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Comment: uploaded mCODE update and tooling slides to minutes.



Liz / Rachel

FHIR-27748 - Rename "Functional Annotation" Component to "Variant Consequence" TRIAGED 

FHIR-27747 - New Component for Functional Effect TRIAGED 
Kevin (discuss what the 'genomics guidance' page should/should not contain)
FHIR-27159 - Update Genomics Guidance page to more clearly point to our IG TRIAGED 

FHIR-16402 - Add material from guidance document TRIAGED 

FHIR-27159 - Update Genomics Guidance page to more clearly point to our IG TRIAGED


  • Bob D: The page should be updated to "don't look at anything here, go to the IG", question is if this page contains information we want to keep (different tracker discussed later)
  • Kevin: could update the page to a landing page telling people to go to the IG
  • FHIR-I was asked yesterday in the FHIR-I joint meeting about including our applied PR to R5 into the R4B release. Couldn't get it into the FHIR 4.0.1 technical correction release, as this isn't considered to be a technical correction but a content change.
  • Kevin: could try to get a updated page into R4B
  • Bob D: remove everything, keep a link to the ig. Could include the content in a part of the IG.
  • Arthur: the page needs a strong statement that implementers should follow the IG
  • Kevin: 3 Options:
    1. move the content into our IG
    2. move the content to Molecular Sequence
    3. create another page in core and move it there
  • Liz: in favour of a clean landing page, move the content into the IG


FHIR-27748 - Rename "Functional Annotation" Component to "Variant Consequence" TRIAGED 

Liz & Rachel presenting the proposal:

  • Proposal to create new LOINC code for molecular consequence
  • extensible value binding to the structural_variant SO branch (SO:0001537)
  • functional annotation will be renamed to molecular consequence, binding will stay the same
  • amino-acid-change-type is also potentially overlapping with the molecular consequence concept, and therefore potentially also be merged
  • Discussion: should amino-acid-change type merge als be included into the tracker disposition? 
    • → breaking change which should discussed in another issue
  •  create Tracker item: merging amino-acid-change-type and molecular consequence


FHIR-27747 - New Component for Functional Effect TRIAGED 


Date: Tuesday 9/22/2020


Quarter3 : 14:00-15:30 ET (Q6)

Minutes Approved as Presented 


  1. mCode (May T)

mcode stu1 current status

alignment with genomics reporting stu2

oncotype DX (breast) use case discussion


mCODE STU2 Update and Tooling Discussion slides: mCODE_Update_HL7WGM_CGWG.pptx 

When genomics reporting IG makes a change on one of the structures pulled into mCODE, some concern from mCODE's business needs to also adopt the change.

~15 orgs have implemented mCODE 

MD Anderson, UT Southwestern, UCSF, Kaiser P, Intermountain, Mayo, Rush, Trinity, Princess Margaret Cancer Centre, Mass General, Dana-Farber, Brigham Health, Memorial Sloan Kett, U Penn, Geisinger, Washington U St. Lou

Greater alignment on terminologies on the horizon

May looking to submit LOINC code for oncotype dx


  1. IG creation/publishing

currently on manual editing of structure definitions

Forge - windows only, needs licenses from HL7

Trifolia - web-based, limited github interaction

FSH/SUSHI + GoFSH (decompiler) may be able to create equivalent structuredefinitions

can use current sdefs in one folder, mark one to be generated by GoFSH, and everything should still connect 




Wednesday 9/



Quarter: 10:00-11:30 ET (Q7)


Image AddedFHIR-16402 - Add material from guidance document Resolved - along lines of FHIR-27159 from yesterday.

Image AddedFHIR-27864 - Update binding to LOINC Diagnostic codes value set Triaged

Needs input Have to confirm LOINC categories for filtering and create more rigid picture of what to bind here beyond the original overall LOINC binding.