bgz-to-omop's Introduction

BGZ-to-OMOP

Poster "Leveraging FHIR for a generic EHR to OMOP-ETL: can we make an ETL process reusable?"
BgZ als FHIR Bundle omzetten naar OMOP voor hergebruik in onderzoek.
Waar lopen we tegenaan?
Later ook proberen IPS, e.g. op basis van de $ips operation van Epic
Definieer StructMaps van OMOP logical models (https://build.fhir.org/ig/HL7/fhir-omop-ig/) naar zibs2017/STU3 FHIR
Eventueel ook kijken naar SQL-on-FHIR (https://build.fhir.org/ig/FHIR/sql-on-fhir-v2/) view definitions

Docker to run IG Publisher

> docker run --name=bgz-to-omop -it -v "$(pwd)":/app node:lts-buster /bin/bash

.. install GoFSH and sushi, see https://fshschool.org/docs/gofsh/installation/

.. install java, jekyll, graphviz (needed for plantuml) in Docker (required for IG tooling)

@> apt update
@> apt install jekyll graphviz
@> dpkg -i jdk-21_linux-x64_bin.deb
@> npm install -g fsh-sushi

N.B. npm gofsh doesnot work in GitHub workflows, but npm fsh-sushi does?

Validate resources

> curl -L https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar -o validator_cli.jar
> java -jar validator_cli.jar -version 3.0.2 input/resources

Build IG

> curl -L https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar -o publisher.jar
> java -jar publisher.jar -ig ig.ini

Bevindingen

SUSHI ondersteund STU3 niet
- WORKAROUND: run sushi to generate R4 en pas de R4 logical models aan naar STU3 en gebruik die als input/resources
  - fhirVersion 3.0.2
  - element.type.targetProfile is geen array in STU3
Logical Models geven error bij valideren, maar IG wordt wel gemaakt
FML niet ondersteund in STU3
- WORKAROUND: definieer StructMaps

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