owl-on-fhir 1.1.5
Python-based non-minimalistic OWL to FHIR converter.
Requires Python: >=3.9.0


# OWL-on-FHIR
![owl-on-fhir logo](https://github.com/hot-ecosystem/owl-on-fhir/blob/master/docs/owl-on-fhir%20logo%20v2.png?raw=true "OWL on FHIR")

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

## Prerequisite
* [Python 3.9+](https://www.python.org/downloads/)
* [Java 11+](https://www.oracle.com/java/technologies/javase/jdk11-archive-downloads.html)

## 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](https://github.com/INCATools/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.