Skills › Scientific Agent Skills › database-lookup › monarch.md
monarch.md
46 lines · skills/database-lookup/references/monarch.md at 5f2bc03
Monarch Initiative API
Raw lines 1 to 211## Key Endpoints
13| Endpoint | Description |
14|----------|-------------|
15| `/search?q={query}` | Text search across all entities |
16| `/autocomplete?q={prefix}` | Autocomplete entity names |
17| `/entity/{id}` | Entity details (gene, disease, phenotype) |
18| `/association?entity={id}` | Associations for an entity |
19| `/association?entity={id}&category={cat}` | Filtered associations |
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) |
/association?entity={id} | Associations for an entity |
/association?entity={id}&category={cat} | Filtered associations |
21## Entity ID Prefixes
22- `MONDO:` — diseases (e.g. `MONDO:0007947`)
23- `HP:` — phenotypes (e.g. `HP:0001250`)
24- `HGNC:` — genes (e.g. `HGNC:3603`)
25- `NCBIGene:` — genes (e.g. `NCBIGene:7157`)
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)
27## Association Categories
28`biolink:GeneToPhenotypicFeatureAssociation`, `biolink:DiseaseToPhenotypicFeatureAssociation`, `biolink:GeneToDiseaseAssociation`
Association Categories
biolink:GeneToPhenotypicFeatureAssociation, biolink:DiseaseToPhenotypicFeatureAssociation, biolink:GeneToDiseaseAssociation
30## Example Calls
31```
32# Search for Marfan syndrome
33https://api.monarchinitiative.org/v3/api/search?q=Marfan+syndrome&limit=5
35# Entity details for a disease
36https://api.monarchinitiative.org/v3/api/entity/MONDO:0007947
38# Gene-to-phenotype for FBN1
39https://api.monarchinitiative.org/v3/api/association?entity=HGNC%3A3603&category=biolink:GeneToPhenotypicFeatureAssociation&limit=10
40```
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/association?entity=HGNC%3A3603&category=biolink:GeneToPhenotypicFeatureAssociation&limit=1042## Response Format
43Paginate search/associations with `limit` and zero-based `offset`. JSON. Search: `items[]` with `id`, `name`, `category`. Associations: `items[]` with `subject`, `predicate`, `object`, `publications`.
Response Format
Paginate search/associations with limit and zero-based offset. JSON. Search: items[] with id, name, category. Associations: items[] with subject, predicate, object, publications.