Associations with an entity on one end

Usage

monarch_associations(entity, end = c("subject", "object"), limit = 200, ...)

Arguments

entity: An entity CURIE, for example "MONDO:0007947".
end: "subject" or "object".
limit: Maximum associations to return.
...: Passed to biohttp::get_json(), for example throttle.

Value

A biohttp envelope whose data is the tibble described in monarch_parse_associations().

One direction per call

end picks which end of the association the entity sits on. Both directions are two calls, and concatenating them returns any association that has the entity on both ends twice. Collapsing those, and deciding what to do with the publications on each copy, is the caller's model rather than Monarch's answer, so this function does neither.

References

Putman et al. (2024). The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Research 52(D1), D938-D949. doi:10.1093/nar/gkad1082

Service documentation: https://monarchinitiative.org/

Examples

# \donttest{
biohttp::body_or_null(monarch_associations("MONDO:0007947"))
#> # A tibble: 189 × 10
#>    subject       subject_label    subject_category predicate object object_label
#>    <chr>         <chr>            <chr>            <chr>     <chr>  <chr>       
#>  1 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Emphysema   
#>  2 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Tricuspid r…
#>  3 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Dolichoceph…
#>  4 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Megalocornea
#>  5 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Abnormality…
#>  6 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Mitral valv…
#>  7 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Tricuspid v…
#>  8 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Abnormal ca…
#>  9 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Neonatal re…
#> 10 MONDO:0017309 neonatal Marfan… biolink:Disease  biolink:… HP:00… Ascending t…
#> # ℹ 179 more rows
#> # ℹ 4 more variables: object_category <chr>, primary_knowledge_source <chr>,
#> #   knowledge_level <chr>, publications <list>
# }