HL7 Clinical Genomics – Implementation Roadmap The HL7 Clinical Genomics SIG Amnon Shabo (Shvo), PhD HL7 Clinical Genomics SIG Co-chair and Modeling Facilitator.

HL7 Clinical Genomics –

Implementation Roadmap

The HL7 Clinical Genomics SIG

Amnon Shabo (Shvo), PhD

HL7 Clinical Genomics SIGCo-chair and Modeling Facilitator

HL7 Structured Documents TCCDA R2 Co-editorCCD Implementation Guide Co-editor

2

Haifa Research Lab

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.

3

Haifa Research Lab

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 v3v2 generator make domain choices Document the gaps Imply missing semantics from the v3 models

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Haifa Research Lab

A Proposed Roadmap for CG Implementations

PersonclassCode*: <= PSNdeterminerCode*: <= INSTANCEid: II [0..1]name: BAG<EN> [0..*]telecom: BAG<TEL> [0..*]administrativeGenderCode: CE CWE [0..1] <=AdministrativeGenderbirthTime: TS [0..1]deceasedInd: BL [0..1] "false"deceasedTime: TS [0..1]raceCode: SET<CE> CWE [0..*] <= RaceethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity

1..1 patientPerson

0..1 providerOrganization

PatientclassCode*: <= PATid: II [0..1]

DeceasedEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode: CD CWE [0..1]value: IVL<PQ> CWE [0..1]

SubjectEstimatedAge

LivingEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode: CD CWE [0..1]value: IVL<PQ> CWE [0..1]

0..* subjectEstimatedAgetypeCode*: <= SBJsubjectOf1

V3 XML ITS

Family History

Implementation

V2 message

generation

Genetic testing

Implementation

Balloted informative implementation specifications

CDISC

SDTM

Pharmacogemomics

Implementation

Implementation

Technologies:

The Clinical Genomics semantics:

represented by normative HL7 V3 ModelsPersonclassCode*: <= PSNdeterminerCode*: <= INSTANCEid: II [0..1]name: BAG<EN> [0..*]telecom: BAG<TEL> [0..*]administrativeGenderCode: CE CWE [0..1] <=AdministrativeGenderbirthTime: TS [0..1]deceasedInd: BL [0..1] "false"deceasedTime: TS [0..1]raceCode: SET<CE> CWE [0..*] <= RaceethnicGroupCode: SET<CE> CWE [0..*] <= Ethnicity

1..1 patientPerson

0..1 providerOrganization

PatientclassCode*: <= PATid: II [0..1]

DeceasedEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode: CD CWE [0..1]value: IVL<PQ> CWE [0..1]

SubjectEstimatedAge

LivingEstimatedAgeclassCode*: <= OBSmoodCode*: <= EVNcode: CD CWE [0..1]value: IVL<PQ> CWE [0..1]

0..* subjectEstimatedAgetypeCode*: <= SBJsubjectOf1

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Haifa Research Lab

Example: The GeneticVariation Model

0..* associatedObservation

typeCode*: <= ActRelationshipType (default=COMP)contextConductionInd: BL [0..1] "TRUE"

sourceOf

0..* associatedProperty

typeCode*: <= DRIVcontextConductionInd: BL [0..1] "TRUE"

derivedFrom

0..* sequenceVariation

typeCode*: <= COMPcontextConductionInd: BL [0..1] "TRUE"

component1

IndividualAlleleclassCode*: <= SEQVARmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]negationInd: BL [0..1]title: ED [0..1]text: ED [0..1]statusCode: CS CNE [0..1] <= ActStatuseffectiveTime*: GTS [1..1]reasonCode: SET<CE> CWE [0..*] <= ActReasonvalue: CD CWE [0..1] <= C:interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretation

GeneticLocusclassCode*: <= LOCmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]code: CE CWE [0..1] (default=Gene)negationInd: BL [0..1]title: ED [0..1]text: ED [0..1]statusCode: CS CNE [0..1] <= ActStatuseffectiveTime*: IVL<TS> [1..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialityreasonCode: SET<CE> CWE [0..*] <= GeneticActReasonvalue*: ANY [1..1]interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode*: SET<CE> CWE [1..1]

0..* individualAllele


component2

SequenceclassCode*: <= SEQmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]code: CD CWE [1..1] (the type of sequence (observed, reference, etc.))text: ED [0..1] (sequence's annotations)effectiveTime: GTS [0..1]reasonCode: SET<CE> CWE [0..*] <= ActReasonvalue: ED [1..1] ((the actual sequence in a recognized bioinformatics content model) (such as BSML)interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode: SET<CE> CWE [0..*] (the sequencing method)

HL7 Clinical Genomics SIGDocument: Genotype Topic - The GeneticVariation ModelRev: POCG_RM000011.v9 Date: November 18, 2007Facilitator: Amnon Shabo (Shvo), IBM Research in Haifa, shabo@il.ibm.com

Note:A related allele that is ata different locus, and hasinterrelation with thesource allele, e.g.,translocated duplicatesof a gene.

0..* phenotype

typeCode*: <= PERTcontextConductionInd: BL [0..1] "TRUE"

pertinentInformation

SequenceVariationclassCode*: <= SEQVARmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]code: CD CWE [0..1]negationInd: BL [0..1]title: ED [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: ANY [0..1]interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode: SET<CE> CWE [0..*]

Note:Code: COPY_NUMBER, ZYGOSITY, DOMINANCY, GENE_FAMILY,etc. For example, if code = COPY_NUMBER, then the value is oftype INT and is holding the no. of copies of this gene or allele.

0..* sequence

typeCode*: <= COMPcomponent2

0..* phenotype



0..* phenotype

typeCode*: <= PERT


Note:The code attribute indicates inwhat molecule the variation occurs,i.e., DNA, RNA or Protein.

Note:Use the associations to the shadowclasses when the variation and orthe sequence data are not at theallelic level.



sourceOf

0..1 associatedObservation


sourceOf

Note:This recursive associationenables the association of anRNA sequence derived froma DNA sequence and apolypeptide sequence derivedfrom the RNA sequence.

0..* phenotype



Note:

This class is a placeholder for specifying a locus on the genome, i.e., a position of a particulargiven sequence in the subject’s genome.Note that the semantics of the locus (e.g., gene) is defined by data assigned in the code & valueattributes of this class, and also by placing additional data relating to this locus into the classes(and CMETs) associated with this class.

Note:The term 'Individual Allele' doesn't refer necessarily to aknown variant of the gene/locus, rather it refers to theindividual patient data regarding the gene/locus, and mightcontain personal variations with unknown significance atthe effective time of this observation.

AssociatedObservationclassCode*: <= GENmoodCode*: <=x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: SET<II> [0..*]code*: CD CWE [1..1]text: ED [0..1]effectiveTime*: GTS [1..1]value: ANY [0..1]methodCode: SET<CE> CWE [0..*]

Note:The code attribute could hold codes like TYPE,POSITION.GENOME, LENGTH, REFERENCE, REGION, etc..The value attribute is populated based on the selected codeand its data type is then setup accordingly during instancecreation. Here are a few examples:If code = TYPE, then the value is of type CV and holds one of thefollowing: SNP (tagSNP), INSERTION, DELETION,TRANSLOCATION, etc.

if code = POSITION, then value is of type INT and holdsthe actual numeric value representing the variation positionalong the gene.

if code = LENGTH, then value is of type INT and holdsthe actual numeric value representing the variation length.

If code = POSITION.GENE, then value is of type CV and is oneof the following codes:INTRON, EXON, UTR, PROMOTER, etc.

If code = POSITION.GENOME, then value is of type CV and is oneof the following codes:NORMAL_LOCUS, ECTOPIC, TRANSLOCATION, etc.

If the code = REFERENCE, then value istype CD and holds the reference gene identifier drawn from areference database like GenBank.

More details about vocabularies for codes and itsrespective values could be found in the specification.

Note:Code: CLASSIFICATION, etc.For example, if code =CLASSIFICATION, then the valueis of type CV and is holding eitherKNOWN or NOVEL.

reference

0..* geneticLocus

typeCode*: <= REFRcontextConductionInd: BL [0..1] "TRUE"

Note:A related locus that has significantinterrelation with the source locusand is not part of this loci set representedin this instance.

reference



Constrained to a restricted BSMLcontent model, specified in aseparate schema.

Constraint: Sequence.value

0..* sequence


component4



component3

AssociatedPropertyclassCode*: <= GENmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)code*: CD CWE [1..1]text: ED [0..1]value: ANY [0..1]



derivedFrom



derivedFrom



derivedFrom1



sourceOf



derivedFrom3derivedFrom2

0..* sequence


Note:Any observation related to the variation and is notan inherent part of the variation observation (the lattershould be represented in the AssociatedProperty class).For example, the zygosity of the variation.

Note:Any observation related to the sequence and is notan inherent part of the sequence observation, e.g.,splicing alternatives.Note that inherent characteristics of the sequenceshould be represented in the AssociatedProperty class.

Note:There could be zero to manyIndividualAllele objects in aspecific instance. A typicalcase would be an allele pair,one on the paternalchromosome and one on thematernal chromosome.

Note:Use this class forinherent dataabout the locus, e.g.chromosome no.

0..* phenotype

typeCode*: <= PERTpertinentInformation

AssociatedProperty

AssociatedProperty

AssociatedProperty

SequenceVariation

Sequence

SequenceVariation

Note:An internal CMET used to representclinical phenotypes, both observed inthe patient and known in thescientific literature.

CMET: (ORGANIZER) A_Phenotype

[universal](POCG_MT000030UV)









Holds the variation expressed with arecognized notation like 269T>C ora markup like BSML or drawn from anexternal reference like OMIM or dbSNP.Data type should be set accordingly.

Constraint: value

If code = "Gene", value data type shall be set to CD and containa code identifying a gene through GenBank GeneID, HUGO name,OMIM ID or any other internationally recognized identification of genes.If the locus is not a gene then the data type should be set to theappropriate type, e.g., ST for locus notation like “10q24.32”.

Constraint: value

GeneticLociclassCode*: <= LOCmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: SET<II> [0..*]code*: CD CWE [1..1] <= GeneticVariationnegationInd: BL [0..1]title: ED [0..1]text: ED [0..1]statusCode*: CS CNE [1..1] <= ActStatuseffectiveTime*: GTS [1..1]confidentialityCode: SET<CE> CWE [1..1] <= ConfidentialityreasonCode: SET<CE> CWE [0..*]interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode: SET<CE> CWE [0..*] <= ObservationMethod

0..* geneticLocus


0..* assignedEntity

typeCode*: <= AUTcontextControlCode: CS CNE [0..1] "OP"

author

0..* assignedEntity

typeCode*: <= VRFcontextControlCode: CS CNE [0..1] "OP"

verifier

0..* assignedEntity

typeCode*: <= PRFcontextControlCode: CS CNE [0..1] "OP"

performer

CMET: (ASSIGNED) R_AssignedEntity

[universal](COCT_MT090000UV)

0..1 roleName

GeneticDocumentclassCode*: <= DOCmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: SET<II> [0..1]code*: CD CWE [1..1] <= DocumentTypetitle: ED [0..1]text: ED [0..1]statusCode*: CS CNE [1..1] <= ActStatuseffectiveTime*: GTS [1..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialitysetId: II [0..1]

0..* geneticDocument

typeCode*: <= DOCcontextConductionInd: BL [0..1] "TRUE"

documentation

relatedDocument


typeCode*: <= x_ActRelationshipDocumentcontextConductionInd: BL [0..1] "TRUE"seperatableInd: BL [0..1]

Note:Use the separation indicator to indicatewhen a document should not be separatedfrom its associated document (like in theEGFR-KRAS2 use case from HPCGG)

Note:There are two ways to refer to a clinical document: 1. Populate the id attribute with the document id 2. Place the entire CDA instance within the text attribute

The other attributes in this class are essential data aboutthe document and they are repeated in the documentinstance itself. It’s meant to ease the parsing process.



sourceOf



0..* phenotype



GeneticVariation(POCG_RM000011UV)

The entry point to the combinedGenetic Loci/Locus model thatrepresent genetic variations data.

0..1 identifiedEntity

typeCode*: <= SBJcontextControlCode: CS CNE [0..1] "OP"

subjectIdentifiedEntityclassCode*: <= IDENTid: SET<II> [0..*]code: CE CWE [0..1] <= RoleCode

ScopingEntityclassCode*: <= LIVdeterminerCode*: <= INSTANCEid: SET<II> [0..*]code: CE CWE [0..1] <= EntityCode

0..1

performer

AssociatedObservation




0..*

author

0..1

performer 0..1

performer

0..1

performer

0..1

performer

If interpretationCode is assigned with a valuea reasonCode shall be assigned a value to setthe context for the interpretation semantics.

Constraint: GeneticLoci.reasonCode&interpretationCode

AssociatedProperty


typeCode*: <= DRIVderivedFrom

Genetic Loci

Genetic

Locus

Individual Allele

Sequence

Variation

Sequence

(observed or reference)

Genetic Document

participants

Associated data (vocab. Controlled)

6

Haifa Research Lab

New ITS Tool: Domain-Specific V3V2 Generator

OBR

OBX



sourceOf



derivedFrom



component1

IndividualAlleleclassCode*: <= SEQVARmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]negationInd: BL [0..1]title: ED [0..1]text: ED [0..1]statusCode: CS CNE [0..1] <= ActStatuseffectiveTime*: GTS [1..1]reasonCode: SET<CE> CWE [0..*] <= ActReasonvalue: CD CWE [0..1] <= C:interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretation

GeneticLocusclassCode*: <= LOCmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]code: CE CWE [0..1] (default=Gene)negationInd: BL [0..1]title: ED [0..1]text: ED [0..1]statusCode: CS CNE [0..1] <= ActStatuseffectiveTime*: IVL<TS> [1..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialityreasonCode: SET<CE> CWE [0..*] <= GeneticActReasonvalue*: ANY [1..1]interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode*: SET<CE> CWE [1..1]



component2

SequenceclassCode*: <= SEQmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]code: CD CWE [1..1] (the type of sequence (observed, reference, etc.))text: ED [0..1] (sequence's annotations)effectiveTime: GTS [0..1]reasonCode: SET<CE> CWE [0..*] <= ActReasonvalue: ED [1..1] ((the actual sequence in a recognized bioinformatics content model) (such as BSML)interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode: SET<CE> CWE [0..*] (the sequencing method)

HL7 Clinical Genomics SIGDocument: Genotype Topic - The GeneticVariation ModelRev: POCG_RM000011.v9 Date: November 18, 2007Facilitator: Amnon Shabo (Shvo), IBM Research in Haifa, shabo@il.ibm.com

Note:A related allele that is ata different locus, and hasinterrelation with thesource allele, e.g.,translocated duplicatesof a gene.

0..* phenotype



SequenceVariationclassCode*: <= SEQVARmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: II [0..1]code: CD CWE [0..1]negationInd: BL [0..1]title: ED [0..1]text: ED [0..1]effectiveTime: GTS [0..1]value: ANY [0..1]interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode: SET<CE> CWE [0..*]

Note:Code: COPY_NUMBER, ZYGOSITY, DOMINANCY, GENE_FAMILY,etc. For example, if code = COPY_NUMBER, then the value is oftype INT and is holding the no. of copies of this gene or allele.

0..* sequence


0..* phenotype



0..* phenotype

typeCode*: <= PERT


Note:The code attribute indicates inwhat molecule the variation occurs,i.e., DNA, RNA or Protein.

Note:Use the associations to the shadowclasses when the variation and orthe sequence data are not at theallelic level.



sourceOf

0..1 associatedObservation


sourceOf

Note:This recursive associationenables the association of anRNA sequence derived froma DNA sequence and apolypeptide sequence derivedfrom the RNA sequence.

0..* phenotype



Note:

This class is a placeholder for specifying a locus on the genome, i.e., a position of a particulargiven sequence in the subject’s genome.Note that the semantics of the locus (e.g., gene) is defined by data assigned in the code & valueattributes of this class, and also by placing additional data relating to this locus into the classes(and CMETs) associated with this class.

Note:The term 'Individual Allele' doesn't refer necessarily to aknown variant of the gene/locus, rather it refers to theindividual patient data regarding the gene/locus, and mightcontain personal variations with unknown significance atthe effective time of this observation.

AssociatedObservationclassCode*: <= GENmoodCode*: <=x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: SET<II> [0..*]code*: CD CWE [1..1]text: ED [0..1]effectiveTime*: GTS [1..1]value: ANY [0..1]methodCode: SET<CE> CWE [0..*]

Note:The code attribute could hold codes like TYPE,POSITION.GENOME, LENGTH, REFERENCE, REGION, etc..The value attribute is populated based on the selected codeand its data type is then setup accordingly during instancecreation. Here are a few examples:If code = TYPE, then the value is of type CV and holds one of thefollowing: SNP (tagSNP), INSERTION, DELETION,TRANSLOCATION, etc.

if code = POSITION, then value is of type INT and holdsthe actual numeric value representing the variation positionalong the gene.

if code = LENGTH, then value is of type INT and holdsthe actual numeric value representing the variation length.

If code = POSITION.GENE, then value is of type CV and is oneof the following codes:INTRON, EXON, UTR, PROMOTER, etc.

If code = POSITION.GENOME, then value is of type CV and is oneof the following codes:NORMAL_LOCUS, ECTOPIC, TRANSLOCATION, etc.

If the code = REFERENCE, then value istype CD and holds the reference gene identifier drawn from areference database like GenBank.

More details about vocabularies for codes and itsrespective values could be found in the specification.

Note:Code: CLASSIFICATION, etc.For example, if code =CLASSIFICATION, then the valueis of type CV and is holding eitherKNOWN or NOVEL.

reference

0..* geneticLocus


Note:A related locus that has significantinterrelation with the source locusand is not part of this loci set representedin this instance.

reference



Constrained to a restricted BSMLcontent model, specified in aseparate schema.

Constraint: Sequence.value

0..* sequence


component4



component3

AssociatedPropertyclassCode*: <= GENmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)code*: CD CWE [1..1]text: ED [0..1]value: ANY [0..1]



derivedFrom



derivedFrom



derivedFrom1



sourceOf



derivedFrom3derivedFrom2

0..* sequence


Note:Any observation related to the variation and is notan inherent part of the variation observation (the lattershould be represented in the AssociatedProperty class).For example, the zygosity of the variation.

Note:Any observation related to the sequence and is notan inherent part of the sequence observation, e.g.,splicing alternatives.Note that inherent characteristics of the sequenceshould be represented in the AssociatedProperty class.

Note:There could be zero to manyIndividualAllele objects in aspecific instance. A typicalcase would be an allele pair,one on the paternalchromosome and one on thematernal chromosome.

Note:Use this class forinherent dataabout the locus, e.g.chromosome no.

0..* phenotype

typeCode*: <= PERTpertinentInformation

AssociatedProperty

AssociatedProperty

AssociatedProperty

SequenceVariation

Sequence

SequenceVariation

Note:An internal CMET used to representclinical phenotypes, both observed inthe patient and known in thescientific literature.











Holds the variation expressed with arecognized notation like 269T>C ora markup like BSML or drawn from anexternal reference like OMIM or dbSNP.Data type should be set accordingly.

Constraint: value

If code = "Gene", value data type shall be set to CD and containa code identifying a gene through GenBank GeneID, HUGO name,OMIM ID or any other internationally recognized identification of genes.If the locus is not a gene then the data type should be set to theappropriate type, e.g., ST for locus notation like “10q24.32”.

Constraint: value

GeneticLociclassCode*: <= LOCmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: SET<II> [0..*]code*: CD CWE [1..1] <= GeneticVariationnegationInd: BL [0..1]title: ED [0..1]text: ED [0..1]statusCode*: CS CNE [1..1] <= ActStatuseffectiveTime*: GTS [1..1]confidentialityCode: SET<CE> CWE [1..1] <= ConfidentialityreasonCode: SET<CE> CWE [0..*]interpretationCode: SET<CE> CWE [0..*] <= GeneticObservationInterpretationmethodCode: SET<CE> CWE [0..*] <= ObservationMethod

0..* geneticLocus


0..* assignedEntity

typeCode*: <= AUTcontextControlCode: CS CNE [0..1] "OP"

author

0..* assignedEntity

typeCode*: <= VRFcontextControlCode: CS CNE [0..1] "OP"

verifier

0..* assignedEntity

typeCode*: <= PRFcontextControlCode: CS CNE [0..1] "OP"

performer

CMET: (ASSIGNED) R_AssignedEntity

[universal](COCT_MT090000UV)

0..1 roleName

GeneticDocumentclassCode*: <= DOCmoodCode*: <= x_ActMoodDefEvnRqoPrmsPrp (default=EVN)id: SET<II> [0..1]code*: CD CWE [1..1] <= DocumentTypetitle: ED [0..1]text: ED [0..1]statusCode*: CS CNE [1..1] <= ActStatuseffectiveTime*: GTS [1..1]confidentialityCode: SET<CE> CWE [0..*] <= ConfidentialitysetId: II [0..1]


typeCode*: <= DOCcontextConductionInd: BL [0..1] "TRUE"

documentation

relatedDocument


typeCode*: <= x_ActRelationshipDocumentcontextConductionInd: BL [0..1] "TRUE"seperatableInd: BL [0..1]

Note:Use the separation indicator to indicatewhen a document should not be separatedfrom its associated document (like in theEGFR-KRAS2 use case from HPCGG)

Note:There are two ways to refer to a clinical document: 1. Populate the id attribute with the document id 2. Place the entire CDA instance within the text attribute

The other attributes in this class are essential data aboutthe document and they are repeated in the documentinstance itself. It’s meant to ease the parsing process.



sourceOf



0..* phenotype



GeneticVariation(POCG_RM000011UV)

The entry point to the combinedGenetic Loci/Locus model thatrepresent genetic variations data.

0..1 identifiedEntity

typeCode*: <= SBJcontextControlCode: CS CNE [0..1] "OP"

subjectIdentifiedEntityclassCode*: <= IDENTid: SET<II> [0..*]code: CE CWE [0..1] <= RoleCode

ScopingEntityclassCode*: <= LIVdeterminerCode*: <= INSTANCEid: SET<II> [0..*]code: CE CWE [0..1] <= EntityCode

0..1

performer





0..*

author

0..1

performer 0..1

performer

0..1

performer

0..1

performer

If interpretationCode is assigned with a valuea reasonCode shall be assigned a value to setthe context for the interpretation semantics.

Constraint: GeneticLoci.reasonCode&interpretationCode

AssociatedProperty


typeCode*: <= DRIVderivedFrom

OBXOBX

OBR

OBXOBXOBX

OBR

OBXOBXOBX

OBR

OBXOBXOBX

Genetic LociGenetic LocusIndividual AlleleSequence Variation

PID

Subject

OBR

OBXOBXOBX

Associated data

User-defin

ed

preferences

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Haifa Research Lab

GeneticVariation in V2 (with V3 similarities)

e.g., GeneticLoci.interpretationCode

V3 GeneticLoci overall ‘summary’

V3 GeneticLocus & SequenceVariatione.g.,

GeneticLocus.value

8

Haifa Research Lab

What Should the V3V2 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

HL7 Clinical Genomics – Implementation Roadmap The HL7 Clinical Genomics SIG Amnon Shabo (Shvo), PhD HL7 Clinical Genomics SIG Co-chair and Modeling Facilitator.

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