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Comment: Uploaded and linked to slides (Bob F)


  1. S4G (first)
  2. Family History (Grant)
  3. FHIR-I prep
  4. examples (cont)

S4G ONC Sync for Genes Update (Bob F)


Phase 4 soliciting groups to participate, reach out to Bob F or 

Discussion Points to consider:

  • Core Vs custom IGs (80/20)
    • eMERGE, HLA, mCODE, phenopackets
  • Collaboration and engagement
    • onc/nlm/nhgri
  • CG WG effort
    • standard development (new)
    • fixes, clarifications, examples (existing)
    • consultation to support adoption
      • deriving from parent profiles (including US core)
        • currently lacking functionality in FHIR validator

Family History (Grant W)

  • GA4GH Clin/Pheno Pedigree subgroup
    • minimum data set for a family health history - work started in 2008 - will result in a live document for comment
      • standard-agnostic list of recommended elements
      • PED format found insufficient by itself
        • each PED is scoped to one particular disease
      • working with app vendor called 'cancer IQ'
    • current FHIR resource is targeted at (vague) family health history statements taken by clinicians - not computable
      • genomics profile on that resource (from R3 work) is still lacking for robust use.
        • ids from PED (family, proband, father, mother, individual)
    • Ancestry (from an ontology if possible-hard to identify one) (HANCESTRO one option, but many ontologies tend to be too narrowly scoped)
    • Considering a place for marking records of pedigree analysis in the EHR

Ancestry as Observation vs other resource? Research-enabling focus rather than solely clinical


Minutes Approved as Presented 


CG Information Modeling

  • overview of where we are
  • update on recent modeling
  • roadmap - priority
    • laundry list of what we can do
  • technical approach to implement into FHIR IG
  • GA4GH alignment


  1. Why
  2. Review Model (preview Definitional Variant)
  3. Roadmap

Feedback / Questions

  • Is Sequence related to an "order panel"?  — No, this is a lower level of data
  • Add an additional sequence representation? — Intent was to focus/"ground" at the conceptual level (Sequence) and let the various representations grow / extend as needed? Patrick Werner
  • Sequence-Based Variant Representation: data types of referenceAllele and alternateAllele maybe should be Allele? — allele name ties back to the names in VCF, SPDI, etc ... but still aligns conceptually to our definition of Sequence in our model.  Can discuss further if needed.

Prioritizing Next Steps (suggestions):

  • "Implications" - struggling on the IG side, perhaps can help
  • How to align logical model to FHIR IG current state and apply

Bob's Crystal Ball (initial guess as CG resources) (Definitional resources)

  • MolecularSequence (all types, representations, GenomeAssembly, annotations+features)
  • MolecularVariation (all types, representations, annotations)
  • Assertion<<SEPIO>> (implications and inferences related to sequences and variations)