hl7 / genomics-reporting

Source for the HL7 Genomics work group's "Clinical Genomics-Reporting" FHIR implementation guide

genomics-reporting

The source repository for the HL7 Clinical Genomics work group's "Clinical Genomics Reporting" FHIR implementation guide.

For history of published builds, review here: http://hl7.org/fhir/uv/genomics-reporting/history.html

To build locally:

• Clone repo
• run '_updatePublisher.{sh | bat}' script (answering Y to the prompts) to ensure you have the latest version of the publisher and templates
• run '_genonce.{sh | bat}' script to run the build
• review the build output for any errors
• review the output/qa.html for any new error/warning/informational entries

genomics-reporting's Issues

ant-launcher?

@lmckenzi Can you shed some light on what https://github.com/HL7/genomics-reporting/blob/master/framework/ant/ant-launcher.jar is used for? I see it is executed from the scripts in the root directory - I am assuming it pulls down the HL7 publishing tool, perhaps a few other things?

Expansion of hgvs ValueSet

Hey!

I have set up an implementation based on this guide. Right now I'm stuck at setting up resource validation.

Right now LOINC, Sequence ontology and both of the HGNC CodeSystems I obtained seem fine, but I'm stuck with HGVS. Also I'm concerned if the current implementation makes sense:
As far as I see HGNC is a recommendation on how to format sequence variants. They can be a good starting point but get very complex and can have multiple representations for the same variation.
Currently HGNC has a strict binding in this implementation guide, resulting in a the requirement for a CodeSystem of http://varnomen.hgvs.org/ that lists all the allowed codes. This is unlikely to generate and also doesn't distinguish between DNA changes and protein changes.

My proposal would be to move away from strict to something less strict like extensible. More optimal would be something like a validation based on regular expressions, but that is not part of the FHIR spec (as far as I know).