This page is part of the Genetic Reporting Implementation Guide (v0.1.0: STU 1 Ballot 1) based on FHIR v3.3.0. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

2.6 StructureDefinition: Genomics Panel

The official URL for this profile is: 

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-gen-panel

2.6.2 Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from Genetic Observation Common Properties

Summary

Mandatory: 3 elements
Must-Support: 20 elements
Prohibited: 1 element

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element Observation.hasMember is sliced based on the value of pattern:resolve().code

This structure is derived from Genetic Observation Common Properties

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Genomics Panel
... obs-recommendedAction S1..1Reference(Task | ServiceRequest | MedicationRequest)Recommended action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-recommendedAction
... code S1..1CodeableConceptGenetic Panel
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-panel"}]}
... value[x] 0..0
... hasMember Reference(Observation | QuestionnaireResponse | Sequence)Slice: Unordered, Open by pattern:resolve().code
... hasMember S0..*Reference(Genomics Panel)Genetic panel
... hasMember S0..1Reference(Genetic analysis overall interpretation)Assessment of overall results
... hasMember S0..1Reference(Deletion-duplication overall interpretation)Assessment of deletion/duplication results
... hasMember S0..1Reference(Chromosome analysis overall interpretation)Assessment of chromosomal abnormalities
... hasMember S0..*Reference(Inherited Disease Pathogenicity)Inherited Disease Pathology
... hasMember S0..*Reference(Somatic Diagnostic Impact)Somatic Diagnostic
... hasMember S0..*Reference(Somatic Prognostic Impact)Somatic Prognostic
... hasMember S0..*Reference(Somatic Predictive Impact)Somatic Predictive
... hasMember S0..*Reference(Genotype medication metabolism impact)Metabolism Impact
... hasMember S0..*Reference(Genotype medication efficacy impact)Efficacy Impact
... hasMember S0..*Reference(High Risk Allele)High-Risk Medication Impact
... hasMember S0..*Reference(Chromosome analysis G-banding panel)Chromosome G-Band results
... hasMember S0..*Reference(Chromosome Analysis FISH panel)Chromosome FISH-test results
... hasMember S0..*Reference(Cytogenic Notation)Cytogenic Notation
... hasMember S0..*Reference(Genotype)Genotype
... hasMember S0..*Reference(Haplotype)Haplotype
... hasMember S0..*Reference(Complex variation)Complex Variant
... hasMember S0..*Reference(Described Variant (Discrete or Structural))Described Variant

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Genomics Panel
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: Common Languages (extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... body-structure SI0..1Reference(BodyStructure)Extension
URL: http://hl7.org/fhir/StructureDefinition/body-structure
... obs-recommendedAction S1..1Reference(Task | ServiceRequest | MedicationRequest)Recommended action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-recommendedAction
.... id 0..1stringxml:id (or equivalent in JSON)
.... url 1..1uri"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-recommendedAction"
.... valueReference 0..1Reference(Task | ServiceRequest | MedicationRequest)Value of extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn SΣ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..*CodeableConceptClassification of type of observation
Binding: Observation Category Codes (preferred)

Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptGenetic Panel
Binding: LOINC Codes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-panel"}]}
... subject SΣ0..1Reference(Patient | Group | Location)Who and/or what this is about
... focus Σ0..1Reference(Resource)The "focal point" of the observation
... context 0..1Reference(Encounter | EpisodeOfCare)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, TimingAssessment of overall results
... issued SΣ0..1instantAssessment of deletion/duplication results
... performer SΣ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Genes, drugs and/or conditions tested with no findings
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comment 0..1stringComments about result
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMED CT Body Structures (example)
... method 0..1CodeableConceptHow it was done
Binding: Observation Methods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceComponent | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: Observation Reference Range Meaning Codes (extensible)
.... appliesTo 0..*CodeableConceptReference range population
Binding: Observation Reference Range Applies To Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember ΣReference(Observation | QuestionnaireResponse | Sequence)Related resource that belongs to the Observation group
Slice: Unordered, Open by pattern:resolve().code
... hasMember SΣ0..*Reference(Genomics Panel)Genetic panel
... hasMember SΣ0..1Reference(Genetic analysis overall interpretation)Assessment of overall results
... hasMember SΣ0..1Reference(Deletion-duplication overall interpretation)Assessment of deletion/duplication results
... hasMember SΣ0..1Reference(Chromosome analysis overall interpretation)Assessment of chromosomal abnormalities
... hasMember SΣ0..*Reference(Inherited Disease Pathogenicity)Inherited Disease Pathology
... hasMember SΣ0..*Reference(Somatic Diagnostic Impact)Somatic Diagnostic
... hasMember SΣ0..*Reference(Somatic Prognostic Impact)Somatic Prognostic
... hasMember SΣ0..*Reference(Somatic Predictive Impact)Somatic Predictive
... hasMember SΣ0..*Reference(Genotype medication metabolism impact)Metabolism Impact
... hasMember SΣ0..*Reference(Genotype medication efficacy impact)Efficacy Impact
... hasMember SΣ0..*Reference(High Risk Allele)High-Risk Medication Impact
... hasMember SΣ0..*Reference(Chromosome analysis G-banding panel)Chromosome G-Band results
... hasMember SΣ0..*Reference(Chromosome Analysis FISH panel)Chromosome FISH-test results
... hasMember SΣ0..*Reference(Cytogenic Notation)Cytogenic Notation
... hasMember SΣ0..*Reference(Genotype)Genotype
... hasMember SΣ0..*Reference(Haplotype)Haplotype
... hasMember SΣ0..*Reference(Complex variation)Complex Variant
... hasMember SΣ0..*Reference(Described Variant (Discrete or Structural))Described Variant
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | Sequence)Related measurements the observation is made from
... component ΣI0..*BackboneElementComponent results
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

This structure is derived from Genetic Observation Common Properties

Summary

Mandatory: 3 elements
Must-Support: 20 elements
Prohibited: 1 element

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element Observation.hasMember is sliced based on the value of pattern:resolve().code

Differential View

This structure is derived from Genetic Observation Common Properties

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Genomics Panel
... obs-recommendedAction S1..1Reference(Task | ServiceRequest | MedicationRequest)Recommended action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-recommendedAction
... code S1..1CodeableConceptGenetic Panel
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-panel"}]}
... value[x] 0..0
... hasMember Reference(Observation | QuestionnaireResponse | Sequence)Slice: Unordered, Open by pattern:resolve().code
... hasMember S0..*Reference(Genomics Panel)Genetic panel
... hasMember S0..1Reference(Genetic analysis overall interpretation)Assessment of overall results
... hasMember S0..1Reference(Deletion-duplication overall interpretation)Assessment of deletion/duplication results
... hasMember S0..1Reference(Chromosome analysis overall interpretation)Assessment of chromosomal abnormalities
... hasMember S0..*Reference(Inherited Disease Pathogenicity)Inherited Disease Pathology
... hasMember S0..*Reference(Somatic Diagnostic Impact)Somatic Diagnostic
... hasMember S0..*Reference(Somatic Prognostic Impact)Somatic Prognostic
... hasMember S0..*Reference(Somatic Predictive Impact)Somatic Predictive
... hasMember S0..*Reference(Genotype medication metabolism impact)Metabolism Impact
... hasMember S0..*Reference(Genotype medication efficacy impact)Efficacy Impact
... hasMember S0..*Reference(High Risk Allele)High-Risk Medication Impact
... hasMember S0..*Reference(Chromosome analysis G-banding panel)Chromosome G-Band results
... hasMember S0..*Reference(Chromosome Analysis FISH panel)Chromosome FISH-test results
... hasMember S0..*Reference(Cytogenic Notation)Cytogenic Notation
... hasMember S0..*Reference(Genotype)Genotype
... hasMember S0..*Reference(Haplotype)Haplotype
... hasMember S0..*Reference(Complex variation)Complex Variant
... hasMember S0..*Reference(Described Variant (Discrete or Structural))Described Variant

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Genomics Panel
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: Common Languages (extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... body-structure SI0..1Reference(BodyStructure)Extension
URL: http://hl7.org/fhir/StructureDefinition/body-structure
... obs-recommendedAction S1..1Reference(Task | ServiceRequest | MedicationRequest)Recommended action
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-recommendedAction
.... id 0..1stringxml:id (or equivalent in JSON)
.... url 1..1uri"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-recommendedAction"
.... valueReference 0..1Reference(Task | ServiceRequest | MedicationRequest)Value of extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn SΣ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..*CodeableConceptClassification of type of observation
Binding: Observation Category Codes (preferred)

Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptGenetic Panel
Binding: LOINC Codes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-panel"}]}
... subject SΣ0..1Reference(Patient | Group | Location)Who and/or what this is about
... focus Σ0..1Reference(Resource)The "focal point" of the observation
... context 0..1Reference(Encounter | EpisodeOfCare)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, TimingAssessment of overall results
... issued SΣ0..1instantAssessment of deletion/duplication results
... performer SΣ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Genes, drugs and/or conditions tested with no findings
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comment 0..1stringComments about result
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMED CT Body Structures (example)
... method 0..1CodeableConceptHow it was done
Binding: Observation Methods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceComponent | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: Observation Reference Range Meaning Codes (extensible)
.... appliesTo 0..*CodeableConceptReference range population
Binding: Observation Reference Range Applies To Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember ΣReference(Observation | QuestionnaireResponse | Sequence)Related resource that belongs to the Observation group
Slice: Unordered, Open by pattern:resolve().code
... hasMember SΣ0..*Reference(Genomics Panel)Genetic panel
... hasMember SΣ0..1Reference(Genetic analysis overall interpretation)Assessment of overall results
... hasMember SΣ0..1Reference(Deletion-duplication overall interpretation)Assessment of deletion/duplication results
... hasMember SΣ0..1Reference(Chromosome analysis overall interpretation)Assessment of chromosomal abnormalities
... hasMember SΣ0..*Reference(Inherited Disease Pathogenicity)Inherited Disease Pathology
... hasMember SΣ0..*Reference(Somatic Diagnostic Impact)Somatic Diagnostic
... hasMember SΣ0..*Reference(Somatic Prognostic Impact)Somatic Prognostic
... hasMember SΣ0..*Reference(Somatic Predictive Impact)Somatic Predictive
... hasMember SΣ0..*Reference(Genotype medication metabolism impact)Metabolism Impact
... hasMember SΣ0..*Reference(Genotype medication efficacy impact)Efficacy Impact
... hasMember SΣ0..*Reference(High Risk Allele)High-Risk Medication Impact
... hasMember SΣ0..*Reference(Chromosome analysis G-banding panel)Chromosome G-Band results
... hasMember SΣ0..*Reference(Chromosome Analysis FISH panel)Chromosome FISH-test results
... hasMember SΣ0..*Reference(Cytogenic Notation)Cytogenic Notation
... hasMember SΣ0..*Reference(Genotype)Genotype
... hasMember SΣ0..*Reference(Haplotype)Haplotype
... hasMember SΣ0..*Reference(Complex variation)Complex Variant
... hasMember SΣ0..*Reference(Described Variant (Discrete or Structural))Described Variant
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | Sequence)Related measurements the observation is made from
... component ΣI0..*BackboneElementComponent results
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

 

Other representations of profile: Schematron

2.6.3 Terminology Bindings

Terminology Bindings

PathNameConformanceValueSet
Observation.languageCommon LanguagesextensibleCommon Languages
Observation.statusObservationStatusrequiredObservationStatus
Observation.categoryObservation Category CodespreferredObservation Category Codes
Observation.codeLOINC CodesexampleLOINC Codes
Observation.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.interpretationObservation Interpretation CodesextensibleObservation Interpretation Codes
Observation.bodySiteSNOMED CT Body StructuresexampleSNOMED CT Body Structures
Observation.methodObservation MethodsexampleObservation Methods
Observation.referenceRange.typeObservation Reference Range Meaning CodesextensibleObservation Reference Range Meaning Codes
Observation.referenceRange.appliesToObservation Reference Range Applies To CodesexampleObservation Reference Range Applies To Codes
Observation.component.codeLOINC CodesexampleLOINC Codes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationObservation Interpretation CodesextensibleObservation Interpretation Codes

2.6.4 Constraints

Constraints

IdPathDetailsRequirements
dom-2ObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-1ObservationIf the resource is contained in another resource, it SHALL NOT contain any narrative
: contained.text.empty()
dom-4ObservationIf a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-3ObservationIf the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource
: contained.all(('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists())
obs-7ObservationIf Observation.code is the same as a Observation.component.code then the value element associated with the code SHALL NOT be present
: value.empty() or component.code.where( (coding.code = %resource.code.coding.code) and (coding.system = %resource.code.coding.system)).empty()
obs-6ObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
ele-1Observation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())
obs-3Observation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())