drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/monarch.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
Monarch Initiative API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/monarch.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

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.