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Extract mappings from ORDO

extract_ordo_mappings.Rd

Extract mappings from the Orphanet Rare Disease Ontology (ORDO). ORDO uses oboInOwl:hasDbXref for mapping with annotations to indicate exact/broad/narrow-ness. Utilizes robot().

Usage

extract_ordo_mappings(
  ordo_path,
  as_skos = TRUE,
  output = NULL,
  tidy_what = "everything"
)

Arguments

ordo_path

The path to the ORDO file, as a string.

as_skos

Whether to convert ORDO's annotated oboInOwl:hasDbXref mappings to their Simple Knowledge Organization System (SKOS) equivalents, as a boolean (default: TRUE).

The ORDO-skos equivalent predicates are as follows:

  • "BTNT" - skos:narrowMatch

  • "NTBT" - skos:broadMatch

  • "E" - skos:exactMatch

  • "ND" - doid:undefinedMatch (supplements SKOS)

  • "W" - doid:notMatch (supplements SKOS)

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.

Value

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

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

If as_skos = FALSE, ORDO's text-based oboInOwl:hasDbXref annotations denoting the type of relationship the Xref represents (simple text code only) will be included in the predicate_modifier column.