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

{
  "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:

{
  "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
• NCBI E-utilities Scraper
• Reactome Pathways Scraper
• Cellosaurus Scraper

Development

$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.