CG WG Call Notes leading to 2015 September WGM

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September 1, 2015 -- Weekly call

Agenda

  • Misc.

Attendees

  • Amnon Shabo (Shvo), Siew Lam, Jeremy Warner, Scott Bolte, Jon Holt, Gil Alterovitz, Larry Babb, Mollie Ullman-Cullere, Oracle rep. (please add your name)

Draft Minutes

  • Jon reported on the status of family health history standardization
  • Gil reported on the precision medicine initiative of the White House
    • Had a call with the chief data scientist (new appointment) telling him about SMART on FHIR
    • Looking for parties interested in prototyping
    • Oracle representative joined the call and expressed interest to learn more about implementation options
  • Larry and Gil reported on Global Alliance activities

August 25, 2015 -- Weekly call

Agenda

  • FHIR discussion
  • ClinGen update

Attendees

  • Amnon Shabo (Shvo), Larry Babb, Bob Milius, Siew Lam, Grant Wood, Gil Alterovitz, Alex (Gil's team), Jon Holt, Jeremy , Perry Mar, Joseph Kane, J. Karp

Draft Minutes

  • Larry reported on the allele registry of ClinGen
    • a way to canonicalize the allele representation
  • Gil had a motion to approve submitting the ballot reconciliation of FHIR genomic observation
  • results: approved as follows - one negative, three abstains, five affirmative

August 11, 2015 -- Weekly call

Agenda

  • FHIR reconciliation

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Scott Bolte, Travis, Bob Milius, Gil Alterovitz, Joseph Kane, Tom (Gil's team), Jon Holt, Lloyd McKenzie

Draft Minutes

  • Gil reviewed the last call where we wnet through major negative comments
  • Discussion of genomic coordinates
  • Discussion of local external coding systems and value sets

August 4, 2015 -- Weekly call

Agenda

  • FHIR reconciliation

Attendees

  • Amnon Shabo (Shvo), Siew Lam, Scott Bolte, Larry Babb, Perry Mar, Grant Wood, Gil Alterovitz, Tom (Gil's team), Jonathan Holt, Travis

Draft Minutes

  • Gil went through of the items in the reconciliation document (is available on the main HL7 Clinical Genomics page)


July 21, 2015 -- Weekly call

Agenda

  • FHIR

Attendees

  • Gil Alterovitz, Mollie Ullman-Cullere, Joseph Kane (Epic), Tom Chen (SMART Genomics), Jonathan Holt, Eric Haas

Draft Minutes

  • Discussed FHIR's new 'component' element recommended to use for the genetics observation profile
    • Component supports key - values pairs.
    • CG needs to use coded keys. LOINC and other options were discussed.
    • Using components for genetic/genomic data will also create a flat structure (not supporting a hierarchy)
  • Unanimously approved use of component and LOINC to address FHIR needs in ballot resolution and preparation of Sept. ballot.

July 14, 2015 -- Weekly call

Agenda

  • Misc.

Attendees

  • Amnon Shabo (Shvo), Siew Lam, Grant Wood, Gil Alterovitz, Larry Babb, Perry Mar, Bob Milius, Mollie Ullman-Cullere, Bob Freimuth, Travis

Draft Minutes

  • How to report absence of variants
  • Larry told about how the IOM EHR genomics effort copes with the above


July 7, 2015 -- Weekly call

Agenda

  • FHIR ballot and editors

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Siew Lam, Grant Wood, Gil Alterovitz, Dan Rutz, Jeremy Warner, Joseph, Scot Bolte, Perry Mar, Bob Freimuth, Bob Milius, Tom (Gil's team)

Draft Minutes

  • Discussed a motion to first take care of ballot reconciliation and then address other comments that actually change the FHIR structure, e.g., remove assessed condition or change to reason for study, etc.


June 30, 2015 -- Weekly call

Agenda

  • CIGAR
  • Jon - letter to HL7, and also Kevin's input
  • Ballot reconciliation

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Jonathan Holt, Grant Wood, Gil Alterovitz, Bob Milius, Larry Babb, Dan Rutz, Jeremy Warner, Travis, Jami (Regenstrief), Lori Dieterle, Scot Bolte

Draft Minutes

  • Jon - CIGAR is a type of interpretation
  • Amnon - I would think of CIGAR as another way to present findings of test/observation
  • Mollie brought up Perry Mar's ballot comments
  • Jon - assessed condition is not a good term, perhaps should use reason for test and in any case it belongs at a higher level
  • Travis - we include on the order
  • Bob M. - for the purpose of ballot reconciliation we need a better definition

June 23, 2015 -- Weekly call

Agenda

  • FHIR stuff and miscellaneous

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Siew Lam, Jonathan Holt, Perry Mar, Grant Wood, Gil Alterovitz, Bob Milius, Jeremy Warner, Harish, Lorie Dieterle, Larry Babb, Travis, Scott Bolte

Draft Minutes

  • Amnon: we need to disallow the use of the base interpretation or point to a separate resource/profile, similarly to the way it's done with assessed condition
  • Mollie: in my understanding, we can't disallow something in the profile, but on the other hand, whatever we don't explicitly specify (e.g., interpretation is not part of the genetic profile) is not part of the our standard
  • Gil: Global alliance is looking to developing standards similar to FHIR and approached us on that
  • Gil: gave an update on the availability of a sand box in FHIR
  • Larry gave updated on the allele registry of ClinGen
  • Mollie reviewed the intro text revision to the FHIR spec "Standard Profile for Genetics (Profile)"
  • Lam: why do we say that the standard can't be used for CDS?
  • Proposed to have a warning on the use of the standard by clinical decision support applications, but can still be used by human experts
  • Revised draft will be circulated


June 16, 2015 -- Weekly call

Agenda

  • FHIR stuff

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Siew Lam, Larry Babb, Jonathan Holt, Perry Mar, Bob Freimuth, Dan, Lori, Travis

Draft Minutes

  • Larry:
    • Went through his FHIR ballot comment
    • We should not be bundling everything into a single flat Observation structure
    • Need a roadmap to show how this work is going to evolve
    • Need to support clinical decision support
  • Amnon:
    • The interpretation of the base Observation resource should be explicitly disallowed
    • Clinical decision support is an important use case


June 9, 2015 -- Weekly call

Agenda

  • Misc.

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Siew Lam, Larry Babb, Jonathan Holt, Jeremy Warner, Dan Rutz, Bob Milius, Jeffery Karp, Scott Bolte, Joseph

Draft Minutes

  • Comments on the FHIR genetic Family Health History FHIR Profile
  • Decided to contact Lloyd and Grahame about issues in the current revision of the FHIR profile of genetic family history as explained by Jonathan Holt


June 2, 2015 -- Weekly call

Agenda

  • Misc.

Attendees

  • Amnon Shabo (Shvo), Mollie Ullman-Cullere, Grant Wood, Larry Babb, Jonathan Holt, Bob Freimuth, Jeremy Warner, Dan Rutz, Bob Milius, Jeffery Karp, Gil Alterovitz, Travis Pittman

Draft Minutes

  • Dan Rutz introduced himself (representing Epic)
  • Grant described the genomics policy meeting in DC
  • The Global Alliance plenary meeting was mentioned
  • Not clear if and which FHIR version is going normative
    • Later confirmed that there will be at least one more DSTU (DSTU 2.1) prior to normative balloting
  • Bob Freimuth:
    • perhaps it's not possible to get to an overarching CG model covering all use cases
    • focus on messaging specifications
  • Amnon:
    • HL7 main mandate is about exchange of information
    • however, the model of exchanged information impacts the internal representation of the data at the sending and receiving sides
    • if the internal representations are very different than the exchanged representation, then it might make semantic interoperability much harder
    • We have to work both bottom up (smaller-scale models for specific use cases) and top down (conceptual and broader modeling) so that we archive progress and learn lessons on the one hand, and still converge on the important principles to be kept in any CG model
    • the DIM effort is currently about two narrower models - Clinical Genomics Statement (just one single gen-phen association) and family history
    • the overarching models meet the concrete specifications by means of constraining, preferably using model-driven tools