This Spring Boot CLI application transforms a collection of HGNC source files into FHIR code systems. It produces two FHIR code systems, one with the gene groups and another one with the gene ids.
You will need Maven installed in your computer. You can build the jar file using Maven.
mvn package
You need a JVM to run the application.
java -jar fhir-hgnc-0.1.0-SNAPSHOT.jar -igg [file] -igi [file] -ogg [file] -ogi [file]
All the parameters are mandatory and the following table shows their descriptions:
| Parameter | Type | Mandatory | Description |
|---|---|---|---|
| -igg | string | No | The gene groups input file, download-all.json, available from this page. |
| -igi | string | Yes | The gene ids input file, hgnc_complete_set.json, available from this page. |
| -ogg | string | No | Gene groups FHIR code system target file. |
| -ogi | string | Yes | Gene ids FHIR code system target file. |