get_: Get functions

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Get functions

Description

Functions to get data objects and extract elements.

Usage

get_hpo(
  lvl = 2,
  force_new = FALSE,
  terms = NULL,
  tag = "v2024-02-08",
  method = "github",
  save_dir = KGExplorer::cache_dir(),
  ...
)

get_hpo_id_direct(term, hpo = get_hpo())

get_mappings(
  terms = NULL,
  to = c("UMLS", "SNOMED", "ICD9", "ICD10"),
  max_dist = 1,
  force_new = FALSE,
  save_dir = KGExplorer::cache_dir(package = "HPOExplorer"),
  ...
)

Arguments

lvl	How many levels deep into the ontology to get ancestors from. For example: 1: "All" 2: "Phenotypic abnormality" 3: "Abnormality of the nervous system" 4: "Abnormality of nervous system physiology" 5: "Neurodevelopmental abnormality" or "Behavioral abnormality"
force_new	Force a new download or creation of a data resource.
terms	A subset of HPO IDs to assign Tiers to.
tag	tag for the GitHub release to which this data should be attached.
method	Method to construct plot with.
save_dir	Directory to save a file to.
...	Arguments passed on to KGExplorer::get_ontology, get_data name <...>Any ontology name from get_ols_options "mondo" Import the Mondo ontology. GitHub.. "hpo" Import the Human Phenotype Ontology. GitHub. filetype File type to search for. import_func Function to import the ontology with. If NULL, automatically tries to choose the correct function. add_metadata Add metadata to the resulting ontology object. add_n_edges Add the number of edges (connections) for each term. add_ontology_levels Add the ontology level for each term. add_version Add the release version to the returned object's attributes file name or vector of names of files to be downloaded. If NULL, all assets attached to the release will be downloaded. repo Repository name in format "owner/repo". Defaults to guess_repo(). overwrite Should any local files of the same name be overwritten? default TRUE.
term	One or more ontology IDs.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
to	Medical ontologies to provide mappings to.
max_dist	Maximum cross-ontology distance to search for mappings. A distance of 1 means only direct mappings are returned. Greater distances mean that mappings are found through intermediate terms and are therefore less reliable.

Value

Data.

ontology_DAG object.

The HPO ID(s) of phenotype(s)

A named list of data.table objects containing mappings.

Functions

• get_hpo(): get_ Get Human Phenotype Ontology (HPO)

  Downloads and imports the "v2024-02-08" release of the Human Phenotype Ontology (HPO) for the purposes of version control and consistency of results. To get the latest version of the HPO, use get_hpo(tag="release", force_new=T) The HPO objects are created from the OBO files distributed via the official HPO GitHub repository.

  By comparison, the hpo data from 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).

• get_hpo_id_direct(): get_ Get HPO term ID direct

  Directly retrieves it from the HPO ontology object.

• get_mappings(): get_ Get Human Phenotype Ontology (HPO) mappings

  Get mappings between HPO terms and their corresponding IDs in other medical ontologies (e.g. SNOMED CT, UMLS, ICD-9/10).

Examples

hpo <- get_hpo()
term = "Phenotypic abnormality"
pheno_abnormality_id <- get_hpo_id_direct(term = term)
mappings <- get_mappings()

neurogenomics/HPOExplorer documentation built on April 17, 2025, 9:25 p.m.