MIABIS on FHIR

FHIR representation of MIABIS

Overview

This repository provides FHIR profile for MIABIS (Minimum Information About BIobank data Sharing) specification. This repository works with SUSHI(SUSHI Unshortens Short Hand Inputs), which acts as an interperter for FSH(FHIR Shorthand). This allows to write FHIR profile specifications with FSH, which provides simple creation of FHIR profiles. These profiles are then uploaded to the Simplifier.

Usage

Files which contain source code for FHIR profiles are Located inside folder MiabisOnFHIR/input/fsh/. In order to generate all the necessary JSON files which are then uploaded to the Simplifier, user needs to have SUSHI installed, for instalation look here. Then following steps are required:

1. open up terminal inside this folder
2. move to MiabisOnFHIR folder : cd MiabisOnFHIR
3. use sushi to generate JSON files from provided files inside the fsh folder. sushi build
4. if the build was successfull, generated files are located inside the MiabisOnFHIR/fsh-generated/ folder.
5. in order to validate the instances based on this IG, you need to download FHIR validator
6. in order to validate the example instances, move your generated *instance.json files to separate folder, and run command java -jar validator_cli.jar -ig {fsh_generated_resources} -version 4.0.1 -extension http://example/org/ -allow-example-urls true {instances}