#' @describeIn get_ get_
#' Get Human Phenotype Ontology (HPO)
#'
#' Updated version of Human Phenotype Ontology (HPO).
#' Created from the OBO files distributed by the HPO project's
#' \href{https://github.com/obophenotype/human-phenotype-ontology}{GitHub}.
#'
#' By comparison, the \code{hpo} data from \pkg{ontologyIndex} is from 2016.
#' Note that the maximum ontology level depth in the 2016 version was 14,
#' whereas in the 2023 version the maximum ontology level depth is 16
#' (due to an expansion of the HPO).
#' @inheritParams KGExplorer::get_ontology
#' @inheritDotParams KGExplorer::get_ontology
#' @returns \link[simona]{ontology_DAG} object.
#'
#' @export
#' @import KGExplorer
#' @examples
#' hpo <- get_hpo()
get_hpo <- function(lvl,
add_ancestors = 2,
force_new = FALSE,
terms=NULL,
## rols imports the international version for some reason
method="github",
save_dir=KGExplorer::cache_dir(package = "HPOExplorer"),
...){
file <- file.path(save_dir,"hp.rds")
if(!file.exists(file) || isTRUE(force_new)){
ont <- KGExplorer::get_ontology(name = "hp",
add_ancestors = add_ancestors,
force_new = force_new,
terms = terms,
method = method,
save_dir = save_dir,
...)
saveRDS(ont,file)
} else {
ont <- readRDS(file)
}
ont <- KGExplorer::filter_ontology(ont = ont,
terms = terms)
return(ont)
}
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