Stream: german/mi-initiative
Topic: Implementation Guide Usage
John (Mar 10 2022 at 17:11):
Hi guys, I am wondering how can I install / Use an Implementation Guide. Unfortunately I couldn't find much documentation how to use them. I want to use "GECCO" implementation guide. Thanks
Julian Sass (Mar 11 2022 at 08:30):
Sure, what is it exactly that you want to do? Install the conformance resources on a server?
John (Mar 11 2022 at 09:17):
Actually we have COVID clinical data and we would like to make use of GECCO profiles and resources, wondering if the work you have done could already give us a head start.
Julian Sass (Mar 11 2022 at 09:36):
I guess what you want to do is implement some sort of ETL pipeline and get your clinical data into FHIR format and then test your implementation by validating against e.g. the GECCO profiles. I would start by choosing a library from here: https://confluence.hl7.org/pages/viewpage.action?pageId=35718838 which will make implementation easier. And then in a second step you can install the implementation guide on a server or use the validator locally.
John (Mar 11 2022 at 10:54):
Thanks for your quick response. We do have clinical synthetic data in FHIR Format as well as real data which we are working to transform in FHIR JSON. What is causing problem is to how to connect these two things. i.e. Clinical Data and Gecco profiles. I guess I need to use a Validator which checks the data conformance against the Gecco profiles ?
- do you know any validator which checks against a particular IG ? I used a standard validator which only checks whether the data is formulated according to FHIR standards or not
- Is there a way / tool to tranform local fhir data / Synthetic data to comply with GECCO specifications ?
- How can I used Gecco IG on Firely Server / any other FHIR server (HAPI) ? I couldn't find an option to use a customised IG ?
Pls excuse me if those questions sound naive but I have done some work with profiling and now trying to make things work together.
Julian Sass (Mar 11 2022 at 11:22):
-
the FHIR validator can check against a particular IG. It's described here: https://confluence.hl7.org/pages/viewpage.action?pageId=35718580#UsingtheFHIRValidator-Validatingagainstanimplementationguide
You need to set the-igparameter to e.g.-ig de.gecco#1.0.5or any other IG. -
I assume there is no such tool because your source data will differ from the data at other hospitals, so you'll need to handle this transformation step yourself. This is specific to CDSIC ODM as source but could be helpful: https://github.com/num-codex/odm2fhir
- Firely and HAPI servers have config settings where you can specify which IGs to load on startup.
Firely Server docs: https://docs.fire.ly/projects/Firely-Server/en/latest/features/conformanceresources.html#conformance-import
HAPI starter https://github.com/hapifhir/hapi-fhir-jpaserver-starter there is an application.yaml with an option to import IGs
John (Mar 11 2022 at 12:28):
Great, thanks a lot
Last updated: Apr 12 2022 at 19:14 UTC
