CG WG Call Notes leading to 2013 September WGM

September 17, 2013 -- Weekly call

Proposed Agenda

• Discuss Cambridge WGM agenda and plans

Attendees

• Amnon Shabo,Gil Alterovitz, Mollie Ullman, Phil Pochon, Grant Wood, Joyce Hernandez, Jenny Cheng, Yan Heras, Scott Bolte, Larry Babb

Draft Minutes

• Discussed the Friday excursion to Harvard
• Discussed draft of PSS for developing HL7 Clinical Genomics Domain Information Model(s)
• Voted on submission of the CG DIM PSS draft to the DE steering division: results - all participants affirmatives

September 10, 2013 -- Weekly call

Proposed Agenda

• Discuss Cambridge WGM agenda and plans

Attendees

• Amnon Shabo,Gil Alterovitz, Mollie Ullman, Phil Pochon, Larry Babb, Bob Milius

Draft Minutes

• Discussed the Friday excursion to Harvard
• Amnon: take care that there is no standards infrastructure talk per se, as it is not a good fit to the goal of discussing the semantics of clinical genomics exchange
• Gil: will talk to Grahame to focus on the genomics resources and LOINC support
• Mollie: need to take care that the current genetic testings are represented as well and not just NGS

September 3, 2013 -- Weekly call

Proposed Agenda

• Discuss draft of PSS for developing HL7 Clinical Genomics Domain Information Model(s)
• Cambridge agenda

Attendees

• Amnon Shabo,Gil Alterovitz, Grant Wood, Mollie Ullman, Scott Bolte,Jenny Cheng, Yan Heras, Phil Pochon, Larry Babb

Draft Minutes

• Discussed the Friday meeting
• Amnon: what's the focus?
• Gil: stakeholders meeting
• Gil: title could be "The HL7 implementer meeting"
• Alternative titles:
  • Amnon: Clinical Genomics Information Exchange
  • Scott: Taking stock of Clinical Genomics Integration Efforts
• Reorganizing the agenda to have a session on HL7 Implementations or have an HL7 talk at the end of each session
• Have an intro on HL7 prior Zac's talk for half an hour
• There should a remote connection

Augsut 6, 2013 -- Weekly call

Proposed Agenda

• Cambridge agenda

Attendees

• Amnon Shabo, Larry Babb, Scott Bolte, Mollie Ullman,Jenny Cheng

Draft Minutes

• Cambridge WGM agenda
  • Tuesday Q4 could be skipped by those wanting to register by day
  • Ask HL7 Hq. for a meeting room for the rest of Thursday, also to prep the field trip on Friday

July 30, 2013 -- Weekly call

Proposed Agenda

• Larry will discuss ClinVar

Attendees

• Amnon Shabo, Larry Babb, Grant Wood, Bob Milius, Scott Bolte, Gil Alterovitz, Mollie Ullman

Draft Minutes

• Larry reviewed ClinVar and related efforts (slides on the U41 Grant are posted here: http://www.hl7.org/Special/committees/clingenomics/docs.cfm?wg_id=7&wg_docs_subfolder_name=presentations)
• HL7 Clinical Genomics Work Group should be on the list of "existing efforts"
• Mollie - concern on lack of healthcare IT people participating in this effort; should be part of the effort right from the beginning
• Amnon - the "Clinical Domain Workgroups" on the combined U01/U41 governance structure might address that concern
• Amnon - intersted in the 'Actionability WG" - is the purpose to get to clinical decisions support, clinical guidelines, workflows, care processes and the like?

July 23, 2013 -- Weekly call

Proposed Agenda

• Discuss the Cambridge WGM agenda
• Discuss if the group wants/needs a project scope statement for the FHIR development
  • If yes, then what should be stated in terms of alignment with the other CG specs (v3, v2, GTR)
  • Could we decide to have the FHIR models (core and extensions) as a single source of semantics for all specs (i.e., v3, v2, GTR and FHIR of course)?

Attendees

• Amnon Shabo, Scott Bolte, Mollie Ullman, Gil Alterovitz, Jenny Cheng and Tom Chen

Draft Minutes

• Discussion took place on how the group need to go about the FHIR genomic resources developed by Gil et. al. and the FHIR family history resource developed by FHIR people
• Gil: we plan on pilots with partners using the FHIR resources
• Mollie: it takes time to vet models for clinical use
• Scott: worthwhile to support the FHIR effort while scoping the use cases it serves
• Amnon: it's an opportunity to come up with the group DIM
• Gil: we don't take ownership on the FHIR Family History resource even though we could contribute to it

July 16, 2013 -- Weekly call

Proposed Agenda

• Discuss the path from DAM to DIM and to technical specs
• Could the FHIR platform facilitate a Clinical Genomics DIM (Domain Information Model)?
• Could we map a FHIR-based DIM to our v3, v2 and CDA specs, so that they're all derived from the same semantics?

Attendees

• Amnon Shabo, Mollie Ullman, Gil Alterovitz, Yan Heras, Grant Wood, Larry Babb, Scott Bolte

Draft Minutes

• Address question on CMET from HL7 Hq.
• Mollie:
  • We missed the deadline for the September ballot
  • We should target at internal review in September and formal ballot in January 2014
• Amnon:
  • Described the HL7 development methodology from DAM to DIM and then to actual specs
  • Mentioned the way our group used this methodology mainly through the v3 development effort
• Larry:
  • What's the relation between the CDC clinical-grade VCF effort and ClinVar efforts?
  • What fits better our standards?
• Grant: Will they be publishing the clinical-grade VCF by January?
• Mollie: in part they are looking to what we are going to publish
• Scott:
  • agile development concepts could be helpful in our effort
  • we still need an overarching structure but one that doesn't limit the development

July 9, 2013 -- Weekly call

Proposed Agenda

• Gil and Jenny will describe the genomic FHIR resources

Attendees

• Amnon Shabo, David Jarvis, Yan Heras, Larry Babb, Scott Bolte,Gil Alterovitz, Jenny Cheng and Tom Chen (Harvard), Joyce Hernandez

Draft Minutes

• Gil et al presented SMART and FHIR resources
  • Presentation: http://smartgenomics.wikispaces.com/file/detail/SMARTGenomicsAPI2_3-1.pdf
  • Web site with FHIR format: http://genomics-advisor.smartplatforms.org:4000/
• Discussed alignment with v2 and GTR
• Discussed the use of VCF and GVF
• Compared to v3 Genetic Locus / Loci model with regard to the core class (sequence vs. locus) and multiple loci representation
• Amnon: need to align the various specs (v2, GTR, FHIR) with a single, computable and agreed-upon model that represents the semantics presented in the DAM (Domain Analysis Model)

July 2, 2013 -- Weekly call

Proposed Agenda

• Cytogenetics discussion

Attendees

• Amnon Shabo, Mollie Ullman, Gil Alterovitz, Scott Bolte, Yan Heras, Grant Wood

Draft Minutes

• Performed ballot reconciliation of the v2 Cytogenetics IG (facilitated by Yan Heras)

June 25, 2013 -- Weekly call

Proposed Agenda

• Discuss the standardization of a clinical-grade VCF and encapsulation and/or referencing of it in HL7
• Continue working on the Clinical Sequencing DAM in preparation to the September ballot

Attendees

• Amnon Shabo, Mollie Ullman, Grant Wood, Bob Milius, Gil Alterovitz, Scott Bolte

Draft Minutes

• Mollie agrees that the v2 message should be taken out of the DAM, but concepts like the association of an overall interpretation with interpretations of discrete testings should be described in detail
• Mollie reported on a conference in Virginia she attended (Mollie - PLEASE FILL IN)
• Gil and Jenny will describe the genomic FHIR resources they're working on in the call in two weeks
• The FHIR resources 'encapsulate' raw data by having the Variant resource holding a line from a VCF file

June 18, 2013 -- Weekly call

Proposed Agenda

• Grant Wood will report on the event "Genomic and Family Health History in Health IT" held in Intermountain
• Status of publsihing the Cytogenetics specification
• Continue working on the Clinical Sequencing DAM in preparation to the September ballot

Attendees

• Amnon Shabo, Mollie Ullman, Larry Babb, Grant Wood, Bob Milius, Joyce Hernandez

Draft Minutes

• Bob Milius is trying to reach out to experts on sequencing for typing purposes
• Grant reported on his talk at the Illumina "Genome Informatics Alliance" conference in Seattle (May 2013)
• Discussed the standardization of the clinically oriented report Illumina presented in the HL7 Phoenix meeting in January 2013
• Grant reported on the conference he organized in Intermountain (SLC)titled "POWERFUL PATIENT DATA: GENOMICS AND FAMILY HEALTH HISTORY IN HEALTH IT"; three Breakout groups: Data Collection; Data Connection; Data Activation. Grant moderated the Data Connection group and promoted the use of the HL7 Pedigree standard for interoperability
• Larry discussed the effort to develop "clinical grade VCF"

June 11, 2013 -- Weekly call

Proposed Agenda

• Finish up the Clinical Sequencing DAM ballot reconciliation
• What does it take to get the GTR into Consolidated CDA?
• Referencing raw data from our standards
• Discuss and approve the Atalanta WGM meeting minutes

Attendees

• Amnon Shabo, Mollie Ullman, Larry Babb, Grant Wood

Draft Minutes

• Finished up the ballot reconciliation of the Clinical Sequencing DAM
• Decided to prepare the Clinical Sequencing DAM to the September ballot Cycle
• Amnon will work out with Mollie to insert wording on (1) warehousing and (2) encapsulation
• Amnon will approach Bob Milius to work out an example of encapsulation of key raw data in tissue typing

June 4, 2013 -- Weekly call

Proposed Agenda

• Review first draft of Atlanta WGM meeting minutes
• Review first draft of Cambridge WGM agenda

Attendees

• Amnon Shabo, Mollie Ullman, Larry Babb, Joyce Hernandez

Draft Minutes

• Discussed FHIR family history and agreed that any effort done should result in FHIR modeling consistent with the Pedigree standard

May 28, 2013 -- Weekly call

Proposed Agenda

• Atlanta meeting recap and minute review and approval
• Review of summer goals
• Draft agenda and goals for Septmeber meeting

Attendees

• Amnon Shabo, Gil Alterovitz, Grant Wood, Scott Bolte, Mollie Ullman, Bob Milius, Deborah Watt (Associate, Research & Faculty Development, Department of Family Practice, University of British Columbia)

Draft Minutes

• Discussed whether we need to split when FHIR s discussed in Cambridge
• Amnon will draft an agenda for Cambridge and see if we can accommodate a joint meeting with FHIR without a split

May 21, 2013 -- Weekly call

Agenda

• Drafting summer goals

Attendees

• Lorie Dieterle (KP - solution consultant working in national IT strategy team), Gil Alterovitz - (HMS/CHIP SMART api to integrate clinical and genomic information), Yan Heras, Grant Wood, Scott Bolte, and Mollie Ullman

Draft Minutes

Goals leading to September meeting

• Grant
  • publishing cytogenetics
  • FH release 2 - Grant does he want this for Sept ballot
  • report on v2.5.1 adoption at Intermountain
  • extensions of v2.5.1
• Mollie
  • prep Clinical Sequencing for ballot in Sept
• Yan
  • help with vocabulary on FH release 2 if needed
  • focus on FHIR family history
• Gill
  • interested in Consolidated CDA working with Amnon and FHIR family history working Yan
• Lorie
  • may be able to help with reviews in process of ballot prep
• Amnon (potential items)
  • Consolidated CDA
  • template for National Bone Marrow program and/or LMM colaboration of GTR
  • Family History 2
• Scott
  • FHIR family history (may have limited bandwidth)

• Important Dates
  • NIB - July 7
  • Deadline for IG's - Aug 5 (with final due Aug 11)

• Mollie to schedule special meeting for ballot reconciliation, to maximize working time on weekly calls - must attend = Amnon, Grant, Mollie