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🧠 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 geneticistsMap patient phenotypes to candidate genes
🔬 Rare disease researchersBuild phenotype profiles for cohorts
🩺 Diagnostic teamsEnrich HPO term picklists
🤖 BioinformaticiansMirror HPO into local pipelines
📊 Pharma R&DTrack phenotypes linked to drug targets
👩‍💻 DevelopersSkip 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

FieldTypeRequiredDescription
searchTermstringNoKeyword or HPO ID like HP:0001250.
maxItemsintegerNoFree 10, paid up to 1,000,000.
includeAssociationsbooleanNoFetch 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

FieldTypeDescription
🆔 hpoIdstringHPO term identifier.
🧠 namestringTerm name.
📖 definitionstringFormal definition.
🔄 synonymsstringExact and related synonyms.
⬆️ parentsstringParent term IDs.
⬇️ childrenstringChild term IDs.
🩺 associatedDiseasesstringOMIM / Orphanet disease names.
🧬 genesstringAssociated gene symbols.
🕒 scrapedAtstringFetch timestamp.
❌ errorstringError 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

ApproachSetupSearchEnrichment
Download OBO and parseHoursBuild your own indexManual joins
HPO API + custom client30 minYesManual
This Actor5 secBuilt-inBuilt-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.

🔗 Recommended Actors

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ParseForge Disease Ontology ScraperDisease Ontology terms.
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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.

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.

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