Scripts used to help with ingestion into FHIR for various datasets.
These are better suited for living outside any particular dataset ingestion repository.
A script has been provided inside the subdirectory, include-codesystems, to download .owl files and convert them to FHIR CodeSystems. Included is a YAML configuration file for pulling Mondo and Human Phenotype ontologies in their entirety.
This script uses a JAR file from https://github.com/aehrc/fhir-owl This currently assumed to have been downloaded into the current working directory.