This page is part of the Genetic Reporting Implementation Guide (v0.3.0: STU 1 Ballot 2) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

StructureDefinition: Described Variant

The official URL for this profile is: 

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-described-variant

Described Variant is a new term that HL7 has assigned to the notion of Simple, Discrete and Structural variants. We have done this because of the difficulty of drawing a clear line between these other labels for variants. The rules are often driven by the registries to which the variants are submitted and are not necessarily consistent. The difference may be driven by testing methodology rather than a difference in the underlying genetic characteristic.

This profile allows a full description of the variant found using properties from a variety of testing approaches and allowing for a variety of descriptive mechanisms. Labs are encouraged to populate what properties they know. In future versions of this implementation guide, HL7 may provide additional guidance on what properties should be sent in which situations and may subdivide Described Variant into multiple sub-profiles with more specific purpose.

Formal Views of Profile Content

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

This structure is derived from Computable Genetic Finding

Summary

Mandatory: 2 elements (51 nested mandatory elements)
Must-Support: 75 elements
Fixed Value: 2 elements

Slices

This structure defines the following Slices:

  • The element Observation.component is sliced based on the value of pattern:code

This structure is derived from Computable Genetic Finding

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Described Variant
... code S1..1CodeableConceptGenetic variant assessment
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]}
... valueCodeableConcept S1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required)
... method S0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (required)
... component BackboneElementSlice: Unordered, Open by pattern:code
... component S0..1BackboneElementDNA Change - Transcript (cHGVS)
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: HGVS (required)
... component S0..1BackboneElementDNA change type
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]}
.... valueCodeableConcept S1..1CodeableConceptWild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Translocation | Substitution | Copy number loss | Copy number variation | Copy number gain +
... component S0..1BackboneElementVariation Code
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementdbSNP ID
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementDNA Change - Genomic (gHGVS)
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: HGVS (required)
... component S0..1BackboneElementGenomic source class
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]}
.... valueCodeableConcept S1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (required)
... component S0..1BackboneElementAmino acid change (pHGVS)
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: HGVS (required)
... component S0..1BackboneElementAmino acid change type
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]}
.... valueCodeableConcept S1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required)
... component S0..1BackboneElementTranscript reference sequence ID
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementGenomic reference sequence ID
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementAllelic Frequency
.... code S1..1CodeableConceptAllelic frequency [NFr]
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]}
.... valueQuantity S1..1Quantity
..... value S1..1decimal
..... system S1..1uriFixed Value: http://unitsofmeasure.org
..... code S1..1codeFixed Value: %
... component S0..*BackboneElementAllelic read depth
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]}
.... valueQuantity S1..1Count
... component S0..1BackboneElementAllelic state
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]}
.... valueCodeableConcept S1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (required)
... component S0..1BackboneElementGenomic structural variant copy number
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]}
.... valueQuantity S1..1Count
... component S0..1BackboneElementGenomic ref allele
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]}
.... valueString S1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
... component S0..1BackboneElementGenomic alt allele
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]}
.... valueString S1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
... component S0..1BackboneElementCoordinate System
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]}
.... valueCodeableConcept S1..1CodeableConceptInterval | Variant method | Alignment method
Binding: GeneticCoordinateSystem (extensible)
... component S0..1BackboneElementGenomic Allele start-end
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]}
.... valueRange S1..1Range
..... low S1..1SimpleQuantityGenomic Allele start
..... high S1..1SimpleQuantityGenomic Allele end
... component S0..1BackboneElementStructural variant length
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]}
.... valueQuantity S1..1Count
... component S0..1BackboneElementStructural variant outer start and end
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]}
.... valueRange S1..1Range
..... low S1..1SimpleQuantity
..... high S1..1SimpleQuantity
... component S0..1BackboneElementStructural variant inner start and end
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]}
.... valueRange S1..1Range
..... low S1..1SimpleQuantity
..... high S1..1SimpleQuantity

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Described Variant
... 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: CommonLanguages (preferred)
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
... 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: ObservationCategoryCodes (preferred)

Required Pattern: {"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]}
... subject SΣ0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
... issued SΣ0..1instantDate/Time this version was made available
... performer SΣ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... valueCodeableConcept SΣI1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... note 0..*AnnotationComments about the observation
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method S0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (required)
... specimen S1..1Reference(Specimen)Specimen examined
... device 0..*Reference(Device FISH Probe | Device Microarray Platform | Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component ΣIBackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (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)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementGene studied ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48018-6"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementCytogenetic (chromosome) location
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48001-2"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementHuman reference sequence assembly version
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"62374-4"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (preferred)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementDNA Change - Transcript (cHGVS)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: HGVS (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementDNA change type
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptWild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Translocation | Substitution | Copy number loss | Copy number variation | Copy number gain +
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementVariation Code
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementdbSNP ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementDNA Change - Genomic (gHGVS)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: HGVS (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic source class
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAmino acid change (pHGVS)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: HGVS (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAmino acid change type
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementTranscript reference sequence ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic reference sequence ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAllelic Frequency
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptAllelic frequency [NFr]
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]}
.... value[x] SΣ1..1QuantityActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... value SΣ1..1decimalNumerical value (with implicit precision)
..... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required)
..... unit Σ0..1stringUnit representation
..... system SΣI1..1uriSystem that defines coded unit form
Fixed Value: http://unitsofmeasure.org
..... code SΣ1..1codeCoded form of the unit
Fixed Value: %
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementAllelic read depth
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]}
.... valueQuantity SI1..1CountA measured or measurable amount
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAllelic state
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic structural variant copy number
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]}
.... valueQuantity SI1..1CountA measured or measurable amount
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic ref allele
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]}
.... value[x] SΣ1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic alt allele
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]}
.... value[x] SΣ1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementCoordinate System
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptInterval | Variant method | Alignment method
Binding: GeneticCoordinateSystem (extensible)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic Allele start-end
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]}
.... value[x] SΣ1..1RangeActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... low SΣ1..1SimpleQuantityGenomic Allele start
..... high SΣ1..1SimpleQuantityGenomic Allele end
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementStructural variant length
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]}
.... valueQuantity SI1..1CountA measured or measurable amount
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementStructural variant outer start and end
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]}
.... value[x] SΣ1..1RangeActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... low SΣ1..1SimpleQuantityLow limit
..... high SΣ1..1SimpleQuantityHigh limit
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementStructural variant inner start and end
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]}
.... value[x] SΣ1..1RangeActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... low SΣ1..1SimpleQuantityLow limit
..... high SΣ1..1SimpleQuantityHigh limit
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (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 Computable Genetic Finding

Summary

Mandatory: 2 elements (51 nested mandatory elements)
Must-Support: 75 elements
Fixed Value: 2 elements

Slices

This structure defines the following Slices:

  • The element Observation.component is sliced based on the value of pattern:code

Differential View

This structure is derived from Computable Genetic Finding

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Described Variant
... code S1..1CodeableConceptGenetic variant assessment
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]}
... valueCodeableConcept S1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required)
... method S0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (required)
... component BackboneElementSlice: Unordered, Open by pattern:code
... component S0..1BackboneElementDNA Change - Transcript (cHGVS)
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: HGVS (required)
... component S0..1BackboneElementDNA change type
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]}
.... valueCodeableConcept S1..1CodeableConceptWild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Translocation | Substitution | Copy number loss | Copy number variation | Copy number gain +
... component S0..1BackboneElementVariation Code
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementdbSNP ID
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementDNA Change - Genomic (gHGVS)
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: HGVS (required)
... component S0..1BackboneElementGenomic source class
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]}
.... valueCodeableConcept S1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (required)
... component S0..1BackboneElementAmino acid change (pHGVS)
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: HGVS (required)
... component S0..1BackboneElementAmino acid change type
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]}
.... valueCodeableConcept S1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required)
... component S0..1BackboneElementTranscript reference sequence ID
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementGenomic reference sequence ID
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]}
.... valueCodeableConcept S1..1CodeableConceptBinding: (unbound) (example)
... component S0..1BackboneElementAllelic Frequency
.... code S1..1CodeableConceptAllelic frequency [NFr]
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]}
.... valueQuantity S1..1Quantity
..... value S1..1decimal
..... system S1..1uriFixed Value: http://unitsofmeasure.org
..... code S1..1codeFixed Value: %
... component S0..*BackboneElementAllelic read depth
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]}
.... valueQuantity S1..1Count
... component S0..1BackboneElementAllelic state
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]}
.... valueCodeableConcept S1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (required)
... component S0..1BackboneElementGenomic structural variant copy number
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]}
.... valueQuantity S1..1Count
... component S0..1BackboneElementGenomic ref allele
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]}
.... valueString S1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
... component S0..1BackboneElementGenomic alt allele
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]}
.... valueString S1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
... component S0..1BackboneElementCoordinate System
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]}
.... valueCodeableConcept S1..1CodeableConceptInterval | Variant method | Alignment method
Binding: GeneticCoordinateSystem (extensible)
... component S0..1BackboneElementGenomic Allele start-end
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]}
.... valueRange S1..1Range
..... low S1..1SimpleQuantityGenomic Allele start
..... high S1..1SimpleQuantityGenomic Allele end
... component S0..1BackboneElementStructural variant length
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]}
.... valueQuantity S1..1Count
... component S0..1BackboneElementStructural variant outer start and end
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]}
.... valueRange S1..1Range
..... low S1..1SimpleQuantity
..... high S1..1SimpleQuantity
... component S0..1BackboneElementStructural variant inner start and end
.... code S1..1CodeableConceptRequired Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]}
.... valueRange S1..1Range
..... low S1..1SimpleQuantity
..... high S1..1SimpleQuantity

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Described Variant
... 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: CommonLanguages (preferred)
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
... 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: ObservationCategoryCodes (preferred)

Required Pattern: {"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptGenetic variant assessment
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD-Described"}]}
... subject SΣ0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
... issued SΣ0..1instantDate/Time this version was made available
... performer SΣ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... valueCodeableConcept SΣI1..1CodeableConceptPresent|Absent|No call|Indeterminate
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... note 0..*AnnotationComments about the observation
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method S0..1CodeableConceptSequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
Binding: LOINC Answer List LL4048-6 (required)
... specimen S1..1Reference(Specimen)Specimen examined
... device 0..*Reference(Device FISH Probe | Device Microarray Platform | Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... component ΣIBackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (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)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementGene studied ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48018-6"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNC (extensible)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementCytogenetic (chromosome) location
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48001-2"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementHuman reference sequence assembly version
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"62374-4"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: LOINC Answer List LL1040-6 (preferred)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementDNA Change - Transcript (cHGVS)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48004-6"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: HGVS (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementDNA change type
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48019-4"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptWild type | Deletion | Duplication | Insertion | Insertion/Deletion | Inversion | Translocation | Substitution | Copy number loss | Copy number variation | Copy number gain +
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementVariation Code
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81252-9"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementdbSNP ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81255-2"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementDNA Change - Genomic (gHGVS)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81290-9"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: HGVS (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic source class
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48002-0"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAmino acid change (pHGVS)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48005-3"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: HGVS (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAmino acid change type
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48006-1"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
Binding: LOINC Answer List LL380-7 (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementTranscript reference sequence ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51958-7"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic reference sequence ID
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"48013-7"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAllelic Frequency
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptAllelic frequency [NFr]
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81258-6"}]}
.... value[x] SΣ1..1QuantityActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... value SΣ1..1decimalNumerical value (with implicit precision)
..... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required)
..... unit Σ0..1stringUnit representation
..... system SΣI1..1uriSystem that defines coded unit form
Fixed Value: http://unitsofmeasure.org
..... code SΣ1..1codeCoded form of the unit
Fixed Value: %
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..*BackboneElementAllelic read depth
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82121-5"}]}
.... valueQuantity SI1..1CountA measured or measurable amount
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementAllelic state
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"53034-5"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (required)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic structural variant copy number
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"82155-3"}]}
.... valueQuantity SI1..1CountA measured or measurable amount
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic ref allele
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69547-8"}]}
.... value[x] SΣ1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic alt allele
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"69551-0"}]}
.... value[x] SΣ1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementCoordinate System
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"TBD"}]}
.... valueCodeableConcept SΣ1..1CodeableConceptInterval | Variant method | Alignment method
Binding: GeneticCoordinateSystem (extensible)
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementGenomic Allele start-end
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81254-5"}]}
.... value[x] SΣ1..1RangeActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... low SΣ1..1SimpleQuantityGenomic Allele start
..... high SΣ1..1SimpleQuantityGenomic Allele end
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementStructural variant length
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81300-6"}]}
.... valueQuantity SI1..1CountA measured or measurable amount
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementStructural variant outer start and end
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81301-4"}]}
.... value[x] SΣ1..1RangeActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... low SΣ1..1SimpleQuantityLow limit
..... high SΣ1..1SimpleQuantityHigh limit
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
... component SΣI0..1BackboneElementStructural variant inner start and end
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code SΣ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"81302-2"}]}
.... value[x] SΣ1..1RangeActual component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... low SΣ1..1SimpleQuantityLow limit
..... high SΣ1..1SimpleQuantityHigh limit
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (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

Terminology Bindings

PathNameConformanceValueSet
Observation.languageCommon LanguagespreferredCommonLanguages
Observation.statusObservationStatusrequiredObservationStatus
Observation.categoryObservation Category CodespreferredObservationCategoryCodes
Observation.codeLOINC CodesexampleLOINCCodes
Observation.valueCodeableConceptLOINC LL1971-2requiredLOINC LL1971-2
Observation.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.bodySiteSNOMED CT Body StructuresexampleSNOMEDCTBodyStructures
Observation.methodLOINC LL4048-6requiredLOINC LL4048-6
Observation.referenceRange.typeObservation Reference Range Meaning CodespreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToObservation Reference Range Applies To CodesexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.value[x].comparatorQuantityComparatorrequiredQuantityComparator
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.valueCodeableConceptGeneticCoordinateSystemextensibleGeneticCoordinateSystem
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.codeLOINC CodesexampleLOINCCodes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason

Constraints

IdPathDetailsRequirements
dom-2ObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.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.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-6ObservationA resource should have narrative for robust management
: text.div.exists()
dom-5ObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
obs-7ObservationIf Observation.code is the same as an 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.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (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() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
qty-3Observation.component.valueQuantityIf a code for the unit is present, the system SHALL also be present
: code.empty() or system.exists()
cnt-3Observation.component.valueQuantityThere SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.
: (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
qty-3Observation.component.valueQuantityIf a code for the unit is present, the system SHALL also be present
: code.empty() or system.exists()
cnt-3Observation.component.valueQuantityThere SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.
: (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
qty-3Observation.component.valueQuantityIf a code for the unit is present, the system SHALL also be present
: code.empty() or system.exists()
cnt-3Observation.component.valueQuantityThere SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.
: (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())

The Described Variant has a large number of properties. However these properties fall into groups, where each group of properties has a purpose (and in some cases represents information that typically appears together). The groups of properties are described below:

Variant Location properties

These are properties that help to describe where a particular variation occurs. Considering the reference sequence genomic-ref-seq:48013-7 and coordinate system coordinate-system:TBD, the component allele-start-end:81254-5 can denote the first and last genomic positions in the reference that correspond to changes. If the observation points to a MolecularSequence resource as a reference sequence, then that resource will carry this information under variant.start and variant.end.

Additionally, if the exact start and end positions are unknown, outer-start-end:81301-4 and inner-start-end:81302-2 can be used to deliver the boundaries of where the variant begins and ends.

Variant Change Components

The components dna-chg:48004-6 and dna-chg-type:48019-4 are used to deliver the Human Genome Variation Society (HGVS) nomenclature for the observed DNA marker and codify the type of change observed. If the described variant is structural, genomic-dna-chg:81290-9 is used instead of dna-chg:48004-6. If a simple variant is observed, the component variation-code:81252-9 is used to report the variant's unique identifier. Alternatively, dbSNP-id:81255-2 can be used to represent the change, and/or the components ref-allele:69547-8 and alt-allele:69551-0 can directly relay the variation from the observed sequence.

Lastly, genomic-source-class:48002-0 can describe the genomic class of the specimen being analyzed, whether it is from inherited genome, cancer genome, or fetal genome.

Allelic State Components

The components allelic-frequency:81258-6, allelic-read-depth:82121-5, and allelic-state:53034-5 indicate infomartion about a particular allele. Namely, they communicate the relative frequency of the allele in the population, the number of reads that identified it, and the observed level of occurence within a set of chromosomes, respectively.

Amino Acid Change Components

The components amino-acid-chg:48005-3 and amino-acid-chg-type:48006-1 are used when communicating a variant in an amino acid sequence. Human Genome Variation Society (HGVS) nomenclature is used.

Genomic Location Components

The components gene-studied:48018-6 and cytogenetic-location:48001-2 are used to describe the cytogenetic chromosome location and the HUGO Gene Nomenclature Committee (HGNC) identifier for a gene studied.