Connectathon 11 Snapshot

This page is part of the FHIR Specification (v1.2.0: STU 3 Draft). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

4.28.13.4 StructureDefinition: ObservationForGenetics

The official URL for this profile is: 

http://hl7.org/fhir/StructureDefinition/observationforgenetics

Describes how the observation resource is used to report structured genetic test results

This profile was published on Wed, Mar 18, 2015 00:00+1100 as a draft by Health Level Seven International (Clinical Genomics).

4.28.13.4.1 Formal Views of Profile Content

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

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Observation
... observation-geneticsSequence 0..1Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsSource 0..1CodeableConceptGenomic source class means category of source of tissue sample used to determine the sequence: Germline / Somatic / Prenatal / Likely Germline / Likely Somatic / Likely Prenatal / Unknown Genomic Origin
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSource
... observation-geneticsVariationHGVS 0..*(Complex)Amino acid / cDNA /RNA variant following HGVS nomenclature
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationHGVS
... observation-geneticsVariationType 0..1CodeableConceptType of variation expressed using Sequence Ontology or LOINC answer list: Wild type / Deletion / Duplication / Insertion / Insertion or Deletion / Inversion / Substitution
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationType
... observation-geneticsGene 0..1CodeableConceptGene in which the sequence is found
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
... observation-geneticsRegion 0..1CodeableConceptDetails of exonic location of variant (e.g. Exon 1)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion
... observation-geneticsAminoAcidVariation 0..1(Complex)HGVS nomenclature for amino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*ObservationMeasurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: Component code SHALL not be same as observation code
... meta ∑0..1MetaMetadata about the resource
... implicitRules ?! ∑0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: IETF BCP-47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... observation-geneticsSequence 0..1Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsSource 0..1CodeableConceptGenomic source class means category of source of tissue sample used to determine the sequence: Germline / Somatic / Prenatal / Likely Germline / Likely Somatic / Likely Prenatal / Unknown Genomic Origin
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSource
... observation-geneticsVariationHGVS 0..*(Complex)Amino acid / cDNA /RNA variant following HGVS nomenclature
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationHGVS
... observation-geneticsVariationType 0..1CodeableConceptType of variation expressed using Sequence Ontology or LOINC answer list: Wild type / Deletion / Duplication / Insertion / Insertion or Deletion / Inversion / Substitution
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationType
... observation-geneticsGene 0..1CodeableConceptGene in which the sequence is found
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
... observation-geneticsRegion 0..1CodeableConceptDetails of exonic location of variant (e.g. Exon 1)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion
... observation-geneticsAminoAcidVariation 0..1(Complex)HGVS nomenclature for amino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier 0..*IdentifierUnique Id for this particular observation
... status ?! ∑1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category 0..1CodeableConceptClassification of type of observation
Binding: Observation Category Codes (example)
... code ∑1..1CodeableConceptType of observation (code / type)
Binding: LOINC Codes (example)
... subject ∑0..1Reference(Patient | Group | Device | Location)Who and/or what this is about
... encounter 0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ∑0..1dateTime, PeriodClinically relevant time/time-period for observation
... issued ∑0..1instantDate/Time this was made available
... performer ∑0..*Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ∑0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: Observation Value Absent Reason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comments 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 | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: Observation Reference Range Meaning Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related ∑0..*BackboneElementResource related to this observation
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1Reference(Observation | QuestionnaireResponse)Resource that is related to this one
... component ∑0..*BackboneElementComponent results
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... code ∑ I1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] ∑0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: Observation Value Absent Reason (extensible)
.... referenceRange 0..*See Observation.referenceRangeProvides guide for interpretation of component result

doco Documentation for this format

todo

Differential View

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Observation
... observation-geneticsSequence 0..1Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsSource 0..1CodeableConceptGenomic source class means category of source of tissue sample used to determine the sequence: Germline / Somatic / Prenatal / Likely Germline / Likely Somatic / Likely Prenatal / Unknown Genomic Origin
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSource
... observation-geneticsVariationHGVS 0..*(Complex)Amino acid / cDNA /RNA variant following HGVS nomenclature
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationHGVS
... observation-geneticsVariationType 0..1CodeableConceptType of variation expressed using Sequence Ontology or LOINC answer list: Wild type / Deletion / Duplication / Insertion / Insertion or Deletion / Inversion / Substitution
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationType
... observation-geneticsGene 0..1CodeableConceptGene in which the sequence is found
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
... observation-geneticsRegion 0..1CodeableConceptDetails of exonic location of variant (e.g. Exon 1)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion
... observation-geneticsAminoAcidVariation 0..1(Complex)HGVS nomenclature for amino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*ObservationMeasurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: Component code SHALL not be same as observation code
... meta ∑0..1MetaMetadata about the resource
... implicitRules ?! ∑0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: IETF BCP-47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... observation-geneticsSequence 0..1Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsSource 0..1CodeableConceptGenomic source class means category of source of tissue sample used to determine the sequence: Germline / Somatic / Prenatal / Likely Germline / Likely Somatic / Likely Prenatal / Unknown Genomic Origin
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSource
... observation-geneticsVariationHGVS 0..*(Complex)Amino acid / cDNA /RNA variant following HGVS nomenclature
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationHGVS
... observation-geneticsVariationType 0..1CodeableConceptType of variation expressed using Sequence Ontology or LOINC answer list: Wild type / Deletion / Duplication / Insertion / Insertion or Deletion / Inversion / Substitution
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariationType
... observation-geneticsGene 0..1CodeableConceptGene in which the sequence is found
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
... observation-geneticsRegion 0..1CodeableConceptDetails of exonic location of variant (e.g. Exon 1)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsRegion
... observation-geneticsAminoAcidVariation 0..1(Complex)HGVS nomenclature for amino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidVariation
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier 0..*IdentifierUnique Id for this particular observation
... status ?! ∑1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category 0..1CodeableConceptClassification of type of observation
Binding: Observation Category Codes (example)
... code ∑1..1CodeableConceptType of observation (code / type)
Binding: LOINC Codes (example)
... subject ∑0..1Reference(Patient | Group | Device | Location)Who and/or what this is about
... encounter 0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ∑0..1dateTime, PeriodClinically relevant time/time-period for observation
... issued ∑0..1instantDate/Time this was made available
... performer ∑0..*Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ∑0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: Observation Value Absent Reason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comments 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 | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: Observation Reference Range Meaning Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related ∑0..*BackboneElementResource related to this observation
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1Reference(Observation | QuestionnaireResponse)Resource that is related to this one
... component ∑0..*BackboneElementComponent results
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... code ∑ I1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] ∑0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: Observation Value Absent Reason (extensible)
.... referenceRange 0..*See Observation.referenceRangeProvides guide for interpretation of component result

doco Documentation for this format

XML Template

JSON Template

todo

 

Other representations of profile: Schematron

4.28.13.4.2 Terminology Bindings

PathNameConformanceValueSet
Observation.language?extrequiredhttp://tools.ietf.org/html/bcp47
Observation.statusObservationStatusrequiredObservationStatus
Observation.categoryObservation Category CodesexampleObservation Category Codes
Observation.codeLOINC CodesexampleLOINC Codes
Observation.dataAbsentReasonObservation Value Absent ReasonextensibleObservation Value Absent Reason
Observation.interpretationObservation Interpretation CodesextensibleObservation Interpretation Codes
Observation.bodySiteSNOMED CT Body StructuresexampleSNOMED CT Body Structures
Observation.methodObservation MethodsexampleObservation Methods
Observation.referenceRange.meaningObservation Reference Range Meaning CodesexampleObservation Reference Range Meaning Codes
Observation.related.typeObservationRelationshipTyperequiredObservationRelationshipType
Observation.component.codeLOINC CodesexampleLOINC Codes
Observation.component.dataAbsentReasonObservation Value Absent ReasonextensibleObservation Value Absent Reason

4.28.13.4.3 Constraints

IdPathDetailsRequirements
obs-6ObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
XPath: not(exists(f:dataAbsentReason)) or (not(exists(*[starts-with(local-name(.), 'value')])))
obs-7ObservationComponent code SHALL not be same as observation code
XPath: not(exists(f:component/f:code)) or count(for $coding in f:code/f:coding return parent::*/f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value and f:system/@value=$coding/f:system/@value])=0
obs-3Observation.referenceRangeMust have at least a low or a high or text
XPath: (exists(f:low) or exists(f:high)or exists(f:text))
.