Skip to contents

Format Logical Axioms

format_axiom.Rd

Format logical axioms in the style of Protege. Input axioms must be in OWL functional syntax.

Usage

format_axiom(
  x,
  property_df = NULL,
  generify_obo = FALSE,
  placeholders = c("<<<", ">>>", "%%%", "@@@"),
  max_phrases = 15L
)

Arguments

x

Complete logical axioms in OWL functional syntax, as a character vector.

property_df

[Optional] A data.frame consisting of relevant annotation and object properties that may be used to make properties more readable in axioms. If provided, data.frame should include two columns:

  • property: Each property's URI.

  • label: Each property's rdfs:label (or equivalent).

See 'Formatting Options' for details.

generify_obo

Whether to make OBO ontology classes and properties generic, as TRUE or FALSE (default). See 'Formatting Options' for details.

placeholders

A set of 4 strings that will be used internally to preserve axiom parentheses [1:2], phrase spacing [3], and complete phrases [4], as a character vector. These should not generally need to be edited and are only exposed in case of conflicts within axioms.

max_phrases

The maximum number of phrases to update in an axiom, as an integer. This protects against an infinite while loops and would only need to be edited if one or more Object* OWL functional phrases are returned unformatted.

Formatting Options

format_axiom() will always rearrange equivalent class and subclass of logical axioms from OWL functional syntax to a more readable form, similar to Protege. However, classes and properties in axioms will be returned as URIs or CURIEs (as formatted in x). This may be desirable for further programmatic examination but will still be difficult for a human to read. To make them more readable, the property_df and generify_obo arguments can be used.

property_df is used to replace OBO ontology property URIs or CURIEs with namespace-prefixed labels: e.g. obo:RO_0004026 would become RO:'disease has location'. Non-OBO properties will not be modified.

generify_obo replaces individual OBO URIs or CURIEs with either namespace-prefixed types, e.g. obo:UBERON_0001032 would become UBERON:anatomy, or namespace only. This format simplifies axioms making basic analysis of axiom patterns easier. See the documentation for generify_obo() for details.