owl

Convert OWL files using fhir-owl (https://github.com/aehrc/fhir-owl)

This plugin is based on 'fhir-owl' by the Australian e-Health Research Center (AEHRC) as CSIRO, Australia. See https://github.com/aehrc/fhir-owl for more information.

Command line usage

/*^babelfsh
owl
   --file FILE [--code-property CODE_PROPERTY] [--code-replace CODE_REPLACE]
   [--definition-property DEFINITION_PROPERTY]
   [--display-property DISPLAY_PROPERTY] [--exclude-labels EXCLUDE_LABELS]
   [--help] [--iri-mappings IRI_MAPPINGS] [--main-namespaces MAIN_NAMESPACES]
   [--no-include-deprecated] [--reasoner REASONER]
   [--synonyms-property SYNONYMS_PROPERTY]
^babelfsh*/

Command line argument reference

Argument name	Description
--file FILE Required	The OWL file to parse
--code-property CODE_PROPERTY --code-prop CODE_PROPERTY --code CODE_PROPERTY	The code property to use
--code-replace CODE_REPLACE	Two strings separated by a comma. Replaces the first string with the second string in all local codes.
--definition-property DEFINITION_PROPERTY --definition-prop DEFINITION_PROPERTY --definition DEFINITION_PROPERTY	Indicates which annotation property contains the concepts' definitions. Default is None.
--display-property DISPLAY_PROPERTY --display-prop DISPLAY_PROPERTY --display DISPLAY_PROPERTY	Indicates which annotation property contains the concepts' displays. Default is 'http://www.w3.org/2000/01/rdf-schema#label'.
--exclude-labels EXCLUDE_LABELS	Comma-separated list of class labels to exclude from the code system.
--help -h	show this help message and exit
--iri-mappings IRI_MAPPINGS	A file containing IRI mappings. The file should be a comma-separated file associating an ontology IRI with a path relative to the BabelFSH file. Default is null.
--main-namespaces MAIN_NAMESPACES --main-ns MAIN_NAMESPACES	Comma-separated list of namespace prefixes that determine which classes are part of the main ontology.
--no-include-deprecated --include-deprecated	Include deprecated concepts in the code system. Default is false.
--reasoner REASONER	The reasoner to use. Choices are elk, jfact. Default is 'elk'
--synonyms-property SYNONYMS_PROPERTY --synonyms-prop SYNONYMS_PROPERTY --synonyms SYNONYMS_PROPERTY	Comma-separated list of OWL annotation properties that contain the concepts' synonyms.