MIABIS on FHIR

FHIR representation of MIABIS (Minimum Information About BIobank Data Sharing).

Goal

The Goal of this project is to provide guidance and all necessary information for adopting the MIABIS on FHIR profiles.

Availability

The implementation guide is available through GitHub Pages here, as well as on the Simplifier.

State

MIABIS on FHIR has been marked active and ready for production use with its 1.0.0 release. It is currently being adopted by the BBMRI-ERIC Federated Search platform. A reference usage of the project can be found in an ETL tool used by BBMRI.cz.

Note

To help with adoption, we have developed a Python library which can be found here.

Overview

This repository provides the source code for the MIABIS (Minimum Information About BIobank Data Sharing) on FHIR Implementation Guide (IG). It works with SUSHI (SUSHI Unshortens Short Hand Inputs), which serves as an interpreter for FSH (FHIR Shorthand). This allows the creation of FHIR profiles using FSH, which simplifies the process of developing and maintaining FHIR profiles.

Usage

The source code for the FHIR profiles is located in the folder Profiles. To generate the necessary JSON files for uploading to Simplifier, the user needs to have SUSHI installed. For installation instructions, see here. This project also has an automated CI pipeline that publishes the Implementation Guide on.

Build the IG

To build the Project, run the following command:

sushi build

Validate the IG

If the build is successful, the generated files will be located in the fsh-generated folder. To validate the instances/examples based on this Implementation Guide (IG), download the FHIR Validator. To validate the example instances, move your generated *instance.json files to a separate folder and run the following command:

java -jar validator_cli.jar -ig {fsh_generated_resources} -version 4.0.1 -extension http://example/org/ -allow-example-urls true {instances}

Running the Publisher

To build HTML content from the IG you need to run the Publisher.

Warning

For the Publisher to work correctly, you need to have Java, Ruby and Jekyll installed.

The Publisher can be downloaded by simply running the provided script:

./_updatePublisher.sh

The page content can be generated using the following command:

java -jar input-cache/publisher.jar -ig ig.ini