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HL7 Clinical Genomics – Implementation Roadmap. The HL7 Clinical Genomics SIG Amnon Shabo (Shvo), PhD HL7 Clinical Genomics SIG Co-chair and Modeling Facilitator HL7 Structured Documents TC CDA R2 Co-editor CCD Implementation Guide Co-editor. V2 :||: V3 Challenges.

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hl7 clinical genomics implementation roadmap

HL7 Clinical Genomics – Implementation Roadmap

The HL7 Clinical Genomics SIG

Amnon Shabo (Shvo), PhD

HL7 Clinical Genomics SIG

Co-chair and Modeling Facilitator

HL7 Structured Documents TC

CDA R2 Co-editor

CCD Implementation Guide Co-editor

v2 v3 challenges
V2 :||: V3 Challenges
  • What should be the position of the HL7 community towards independent modeling attempts of v2 messages applied to new domains that have been solely modeled in v3?
  • What’s the long term vision?
    • Gradual conversion to v3 until v2 is deprecated? Or -
    • V2/V3 Co-existent? If so - how?
  • Divergence is the current situation:
    • V3 and V2 ‘languages’ have different semantics
    • V2 - V3 ‘attribute mapping’ does NOT help when semantics at the source level is different, e.g., different structures, dynamics, etc.
proposed approach
Proposed Approach
  • Recognize V3 models as a single source of semantics
  • Refer to V2 messages is a partial v3 implementation
  • Automatically generate v2 messages from v3 models, much like the V3 XML ITS
  • Acknowledge the incompleteness of the v2 implementation, but
    • Address specific requirements of use cases
    • Let the operator of the v3v2 generator make domain choices
    • Document the gaps
    • Imply missing semantics from the v3 models
a proposed roadmap for cg implementations
A Proposed Roadmap for CG Implementations

The Clinical Genomics semantics:

represented by normative HL7 V3 Models

CDISC

SDTM

V2 message

generation

V3 XML ITS

Implementation

Technologies:

Family History

Implementation

Pharmacogemomics

Implementation

Genetic testing

Implementation

Balloted informative implementation specifications

example the geneticvariation model

Genetic Loci

Genetic Locus

Example: The GeneticVariation Model

Associated data (vocab. Controlled)

participants

Individual Allele

Genetic Document

Sequence

(observed or reference)

Sequence Variation

new its tool domain specific v3 v2 generator
New ITS Tool: Domain-Specific V3V2 Generator

Subject

Associated data

PID

OBR

OBX

OBX

OBX

Sequence Variation

Individual Allele

Genetic Locus

Genetic Loci

User-defined

preferences

OBR

OBR

OBR

OBR

OBX

OBX

OBX

OBX

OBX

OBX

OBX

OBX

OBX

OBX

OBX

OBX

geneticvariation in v2 with v3 similarities
GeneticVariation in V2 (with V3 similarities)

V3 GeneticLoci overall ‘summary’

e.g., GeneticLoci.interpretationCode

V3 GeneticLocus & SequenceVariation

e.g., GeneticLocus.value

what should the v3 v2 its tool facilitate
What Should the V3V2 ITS Tool Facilitate?
  • Consistently capture v3 structural codes & clone names in v2 fields (is it doable?)
  • The choice of v2 ‘common patterns’, e.g.:
    • Patterns of implementing v3 nesting clones (Sub-ID? Parent id?)
  • Document common gaps like v3 associations
  • Transform v3 XML schemas to v2 XML-encoded and on to v2 ASCII