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Extract Mappings from an OBO Foundry Ontology

extract_obo_mappings.Rd

Extract mappings from the OBO Foundry Ontology as SSSOM. .

Usage

extract_obo_mappings(
  onto_path,
  id = NULL,
  version_as = "release",
  output = NULL,
  tidy_what = c("header", "unnest"),
  split_prefix_date = TRUE
)

Arguments

onto_path

The path to an ontology file recognizable by ROBOT, as a string.

id

A character vector of IRIs or CURIEs to filter results to or NULL (default) to return all mappings.

version_as

The format for subject_source_version, if a versionIRI is found, as a string. One of:

  • "release" (default): Use the ontology's release version as a string. Assumes that the release version in the versionIRI follows release/ or releases/. Will return full versionIRI as fallback.

  • "iri": Use the ontology's full versionIRI.

output

The path where output will be written, as a string, or NULL (default) to load data directly.

tidy_what

The elements of a SPARQL-created data.frame to tidy, as a character vector. One or more of the following:

  • "everything" to apply all tidy operations (has precedence over "nothing").

  • "header" to remove leading ? from header labels.

  • "unnest" to unnest list columns with unnest_cross().

  • "uri_to_curie" to convert all URIs recognized by DO.utils to CURIEs with to_curie().

  • "lgl_NA_FALSE" to replace NA in logical columns with FALSE.

  • "as_tibble" to make the output a tibble.

  • "rm_lang_tag" to remove language tags. Tags will only be removed from character class columns, and then only if there is one unique language tag in the given column.

  • "nothing" to prevent all tidying.

split_prefix_date

Whether to extract date suffixes, which may exist in some object_ids, out as the object_source_version and remove them from the object_id, as a boolean (default: TRUE).

Value

If output is specified, the path to the output file with the data. Otherwise, the data as a tibble.

Mappings data will be formatted according to the SSSOM specification, with an additional status column indicating the status (active, deprecated, etc.) of each subject_id.

subject_source_version will be the ontology versionIRI (formatted according to version_as or today's date if versionIRI is not defined.