Search Monarch for an entity — monarch

Turns typed text into the entity id the other calls need.

Usage

monarch_search(text, limit = 10, ...)

Arguments

text: Free text, for example a gene symbol or a disease name.
limit: Maximum matches to return.
...: Passed to biohttp::get_json(), for example throttle.

Value

A biohttp envelope whose data is a list of matches (the tibble from monarch_parse_search()) and total. total is Monarch's own count, not the page size, so a caller can say how much was left behind rather than presenting the first few as everything.

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_search("Marfan syndrome"))$matches
#> # A tibble: 10 × 6
#>    id            name                      category description taxon source_url
#>    <chr>         <chr>                     <chr>    <chr>       <chr> <chr>     
#>  1 MONDO:0007947 Marfan syndrome           biolink… A disorder… NA    https://m…
#>  2 MONDO:0017309 neonatal Marfan syndrome  biolink… Neonatal M… NA    https://m…
#>  3 MONDO:1010296 Marfan syndrome, non-hum… biolink… Marfan syn… NA    https://m…
#>  4 MONDO:1011155 Marfan syndrome, FBN1-re… biolink… Marfan syn… NA    https://m…
#>  5 MONDO:1011156 Marfan syndrome, FBN1-re… biolink… Marfan syn… NA    https://m…
#>  6 MONDO:0008426 Shprintzen-Goldberg synd… biolink… Shprintzen… NA    https://m…
#>  7 MONDO:0007948 marfanoid hypermobility … biolink… NA          NA    https://m…
#>  8 MONDO:0013574 cutis laxa - Marfanoid s… biolink… NA          NA    https://m…
#>  9 MONDO:0009565 microcephaly-glomerulone… biolink… This syndr… NA    https://m…
#> 10 MONDO:0009566 marfanoid habitus-autoso… biolink… Marfanoid … NA    https://m…
# }