Skillintermediate

Monarch Initiative API

| Endpoint | Description | |----------|-------------| | `/search?q={query}` | Text search across all entities | | `/autocomplete?q={prefix}` | Autocomplete entity names | | `/entity/{id}` | Entity details (gene, disease, phenotype) | | `/entity/{id}/associations` | Associations for an entity | | `/entity/{id}/associations?category={cat}` | Filtered associations |

Claude Code Knowledge Pack7/10/2026

Overview

Monarch Initiative API

Base URL

https://api.monarchinitiative.org/v3/api

Auth

No API key required.

Key Endpoints

Endpoint	Description
`/search?q={query}`	Text search across all entities
`/autocomplete?q={prefix}`	Autocomplete entity names
`/entity/{id}`	Entity details (gene, disease, phenotype)
`/entity/{id}/associations`	Associations for an entity
`/entity/{id}/associations?category={cat}`	Filtered associations

Entity ID Prefixes

MONDO: — diseases (e.g. MONDO:0007947)
HP: — phenotypes (e.g. HP:0001250)
HGNC: — genes (e.g. HGNC:3603)
NCBIGene: — genes (e.g. NCBIGene:7157)

Association Categories

biolink:GeneToPhenotypicFeatureAssociation, biolink:DiseaseToPhenotypicFeatureAssociation, biolink:GeneToDiseaseAssociation

Example Calls

# Search for Marfan syndrome
https://api.monarchinitiative.org/v3/api/search?q=Marfan+syndrome&limit=5

# Entity details for a disease
https://api.monarchinitiative.org/v3/api/entity/MONDO:0007947

# Gene-to-phenotype for FBN1
https://api.monarchinitiative.org/v3/api/entity/HGNC:3603/associations?category=biolink:GeneToPhenotypicFeatureAssociation&limit=10

Response Format

JSON. Search: items[] with id, name, category. Associations: items[] with subject, predicate, object, publications.

Rate Limits

No published limits. Be reasonable.