owl-on-fhir 1.1.5

Python-based non-minimalistic OWL to FHIR converter.

OWL-on-FHIR

A Python-based non-minimalistic OWL to FHIR converter.

Prerequisite

• Python 3.9+
• Java 11+

Installation

pip install owl-on-fhir

Usage

Syntax

owl-on-fhir --input-path-or-url FILENAME --code-system-id ID --native-uri-stems "URL_1,...,URL_N" --code-system-url URL [NON_REQUIRED_OPTIONS]

Examples

owl-on-fhir --input-path-or-url comploinc.owl --code-system-id comploinc --native-uri-stems "https://loinc.org/" --code-system-url https://github.com/loinc/comp-loinc/releases/latest/download/merged_reasoned_loinc.owl

CLI options

Short Flag	Long Flag	Required	Description
-h	--help		Show this help message and exit.
-i	--input-path-or-url	True	URL or path to OWL file to convert.
-s	--code-system-id	True	The code system ID to use for identification on the server uploaded to. See: https://hl7.org/fhir/resource-definitions.html#Resource.id
-S	--code-system-url	True	Canonical URL for the code system. See: https://hl7.org/fhir/codesystem-definitions.html#CodeSystem.url
-u	--native-uri-stems	True	A comma-separated list of URI stems that will be used to determine whether a concept is native to the CodeSystem. For example, for OMIM, the following URI stems are native: https://omim.org/entry/,https://omim.org/phenotypicSeries/PS". As of 2023-01-15, there is still a bug in the Obographs spec and/or robot where certain nodes are not being converted. This converter adds back the nodes, but to know which ones belong to the CodeSystem itself and are not foreign concepts, this parameter is necessary. OAK also makes use of this parameter. See also: https://github.com/geneontology/obographs/issues/90
-o	--out-dir	False	The directory where results should be saved.
-n	--out-filename	False	Filename for the primary file converted, e.g. CodeSystem.
-p	--include-only-critical-predicates	False	If present, includes only critical predicates (is_a/parent) rather than all predicates in CodeSystem.property and CodeSystem.concept.property.
-c	--use-cached-intermediaries	False	Use cached intermediaries if they exist?
-r	--retain-intermediaries	False	Retain intermediary files created during conversion process (e.g. Obograph JSON)?
-I	--convert-intermediaries-only	False	Convert intermediaries only?
-d	--dev-oak-path	False	If you want to use a local development version of OAK, specify the path to the OAK directory here. Must be used with --dev-oak-interpreter-path.
-D	--dev-oak-interpreter-path	False	If you want to use a local development version of OAK, specify the path to the Python interpreter where its dependencies are installed (i.e. its virtual environment). Must be used with --dev-oak-path.

More

Alternative OWL to FHIR converters

FHIR-OWL

https://github.com/aehrc/fhir-owl
Takes a minimalistic approach. Can convert top-level CodeSystem properties, concepts, and also supports some predicates, such as synonyms. Uses Java owl-api.

Ontology Access Kit (OAK)

https://github.com/INCATools/ontology-access-kit/ OWL-on-FHIR is largely a wrapper around Ontology Access Kit (OAK)'s FHIR converter. It adds some extra automation such as an intermediary conversion to Obographs JSON, which is currently a required input for OAK for most ontologies, given the current state of development.