Stream: implementers
Topic: US GINA Implementation Guide
Abbie Watson (Oct 11 2017 at 18:56):
@Grahame Grieve - Hi, just fyi... I'm going through the Implementation Guide documentation as we bring Symptomatic and Meteor on FHIR up to compliance with US Core specifications. A fair bit of this is insufficient for the needs of our genomics module, and our interest in a blockchain HIE. Could you tentatively put me down as working on a US GINA Implementation Guide? Might take me 6 months or more; but I've got some ideas I'm already starting to draft out with regards to genomic data extensions and genomic value sets.... i.e. Karyotypes, Chromsomes, Sequences, Chimerism/OrganTransplants, Microbiomes, Geneology, etc.
Bob Milius (Oct 11 2017 at 19:11):
@Abigail Watson Please take a look at the Genomics Implementation Guidance (http://build.fhir.org/genomics.html) and the Clinical Sequencing DAM (http://www.hl7.org/implement/standards/product_brief.cfm?product_id=446). There may be material there you can use. The Clinical Genomics Workgroup would be happy to work with you on this. @Gil Alterovitz @Kevin Power
Abbie Watson (Oct 11 2017 at 19:19):
@Abigail Watson Please take a look at the Genomics Implementation Guidance (http://build.fhir.org/genomics.html) and the Clinical Sequencing DAM (http://www.hl7.org/implement/standards/product_brief.cfm?product_id=446). There may be material there you can use. The Clinical Genomics Workgroup would be happy to work with you on this. @Gil Alterovitz @Kevin Power
Hi Bob,
Yes, I've been following the Clinical Genomics Workgroup for the past year or so! The work you all are doing is very much an inspiration, and my goal is to get a working implementation using the Meteor on FHIR framework and Symptomatic. :)
Basically, as I do the formal implementation, part of that process is going to be making sure that a bunch of the value sets, libraries, profiles, etc. are all published as libraries and packages for the Meteor.js ecosystem. It will mostly be Node libraries, but the raw JSON will be available for downlowd for other people's use. As that happens, it will be a natural time to document as we go along. So an Implementation Guide of some sort is probably going to be a natural byproduct. And if there's a specification on how to write that Implementation Guide? And there's not one listed yet in the Implementation Guide Registry? Well, I have no need to reinvent wheels; and I seem like I'm rolling into this work anyhow.
So, yes... looking forward to basing it on the Genomics Implementation Guidance, and contributing an iteration.
Bob Milius (Oct 11 2017 at 19:24):
Yes, I agree with the need for a compliant clinical genomics IG, in addition to our 'guidance'. Hope to learn more on how to do that. Is this the Meteor on FHIR you're referring to: https://github.com/clinical-meteor/meteor-on-fhir ?
Abbie Watson (Oct 15 2017 at 00:45):
Yes, indeed. Well, mostly. What you've linked to is the Meteor on FHIR boilerplate/demo, which is licensed under the GPL, architected with a Wordpress model with plugins, and is loosely designed after the Mirth interface engine. The genomics module and genetic counseling module that I've been working on is currently structured as a plugin and kept in a private repository.
However, the Meteor on FHIR app is built using a number of MIT licensed FHIR resource packages, which you can find by searching the clinical-meteor GitHub organization for hl7-resource, like so:
https://github.com/clinical-meteor?utf8=%E2%9C%93&q=hl7-resource&type=&language=
So, we've got a 3 tier intellectual property structure: the FHIR schemas and interoperability components are MIT license; the base CRUD UI components are GPL; and proprietary workflow is able to be kept in plugins to retain trade secrets and other intellectual property.
Of particular interest will probably be the hl7-resource-sequence package.
https://github.com/clinical-meteor/hl7-resource-sequence
Right now, the last time I spent time on the Sequence schema was nearly 2 years ago. So, it's probably on v1.0.2 or v1.1.0. As I bring that package up to version 3.0.1, I'll probably start looking at how to add value sets from the Genomics Implementation Guidance and Clinical Sequencing DAM.
Long story short, the ValueSets and US-Gina ImplementationGuide will probably wind up in the clinical-meteor/hl7-resource-sequence repository.
Last updated: Apr 12 2022 at 19:14 UTC
