Get ontology from GitHub and import it via import_ontology.

Get ontology from GitHub and import it via import_ontology.

get_ontology_github(
  name,
  repo,
  filetype = ".obo",
  file = paste0(name, filetype),
  tag = "latest",
  add_metadata = TRUE,
  add_n_edges = TRUE,
  add_ontology_levels = TRUE,
  lvl = 2,
  save_dir = cache_dir(subdir = "ontologies"),
  force_new = FALSE,
  ...
)

Arguments

name

• <...>Any ontology name from get_ols_options

• "mondo" Import the Mondo ontology. GitHub..

• "hpo" Import the Human Phenotype Ontology. GitHub.

repo

Repository name in format "owner/repo". Defaults to guess_repo().

filetype

File type to search for.

file

Can be one of the following:

• "ontology"Creates an ontology_DAG R object by importing the OBO file directly from the official uPheno GitHub repository.

• "bestmatches"Returns a merged table with the best matches between human and non-human homologous phenotypes (from multiple species). Distributed by the official uPheno GitHub repository.

• "upheno_mapping"Return a merged table with matches between human and non-human homologous phenotypes (from multiple species). Distributed by the Monarch Initiative server.

tag

tag for the GitHub release to which this data should be attached.

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.

lvl

Depth of the ancestor terms to add. Will get the closest ancestor to this level if none have this exact level.

save_dir

Directory to save a file to.

force_new

If TRUE, force a new download.

...

Arguments passed on to simona::import_ontology

verbose

Whether to print messages.

robot_jar

The path of the robot.jar file. It can be downloaded from https://github.com/ontodev/robot/releases. Internally, the file is converted to the obo format and parsed by import_obo(). The value of robot_jar can be set as a global option simona_opt$robot_jar = ....

JAVA_ARGS

Options for java. For example you can set -Xmx20G if you want to increase the memory to 20G for java.

Value

ontology_DAG