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Attendance form: 2019-01 CG WGM Attendance (Jira account needed)

Date: Monday, Jan 14

Quarter: Q3

Minutes Approved as Presented 



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Goals

To Welcome everyone to the Work Group Meeting, cover what was recently worked on in the Connectathon, and prepare for the following sessions.

Discussion items

TimeItemWhoNotes

Introductions



Connectathon Recap


https://tinyurl.com/cgwgmslides

https://tinyurl.com/cgconnectathon


Overview Trackers from the Connectathon
https://tinyurl.com/HL7CGWGM

Overview Ballot Trackers
https://docs.google.com/spreadsheets/d/1XUnXeycpRszakfgQO-MKszBhKUmLQv88gb5518NMlS4/edit#gid=0

Prepare for meeting with FHIR-I




Any other business (likely trackers)

https://docs.google.com/spreadsheets/d/1XUnXeycpRszakfgQO-MKszBhKUmLQv88gb5518NMlS4/edit#gid=0

Discussion with May: looking at GTR connections guidance, would like a stable id to a genetic report we are receiving.

A: we mostly focus on structuring test outcome data back into the system. The order side of things is still very young and will need to consider GTR as a genomic extension. Depends on how much info labs (voluntarily) submit to GTR. Need to standardize this area, likely with O&O.

Next steps: should look to integrate into the DAM and/or a future connectathon.

Action items

  •  





Date: Monday, Jan 14 / Quarter: Q4

Minutes Approved as Presented 


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Discussion items

TimeItem
Notes

Approve minutes


Joint with FHIR-I

-upcoming deadlines

-Scopes for code system URI

-FHIR related deadlines now that R4 is published

-Family member history - requirements have changed, any updates here towards FMM2?

-Should create a separate GForge ticket for each externally defined CodeSystem, to assign a CodeSystem URI - then Grahame can help shepherd these through vocab



Any other Business (start trackers)

allow Haplotype to be derivedFrom other Haplotypes

Motion to add Haplotype to the derivedFrom relation on Haplotype

Nay/Abstain/Yay

Bob F+Kevin/7/8 (Yay's counted by show of hands)

Result: Motion Passes

Action items

  •  







Date: Tuesday, Jan 15

Quarter: Q1

Minutes Approved as Presented 


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Discussion items

TimeItemWhoNotes

Review Agenda

Bob M2019-01 CG WGM Agenda

ElectionsBob M

CG has two elections during this WGM

  • Regular: 2 seats open
  • Interim: 1 seat open, announced via listserv on Sunday morning
    • Consensus: if no nominees are received, the 3rd place finisher of the regular election shall be appointed to the interim seat

Review of CG for newcomersBob M


IG ballot reconciliation

Bob M

https://docs.google.com/spreadsheets/d/1XUnXeycpRszakfgQO-MKszBhKUmLQv88gb5518NMlS4/edit#gid=0

  • Tracker 19870
    • High level diagram
    • Support for adding the diagram to the IG
      • Needs a legend with description about how to use it; minor formatting/organizational suggestions
    • Support for another diagram at an even higher level, with everything that is in the IG, to provide a complete road map; readers could then drill down to into the existing diagram
  • Tracker 16253
    • See discussion for 19870
  • Tracker 19936
    • See figs 3 and 5 in general genomic reporting
    • Remove Descriptive Genetic Finding? It was to support cytogenetics, and this profile was removed previously.
    • Consensus: keep Cytogenetic Nomenclature for now, but we could explore communicating it as a component in another profile

Action items

  • Remove "Descriptive Genetic Finding" from fig 5 in general genomic reporting (19936)





Date: Tuesday, Jan 15 / Quarter: Q2

Minutes Approved as Presented 


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Discussion items

TimeItemWhoNotes

Ballot ReconciliationKevin P

https://docs.google.com/spreadsheets/d/1XUnXeycpRszakfgQO-MKszBhKUmLQv88gb5518NMlS4/edit#gid=0

Tracker 19936 (continued)

  • Consensus: rename Cytogenetic Nomenclature to "Structural Genetic Finding"
    • Even split on whether to include "ISCN" in the name
  • Issue: it is possible to define a Complex Variant as a Haplotype, and vise versa
    • Bob M: we need to support the concept of haplotypes being derived from other haplotypes
    • Complex Variant.type has a typo ("hemizygouse")
    • This needs to be fixed, will create a separate tracker for it

Tracker 19981

  • Re: wording of bullets on IG home page, under Scope
  • Consensus: change wording to "This guide covers all aspects of human genetic reporting, including:" and then remove the first bullet ("human and vet...")

Tracker 19937 and Tracker 16108

  • If it were possible to refer to Diagnostic Reports, we may not need Panel
    • See DiagnosticReport extension "extends"
  • We will ask OO if they agree with our proposed resolution to tracker 19937

Action items

  • Rename Cytogenetic Nomenclature to "Structural Genetic Finding" (19936)
  • Create new tracker to reconcile Haplotype and Complex Variant (19936) Bob Milius
  • Update wording on IG home page regarding scope (19981)




Date: Tuesday, Jan 15 / Quarter: Q3

Minutes Approved as Presented 


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Discussion items


TimeItemWhoNotes

Ballot ReconciliationKevin P

https://docs.google.com/spreadsheets/d/1XUnXeycpRszakfgQO-MKszBhKUmLQv88gb5518NMlS4/edit#gid=0

Tracker 16108

  • "Genetics Panel: Suggest removing"
  • persuasive with mod - will remove, but need guidance on how to use diagnostic-report summary-of extension
  • motion - Bret/Patrick
    • discussion- none
    • yea - 12
    • nay - 0
    • abstain - 2
    • motion passes

Tracker #19935

  • "Remove FISH and microarray platform"
  • Should device must be supported (for observations)?
    • consensus is no
  • Persuasive

Tracker # 19933

  • "Remove Copy Number Change"
  • Persuasive with Mod
    • move arrCGH to Described-Variant
    • move chromosome-copy-number-change-type to Described-Variant
    • remove Copy-Number-Change

Tracker #19934

  • 'Change name of “described variant” to “discrete variant”.'
  • Persuasive with mod
    • combine Complex Variant with Described Variant, call it Variant, hasMember to itself.
    • need to determine appropriate observation.code

Tracker #19859

  • 'Rename "Described Variant" profile to "Variant"'
  • same as #19934

Tracker #16913

  • "Interpretation vs. impact - 2018-May Genomics #69"
  • continue in Q4







Action items

  • Lots of stuff.  See notes above.




Date: Tuesday, Jan 15 / Quarter: Q4

Minutes Approved as Presented 


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Goals

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Discussion items

TimeItemWhoNotes

Ballot ReconciliationKevin P

https://docs.google.com/spreadsheets/d/1XUnXeycpRszakfgQO-MKszBhKUmLQv88gb5518NMlS4/edit#gid=0

Tracker #16913

  • "Interpretation vs. impact - 2018-May Genomics #69"
  • continue discussion from Q3
  • persuasive with mod
    • change impact to implication

Tracker #16935

  • "types of overall interpretation - 2018-May Genomics #77"
  • persuasive with mod
    • delete "Deletion-Duplication Overall Interpretation"

Tracker #16923

  • "genetic finding - 2018-May Genomics #73"
  • not persuasive

Tracker #16929

  • "from descriptive to computable - 2018-May Genomics #75"
  • see Tracker 19936 (Tue-Q1)

Tracker #16910

  • "phenotype ontology - 2018-May Genomics #68"
  • not persuasive

Tracker #16938

  • knowledge representation - 2018-May Genomics #78
  • Not persuasive
    • It is not CG's job to create knowledge resource
    • We will advocate for creation of knowledge resource in FHIR to add addition profile based on knowledge resource to our IG

Tracker #16900

  • pre-coordination - 2018-May Genomics #65
  • not persuasive
    • We have designed our profiles to meet the needs of exchanging clinical genomic information in current clinical practice. If other provenance/details is needed to, new profiles may be created or existing ones existing.

Tracker #19912

  • code systems for genomics
  • not addressed

Tracker #19103

  • obs-comp-gen-finding gene studied code could be approved name
  • not addressed

Tracker #1687616876

  • Use of publically available external coding systems and autocomplete lookup tables - 2018-May Genomics #58
  • not addressed



WG consensus:  Props to Kevin Power for all the pre-work to get these organized.  Clem is happy so everyone is happy.

And so ends day 1.  Discussion may or may not continue at the TNP.


Action items

  • Change impact to implication (16913)
  • Delete "Deletion-Duplication Overall Interpretation" (16935)
  • Determine how CG WG could advocate for the creation of a FHIR knowledge resource (16938)




Date: Wednesday, Jan 16

Quarter: Q1

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Discussion items


Interim co-chair election

  • anonymous ranked choice voting
  • write your top three choices, ranked

Nominees:

  • Kevin Power
  • Bob Freimuth
  • Patrick Werner


  • Bob M collected 15 paper ballots

Bob M

Answers to Grahame's questions, proposed wording:

Q: Which resources will be candidates for normative in R5?
A: None. Clinical Genomics is responsible for only one Resource (MolecularSequence), which is NOT a candidate for normative in R5.


Q: In a single sentence, what are our plans for R5?
A: Clinical Genomics will continue to work on refining MolecularSequence, move content of current profiles of core resources (e.g., Observation-Genetics, etc) to the Genomics Reporting IG to remove redundancy, update genetics examples in core resources to improve accuracy and completeness, and work with patient care on the family history pedigree representation/profiles.

  • consensus ok
Bob M

WG communications procedures / Publicizing our activities

move this to end of Q3

Bob F

Review CG Information Model (IM)

  • Bob F presented slides (https://drive.google.com/open?id=1cwk5-AF35e1rIuFZx9Eh9yMdT9_YxVwi)
  • Examples
    • Sequence from blood from human patient X
      • Sequence from hHuman subject
    • Sequence from virus in human blood of patient X
    • Mother/Fetus
      • Fetus is modeled as BiologicalSubject
        • Pattern can be used for donor/recipient
      • Fetus can be modeled as anatomical site
  • Sequences Features
    • Types of Annotations/Features
      • GA4GH VA survey of terms for molecular consequence
    • Generic Feature Format (GFF)
      • GFF3 released as part of Sequence Ontology
    • SequenceLocation acts a glue between Sequence and SequencFeature
  • Roadmap of Modelling Activities
    • Sequence Annotations
    • Definitional Sequences, alleles, haplotypes, genotypes
      • ref: Sequence, Interval, Feature, etc
      • Patient agnostic knowledge
    • Sequence Alignments
      • ref: Sequence, Interval, Activity, Assertion, Feature
    • Variants
    • Observational Seqs/Alleles/Haplotypes/Genotypse/Var
Bob F



Planning model development (including alignment with GA4GH)Bob F

Action items

  •  




Date: Wednesday, Jan 16 / Quarter: Q2

Minutes Approved as Presented 

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Goals

Joint session with O&O

Discussion items


Mesquite

  • Attaching VCF files: Observation-Media-DocumentReference Shared interest topic discussions/reviews/updates
  • Bob gave update on IG ballot, and R5 plans (Answer to Grahame's question about R5)
  • from OO minutes for Tues Q4:
    • Option 1: Dissolve Media into DocRef and Attachment DT and add Attachment as valueAttachment. Elliot, Jonathan
    • Option 2:  Keep Media and DocRef, and add Attachment as valueAttachment to Obsv.  Revert Media to DSTU 2/3-ish (less eventish).  Eric Haas, David Burgess
    • Option 3:  Keep as-is and clarify how to query and get data expressed either in Obsv or DxRpt. JD Nolen, Dan Rutz, Grahame Grieve
  • Names after each option have volunteered to research that option and provide pros/cons.
  • Add CG use case(s) to OO Workspace for Attachment/Media Use Cases
  • Plan is to settle this by Sep 2019.
  • Need to understand boundaries between:
    • observation and media
    • document reference and media
    • clinical note and diagnostic report
      • clinical note -
        • note from a clinician,
        • may include references to lab results,
        • signed by single person, maybe co-signature if a resident,
        • pulls in summaries of other reports
        • lots of variations
        • Clinical notes are not ordered
        • could extend to comments about a diagnostic report (technician's comments) but may not included in final report
      • may be a continuum from clinical note to diagnostic report
      • options for ClinicalNotes
        • category of DocRef
        • profile of composition
        • profile of DocRef
        • separate resource
      • FHIR R4 US Core => DocRef.category=ClinicalNotes / DocRef.type is LOINC




Tracker 19937 and Tracker 16108

Action items

  •  






Date: Wednesday, Jan 16 / Quarter: Q3

Minutes Approved as Presented 

This is to approve minutes via general consent. "You have received the minutes. Are there any corrections to the minutes? (pause) Hearing none, if there are no objections, the minutes are approved as printed."

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Discussion items


Summary of joint meeting with OO Q2

  • see minutes above
  • We need to add our VCF attachment use case to OO Workspace for Attachment/Media Use Cases
    • who? JD will add genetic counseling, and VCF
    • need use case for nesting DiagnosticReports - Alexander & Raymond from Philips will do this



WG call schedules

  • FHIR - Mondays, 11am EST
  • Main - Tuesdays, 11am EST
  • Information Modeling, Thursdays, 10am EST
  • consensus to leave it as it is



WG roles and positions

  • Regular election (2 seats open)
    • two-yr term = e-vote!
  • Interim election (1 seat open)
    • voted in Q1 today (see minutes)
    • winner will be announced after the results of the regular election are announced
    • term: Jan to May 2019
    • This seat will be filled in a Regular Election (2-year term) to be held at the May WGM
  • Facilitators
    • http://www.hl7.org/documentcenter/public/membership/Facilitators%20Summary%20List.pdf
    • Vocabulary facilitator selection
      • "Vocabulary Facilitators These facilitators are the primary vocabulary and terminology support to the group they are associated with. In general, you need to be very familiar with vocabulary and good vocabulary practices. This is to be accomplished by attending all of the vocabulary tutorials offered by HL7 as well as Practical sessions during vocabulary facilitator's meetings. Attendance at vocabulary facilitators meetings held during regular Working Group Meetings is required. Facilitators are also encouraged to attend their designated Domain Work Group when vocabulary issues are discussed as well as RIM Harmonization meetings." 
      • Joel Schneider has volunteered
        • member and active participant of CG and Vocabulary workgroups
        • motion to appoint Joel: Kevin P/Bob F
        • discussion - none
        • abstain - 0
        • nays - 0
        • yeas - 9
        • motion passes
    • Modeling & Methodology facilitator selection?
      • "These facilitators are the primary methodology and message design support to the group they are associated with. In general, you need to become familiar with the HL7 Development Framework, the messaging design methodology and use of the HL7 Design Tools. One of the most important responsibilities is to be aware of and participate in the various activities that harmonize models across domains. In particular, attendance at the Sunday pm Modeling and Methodology sessions is strongly encouraged to get the most up to date information on methodology and tooling. Facilitator orientation is generally scheduled Monday Q1 and a Facilitator round-table session summarizing the each committee's accomplishments and modeling issues is scheduled for Thursday evening."
      • Amnon fulfilled this role
      • conversations with Lloyd = if we aren't doing RIM/V3 we don't need one (paraphrased)
      • contact Amnon to find out his interest in being active in this position, given Lloyd's advice above
      • consensus - remove this position if Amnon doesn't express an interest in continuing.



Upcoming deadlines (report from chairs and Clinical Steering Div)

  • New HL7 Calendar(s)
  • May ballot cycle
    • Jan 27: deadline to submit PSS to Clinical Steering Division and PMO
    • Feb 17: NIB deadline
  • Sept ballot cycle
    • PSSs must be totally approved by Apr 7



WG documents and refreshes

Work group health








Planning for May WGM

  • Room requirements
    • Keep same as Jan WGM?
      • MQ3-Q4, TueQ1-4, WedQ1-Q4
      • consideration of Genomics tutorial conflict for Wed Q3-4
      • consensus to keep
  • Connectathon tracks and process
    • explicit focus on R4 and IG?
    • In stead of copying all scenarios forward, only include scenarios with at least two attendees with intent to participate?
    • Gil would like to be part of this discussion, will summarize and continue in a call







WG communications procedures / Publicizing our activities

  • Bob F
    • little guidance for communicating our activities internally and externally
    • different members are making connections without communicating to each other
    • don't want to appear uncoordinated
    • unified front to external stakeholders
    • (last thing we need is more overhead by WG)
    • Bob F has seen how other orgs operate
  • Grant W
    • today more people involved compared to early days
    • with FHIR, have more content/artifacts that are consumed externally
    • how do we manage the work we do, and also help external stakeholders take advantage of the work we produce?
  • consensus: create a page in Confluence to proactively announce upcoming opportunities, all WG members can add entries as needed


Action items

  •  Create Confluence page to track WG communications




Date: Wednesday, Jan 16 / Quarter: Q4

Minutes Approved as Presented 


This is to approve minutes via general consent. "You have received the minutes. Are there any corrections to the minutes? (pause) Hearing none, if there are no objections, the minutes are approved as printed."

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Discussion items


eMERGE adoption and feedback

  • propose ad hoc call, maybe squeeze them into a Tues call
  • is this more appropriate for a Mon FHIR call?
    • bandwidth for ballot reconciliation?
  • sounds like exactly what the group is looking forward
  • they are using the IG
  • NIH grant, might be considered a one-off from the implementation point of view




FHIR & IG summary

  • Question about slicing: should we leave the slicing open or closed in our profiles.
    • closed slicing would prevent derived IGs/profiles to add new slices. Even if open slicing has the downside of not be able to validate as exact as a closed slicing this is a trade-off we have to make.
  • gForge issue for each code system (for Vocab workgroup)
    • purpose of gforge issue is to record where issue came from and what has been decided
    • don't create 5000 gforge issues
    • code systems only in an IG is uncommon, not impossible; generally want more public
  • Ballot reconciliation
    • We want to publish soon
    • We have a lot of changes planned (renaming/removing/consolidating)
    • At what point do we need to do a new ballot (again)
    • we are not obligated to re-ballot
    • Question if a balloter who approved would be upset with changes
    • from FMG perspective, want content to be ready for ballot, and don't want continuous re-balloting.
    • several connectathons before balloting again
  • Answers to Grahame's questions, proposed wording:

    Q: Which resources will be candidates for normative in R5?
    A: None. Clinical Genomics is responsible for only one Resource (MolecularSequence), which is NOT a candidate for normative in R5.


    Q: In a single sentence, what are our plans for R5?
    A: Clinical Genomics will continue to work on refining MolecularSequence, move content of current profiles of core resources (e.g., Observation-Genetics, etc) to the Genomics Reporting IG to remove redundancy, update genetics examples in core resources to improve accuracy and completeness, and work with patient care on the family history pedigree representation/profiles.


    • The FMG has identified the following topics we'd like work groups to discuss at this WGM (possibly in your joint sessions w/ FHIR-I)

       

      1. Thank you for your work getting R4 out.  We know how much everyone put in developing content and examples, performing and applying QA, resolving tracker items, etc.  That effort is much appreciated.

      you're welcome!

       

      2. What resources your WG is responsible for are candidates for normative in R5?  What timeframe is reasonable to get those resources to that point?

       None will be normative in R5. MolecularSequence will be vetted more fully once the GenomicsReporting IG is published.

       

      3. What are your FMM targets for your other resources?  Any issues getting to those targets?

       MolecularSequence 3 (? currently at 1); issues include vetting it in more diverse use cases, in concert with the Genomics Reporting IG, and analytics of uploaded data

       

      4. Do you have resources that are not progressing through FMM levels and, if so, what are the issues getting them to move?

      Just MolecularSequence (see above)

       

      5. Are you expecting to be working on implementation guides or other FHIR activities beyond core work?

      Yes, Genomics Reporting IG

       

      6. Any issues keeping up with your tracker items?

      Just available time/resources

       

      7. Any other issues?

       always… :)

    • Discussion with Lloyd

      • New tooling for IGs (Trifolia) will be available after April, can migrate after that point and use for Sept ballot

        • Will migrate from spreadsheets to Trifolia, cannot go backwards, suggest to wait for Lloyd's testing to be completed to start using





WG PSSs

  • 564: Connection with decision support
  • 844: Family Health History and Pedigree standard, Release 2
  • 1050: HL7 Clinical Genomics Domain Information Model(s)
  • 460: CDA Implementation Guide for Genetic Testing Reports
  • 1217: Develop FHIR sequence resource for Clinical Genomics
    • Gil has started on this

advice from Lloyd

  • if scope of PSS hasn't significantly changed, but timelines have, consider writing an addendum and submit for approval.
  • if scope has significantly changed, consider retiring old PSS, and writing a new one




Action items

  •