60 lines
1.7 KiB
Markdown
60 lines
1.7 KiB
Markdown
---
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title: "Monarch Initiative API"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/monarch.md
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upstream_sha: 9c9bd2e9
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# Monarch Initiative API
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## Base URL
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```
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https://api.monarchinitiative.org/v3/api
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```
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## Auth
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No API key required.
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## Key Endpoints
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| Endpoint | Description |
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|----------|-------------|
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| `/search?q={query}` | Text search across all entities |
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| `/autocomplete?q={prefix}` | Autocomplete entity names |
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| `/entity/{id}` | Entity details (gene, disease, phenotype) |
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| `/entity/{id}/associations` | Associations for an entity |
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| `/entity/{id}/associations?category={cat}` | Filtered associations |
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## Entity ID Prefixes
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- `MONDO:` — diseases (e.g. `MONDO:0007947`)
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- `HP:` — phenotypes (e.g. `HP:0001250`)
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- `HGNC:` — genes (e.g. `HGNC:3603`)
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- `NCBIGene:` — genes (e.g. `NCBIGene:7157`)
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## Association Categories
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`biolink:GeneToPhenotypicFeatureAssociation`, `biolink:DiseaseToPhenotypicFeatureAssociation`, `biolink:GeneToDiseaseAssociation`
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## Example Calls
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```
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# Search for Marfan syndrome
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https://api.monarchinitiative.org/v3/api/search?q=Marfan+syndrome&limit=5
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# Entity details for a disease
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https://api.monarchinitiative.org/v3/api/entity/MONDO:0007947
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# Gene-to-phenotype for FBN1
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https://api.monarchinitiative.org/v3/api/entity/HGNC:3603/associations?category=biolink:GeneToPhenotypicFeatureAssociation&limit=10
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```
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## Response Format
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JSON. Search: `items[]` with `id`, `name`, `category`. Associations: `items[]` with `subject`, `predicate`, `object`, `publications`.
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## Rate Limits
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No published limits. Be reasonable.
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