drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/hpo.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
HPO (Human Phenotype Ontology)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/hpo.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

HPO (Human Phenotype Ontology)

Base URL

https://ontology.jax.org/api/hp

Auth

No API key required.

Important: URL-encode colons in HP IDs — HP:0001250 becomes HP%3A0001250

Key Endpoints

Endpoint	Description
/hpo/search?q={query}&max={n}	Search HPO terms by name
/hpo/term/{id}	Term details
/hpo/term/{id}/genes	Genes associated with a phenotype
/hpo/term/{id}/diseases	Diseases associated with a phenotype
/hpo/term/{id}/children	Child terms in hierarchy
/hpo/term/{id}/parents	Parent terms
/hpo/gene/{gene_id}	Phenotypes for a gene (Entrez ID)
/hpo/disease/{disease_id}	Phenotypes for a disease (OMIM/ORPHA)

Example Calls

# Search for "seizure"
https://ontology.jax.org/api/hp/hpo/search?q=seizure&max=5

# Term details for Seizure
https://ontology.jax.org/api/hp/hpo/term/HP%3A0001250

# Genes associated with Seizure
https://ontology.jax.org/api/hp/hpo/term/HP%3A0001250/genes

# Diseases for Seizure
https://ontology.jax.org/api/hp/hpo/term/HP%3A0001250/diseases

# Phenotypes for SCN1A (Entrez 6323)
https://ontology.jax.org/api/hp/hpo/gene/6323

Response Format

JSON. Terms: id, name, definition, synonyms. Gene associations: genes[] with geneId, geneSymbol. Diseases: diseases[] with diseaseId, diseaseName.

Rate Limits

No published limits. Bulk annotation files at https://hpo.jax.org/data/annotations