Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Variant

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant Version: 4.0.0-cibuild
Standards status: Trial-use Maturity Level: 2 Computable Name: Variant

Copyright/Legal: This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.

Details about a set of changes in the tested sample compared to a reference sequence.

Scope and Usage

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 Variant into multiple sub-profiles with more specific purpose.

Other Guidance

See Variant Reporting for details on use.

A variety of annotations (see variant implications) can be applied to identified variants, such as: (1) predicted molecular consequences (e.g. a prediction that a variant leads to loss of gene function); (2) diagnostic implications (e.g. presence of a variant indicates increased risk for breast cancer); (3) therapeutic implications (e.g. presence of a somatic variant is associated with sensitivity to a particular drug or eligibility into a clinical trial).

Most human genes are transcribed into multiple transcripts. The molecular consequences profile can be used to indicate transcript-specific predicted consequences, for one or more transcripts. In the Variant instance itself, one can also indicate a representative transcript-level HGVS and/or protein HGVS.

If implementers have additional variant annotations, the Variant profile is defined to allow flexibility. See the section on flexibility for additional guidance, especially the guidance for the Open Slicing allowed on Observation.component.

Note on Molecular Consequence in STU2

The STU2 Variant profile contained the component slice molecular-consequence, which is no longer present in this profile. The functionality to communicate predicted molecular consequences has been moved to the Molecular Consequence profile. For those that have already implemented the STU2 solution and are in a transition, open slicing allows components above and beyond those specified in the Implementation Guide and therefore the STU2 method of communicating molecular consequence will not cause conformance errors. This approach should be used carefully and only during a transition period to ensure full compatibility with other systems that implement the full features of this guide.

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.Slices for extension Content/Rules for all slices
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary 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): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.code This element is included in summaries. 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69548-6"
    }
  ]
}
Observation.Slices for value[x] This element is included in summaries. C 0..1 Actual result
Slice: Unordered, Closed by type:$this
Slicing Note: Other type slices that contain no new information are not shown in this view
Observation.Slices for value[x].valueQuantity Quantity
Observation.Slices for value[x].valueCodeableConcept CodeableConcept
Observation.Slices for value[x].valueString string
Observation.Slices for value[x].valueBoolean boolean
Observation.Slices for value[x].valueInteger integer
Observation.Slices for value[x].valueRange Range
Observation.Slices for value[x].valueRatio Ratio
Observation.Slices for value[x].valueSampledData SampledData
Observation.Slices for value[x].valueTime time
Observation.Slices for value[x].valueDateTime dateTime
Observation.Slices for value[x].valuePeriod Period
Observation.Slices for value[x].value[x]:valueCodeableConcept This element is included in summaries. C 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
Observation.method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
Observation.Slices for component.component:representative-coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:representative-coding-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:representative-coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:genomic-hgvs This element is included in summaries. 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
Observation.Slices for component.component:genomic-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-hgvs.code This element is included in summaries. 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81290-9"
    }
  ]
}
Observation.Slices for component.component:genomic-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:cytogenomic-nomenclature This element is included in summaries. 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
Observation.Slices for component.component:cytogenomic-nomenclature.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenomic-nomenclature.code This element is included in summaries. 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81291-7"
    }
  ]
}
Observation.Slices for component.component:cytogenomic-nomenclature.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:genomic-ref-seq This element is included in summaries. 0..1 BackboneElement Genomic Reference Sequence
Observation.Slices for component.component:genomic-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48013-7"
    }
  ]
}
Observation.Slices for component.component:genomic-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:representative-protein-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:representative-protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:representative-transcript-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:representative-transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:exact-start-end This element is included in summaries. 0..1 BackboneElement Exact Start-End
Observation.Slices for component.component:exact-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:exact-start-end.code This element is included in summaries. 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81254-5"
    }
  ]
}
Observation.Slices for component.component:exact-start-end.value[x] This element is included in summaries. 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
Observation.Slices for component.component:inner-start-end This element is included in summaries. 0..1 BackboneElement Inner Start-End
Observation.Slices for component.component:inner-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:inner-start-end.code This element is included in summaries. 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81302-2"
    }
  ]
}
Observation.Slices for component.component:inner-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant inner-bounding range
Observation.Slices for component.component:outer-start-end This element is included in summaries. 0..1 BackboneElement Outer Start-End
Observation.Slices for component.component:outer-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:outer-start-end.code This element is included in summaries. 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81301-4"
    }
  ]
}
Observation.Slices for component.component:outer-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant outer-bounding range
Observation.Slices for component.component:coordinate-system This element is included in summaries. 0..1 BackboneElement Coordinate System
Observation.Slices for component.component:coordinate-system.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coordinate-system.code This element is included in summaries. 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92822-6"
    }
  ]
}
Observation.Slices for component.component:coordinate-system.value[x] This element is included in summaries. 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
Observation.Slices for component.component:ref-allele This element is included in summaries. 0..1 BackboneElement Genomic Ref Allele
Observation.Slices for component.component:ref-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:ref-allele.code This element is included in summaries. 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69547-8"
    }
  ]
}
Observation.Slices for component.component:ref-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:alt-allele This element is included in summaries. 0..1 BackboneElement Genomic Alt Allele
Observation.Slices for component.component:alt-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:alt-allele.code This element is included in summaries. 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69551-0"
    }
  ]
}
Observation.Slices for component.component:alt-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:coding-change-type This element is included in summaries. 0..1 BackboneElement Coding DNA Change Type
Observation.Slices for component.component:coding-change-type.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coding-change-type.code This element is included in summaries. 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48019-4"
    }
  ]
}
Observation.Slices for component.component:coding-change-type.value[x] This element is included in summaries. 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
Observation.Slices for component.component:genomic-source-class This element is included in summaries. 0..1 BackboneElement Genomic Source Class
Observation.Slices for component.component:genomic-source-class.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-source-class.code This element is included in summaries. 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48002-0"
    }
  ]
}
Observation.Slices for component.component:genomic-source-class.value[x] This element is included in summaries. 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
Observation.Slices for component.component:sample-allelic-frequency This element is included in summaries. 0..1 BackboneElement Sample Allelic Frequency
Observation.Slices for component.component:sample-allelic-frequency.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:sample-allelic-frequency.code This element is included in summaries. 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81258-6"
    }
  ]
}
Observation.Slices for component.component:sample-allelic-frequency.value[x] This element is included in summaries. 0..1 Quantity Relative frequency in the sample
Observation.Slices for component.component:sample-allelic-frequency.value[x].comparator This element is a modifier element. This element is included in summaries. 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
Observation.Slices for component.component:sample-allelic-frequency.value[x].system This element is included in summaries. C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org (extensions allowed)
Observation.Slices for component.component:allelic-read-depth This element is included in summaries. 0..1 BackboneElement Allelic Read Depth
Observation.Slices for component.component:allelic-read-depth.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-read-depth.code This element is included in summaries. 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82121-5"
    }
  ]
}
Observation.Slices for component.component:allelic-read-depth.value[x] This element is included in summaries. 0..1 Quantity Unfiltered count of supporting reads
Observation.Slices for component.component:allelic-state This element is included in summaries. 0..1 BackboneElement Allelic State
Observation.Slices for component.component:allelic-state.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-state.code This element is included in summaries. 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53034-5"
    }
  ]
}
Observation.Slices for component.component:allelic-state.value[x] This element is included in summaries. 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
Observation.Slices for component.component:variant-inheritance This element is included in summaries. 0..1 BackboneElement Origin of germline genetic variant
Observation.Slices for component.component:variant-inheritance.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance.code This element is included in summaries. 1..1 CodeableConcept 94186-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "94186-4"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance.value[x] This element is included in summaries. 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
Observation.Slices for component.component:variant-inheritance-basis This element is included in summaries. 0..1 BackboneElement Evidential basis for variant inheritance
Observation.Slices for component.component:variant-inheritance-basis.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance-basis.code This element is included in summaries. 1..1 CodeableConcept Basis for allelic phase
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82309-6"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance-basis.value[x] This element is included in summaries. 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
Observation.Slices for component.component:variation-code This element is included in summaries. 0..* BackboneElement Variation Code
Observation.Slices for component.component:variation-code.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variation-code.code This element is included in summaries. 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81252-9"
    }
  ]
}
Observation.Slices for component.component:variation-code.value[x] This element is included in summaries. 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
Observation.Slices for component.component:representative-protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:representative-protein-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:representative-protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:copy-number This element is included in summaries. 0..1 BackboneElement Genomic Structural Variant Copy Number
Observation.Slices for component.component:copy-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:copy-number.code This element is included in summaries. 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82155-3"
    }
  ]
}
Observation.Slices for component.component:copy-number.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:copy-number.value[x].valueQuantity Quantity
Observation.Slices for component.component:copy-number.value[x].valueRange Range
Observation.Slices for component.component:variant-confidence-status This element is included in summaries. 0..1 BackboneElement Variant Confidence Status
Observation.Slices for component.component:variant-confidence-status.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-confidence-status.code This element is included in summaries. 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "variant-confidence-status"
    }
  ]
}
Observation.Slices for component.component:variant-confidence-status.value[x] This element is included in summaries. 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
Observation.Slices for component.component:repeat-motif This element is included in summaries. 0..* BackboneElement Repeat Motif
Observation.Slices for component.component:repeat-motif.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-motif.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-motif.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-motif.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-motif.code This element is included in summaries. 1..1 CodeableConcept repeat-motif
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-motif"
    }
  ]
}
Observation.Slices for component.component:repeat-motif.value[x] This element is included in summaries. 1..1 string CAG
Observation.Slices for component.component:repeat-number This element is included in summaries. 0..* BackboneElement Repeat Number
Observation.Slices for component.component:repeat-number.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-number.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-number.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-number.code This element is included in summaries. 1..1 CodeableConcept repeat-number
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-number"
    }
  ]
}
Observation.Slices for component.component:repeat-number.value[x] This element is included in summaries. 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.method Base extensible LOINC Answer Codes for LL4048-6 ∅ unknown?
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-cibuild This IG
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-cibuild This IG
Observation.component:repeat-motif.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If 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-4 error Observation If 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-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If 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.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicFinding Variant
Observation.code 1..1 CodeableConcept 69548-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69548-6"
    }
  ]
}
Observation.Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual result
Slice: Unordered, Open by type:$this
Slicing Note: Other type slices that contain no new information are not shown in this view
Observation.Slices for value[x].value[x]:valueCodeableConcept 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
Observation.method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
Observation.Slices for component.component:representative-coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:representative-coding-hgvs.code 1..1 CodeableConcept 48004-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:representative-coding-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:genomic-hgvs 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
Observation.Slices for component.component:genomic-hgvs.code 1..1 CodeableConcept 81290-9
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81290-9"
    }
  ]
}
Observation.Slices for component.component:genomic-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:cytogenomic-nomenclature 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
Observation.Slices for component.component:cytogenomic-nomenclature.code 1..1 CodeableConcept 81291-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81291-7"
    }
  ]
}
Observation.Slices for component.component:cytogenomic-nomenclature.value[x] 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:genomic-ref-seq 0..1 BackboneElement Genomic Reference Sequence
Observation.Slices for component.component:genomic-ref-seq.code 1..1 CodeableConcept 48013-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48013-7"
    }
  ]
}
Observation.Slices for component.component:genomic-ref-seq.value[x] 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:representative-protein-ref-seq.code 1..1 CodeableConcept protein-ref-seq
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:representative-protein-ref-seq.value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-transcript-ref-seq 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:representative-transcript-ref-seq.code 1..1 CodeableConcept 51958-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:representative-transcript-ref-seq.value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:exact-start-end 0..1 BackboneElement Exact Start-End
Observation.Slices for component.component:exact-start-end.code 1..1 CodeableConcept 81254-5
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81254-5"
    }
  ]
}
Observation.Slices for component.component:exact-start-end.value[x] 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
Observation.Slices for component.component:inner-start-end 0..1 BackboneElement Inner Start-End
Observation.Slices for component.component:inner-start-end.code 1..1 CodeableConcept 81302-2
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81302-2"
    }
  ]
}
Observation.Slices for component.component:inner-start-end.value[x] 0..1 Range Imprecise variant inner-bounding range
Observation.Slices for component.component:outer-start-end 0..1 BackboneElement Outer Start-End
Observation.Slices for component.component:outer-start-end.code 1..1 CodeableConcept 81301-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81301-4"
    }
  ]
}
Observation.Slices for component.component:outer-start-end.value[x] 0..1 Range Imprecise variant outer-bounding range
Observation.Slices for component.component:coordinate-system 0..1 BackboneElement Coordinate System
Observation.Slices for component.component:coordinate-system.code 1..1 CodeableConcept 92822-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92822-6"
    }
  ]
}
Observation.Slices for component.component:coordinate-system.value[x] 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
Observation.Slices for component.component:ref-allele 0..1 BackboneElement Genomic Ref Allele
Observation.Slices for component.component:ref-allele.code 1..1 CodeableConcept 69547-8
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69547-8"
    }
  ]
}
Observation.Slices for component.component:ref-allele.value[x] 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:alt-allele 0..1 BackboneElement Genomic Alt Allele
Observation.Slices for component.component:alt-allele.code 1..1 CodeableConcept 69551-0
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69551-0"
    }
  ]
}
Observation.Slices for component.component:alt-allele.value[x] 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:coding-change-type 0..1 BackboneElement Coding DNA Change Type
Observation.Slices for component.component:coding-change-type.code 1..1 CodeableConcept 48019-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48019-4"
    }
  ]
}
Observation.Slices for component.component:coding-change-type.value[x] 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
Observation.Slices for component.component:genomic-source-class 0..1 BackboneElement Genomic Source Class
Observation.Slices for component.component:genomic-source-class.code 1..1 CodeableConcept 48002-0
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48002-0"
    }
  ]
}
Observation.Slices for component.component:genomic-source-class.value[x] 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
Observation.Slices for component.component:sample-allelic-frequency 0..1 BackboneElement Sample Allelic Frequency
Observation.Slices for component.component:sample-allelic-frequency.code 1..1 CodeableConcept 81258-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81258-6"
    }
  ]
}
Observation.Slices for component.component:sample-allelic-frequency.value[x] 0..1 Quantity Relative frequency in the sample
Observation.Slices for component.component:sample-allelic-frequency.value[x].system 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org (extensions allowed)
Observation.Slices for component.component:allelic-read-depth 0..1 BackboneElement Allelic Read Depth
Observation.Slices for component.component:allelic-read-depth.code 1..1 CodeableConcept 82121-5
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82121-5"
    }
  ]
}
Observation.Slices for component.component:allelic-read-depth.value[x] 0..1 Quantity Unfiltered count of supporting reads
Observation.Slices for component.component:allelic-state 0..1 BackboneElement Allelic State
Observation.Slices for component.component:allelic-state.code 1..1 CodeableConcept 53034-5
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53034-5"
    }
  ]
}
Observation.Slices for component.component:allelic-state.value[x] 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
Observation.Slices for component.component:variant-inheritance 0..1 BackboneElement Origin of germline genetic variant
Observation.Slices for component.component:variant-inheritance.code 1..1 CodeableConcept 94186-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "94186-4"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance.value[x] 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
Observation.Slices for component.component:variant-inheritance-basis 0..1 BackboneElement Evidential basis for variant inheritance
Observation.Slices for component.component:variant-inheritance-basis.code 1..1 CodeableConcept Basis for allelic phase
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82309-6"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance-basis.value[x] 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
Observation.Slices for component.component:variation-code 0..* BackboneElement Variation Code
Observation.Slices for component.component:variation-code.code 1..1 CodeableConcept 81252-9
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81252-9"
    }
  ]
}
Observation.Slices for component.component:variation-code.value[x] 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
Observation.Slices for component.component:representative-protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:representative-protein-hgvs.code 1..1 CodeableConcept 48005-3
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:representative-protein-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:copy-number 0..1 BackboneElement Genomic Structural Variant Copy Number
Observation.Slices for component.component:copy-number.code 1..1 CodeableConcept 82155-3
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82155-3"
    }
  ]
}
Observation.Slices for component.component:copy-number.value[x] 0..1 Actual component result
Observation.Slices for component.component:copy-number.value[x].valueQuantity Quantity
Observation.Slices for component.component:copy-number.value[x].valueRange Range
Observation.Slices for component.component:variant-confidence-status 0..1 BackboneElement Variant Confidence Status
Observation.Slices for component.component:variant-confidence-status.code 1..1 CodeableConcept variant-confidence-status
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "variant-confidence-status"
    }
  ]
}
Observation.Slices for component.component:variant-confidence-status.value[x] 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
Observation.Slices for component.component:repeat-motif 0..* BackboneElement Repeat Motif
Observation.Slices for component.component:repeat-motif.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-motif.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-motif.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-motif.code 1..1 CodeableConcept repeat-motif
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-motif"
    }
  ]
}
Observation.Slices for component.component:repeat-motif.value[x] 1..1 string CAG
Observation.Slices for component.component:repeat-number 0..* BackboneElement Repeat Number
Observation.Slices for component.component:repeat-number.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-number.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-number.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-number.code 1..1 CodeableConcept repeat-number
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-number"
    }
  ]
}
Observation.Slices for component.component:repeat-number.value[x] 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.method Base extensible LOINC Answer Codes for LL4048-6 ∅ unknown?
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-cibuild This IG
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-cibuild This IG
NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7
Observation.id This element is included in summaries. 0..1 id Logical id of this artifact
Observation.meta This element is included in summaries. 0..1 Meta Metadata about the resource
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
Observation.text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
Observation.contained 0..* Resource Contained, inline Resources
Observation.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary 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): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.identifier This element is included in summaries. 0..* Identifier Business Identifier for observation
Observation.basedOn This element is included in summaries. 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
Observation.partOf This element is included in summaries. 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:labCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:labCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:geCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.Slices for category.category:geCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.code This element is included in summaries. 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69548-6"
    }
  ]
}
Observation.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) Who and/or what the observation is about
Observation.focus This element is included in summaries. 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
Observation.encounter This element is included in summaries. 0..1 Reference(Encounter) Healthcare event during which this observation is made
Observation.effective[x] This element is included in summaries. 0..1 Clinically relevant time/time-period for observation
Observation.effective[x].effectiveDateTime dateTime
Observation.effective[x].effectivePeriod Period
Observation.effective[x].effectiveTiming Timing
Observation.effective[x].effectiveInstant instant
Observation.issued This element is included in summaries. 0..1 instant Date/Time this version was made available
Observation.performer This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
Observation.Slices for value[x] This element is included in summaries. C 0..1 Actual result
Slice: Unordered, Closed by type:$this
Slicing Note: Other type slices that contain no new information are not shown in this view
Observation.Slices for value[x].valueQuantity Quantity
Observation.Slices for value[x].valueCodeableConcept CodeableConcept
Observation.Slices for value[x].valueString string
Observation.Slices for value[x].valueBoolean boolean
Observation.Slices for value[x].valueInteger integer
Observation.Slices for value[x].valueRange Range
Observation.Slices for value[x].valueRatio Ratio
Observation.Slices for value[x].valueSampledData SampledData
Observation.Slices for value[x].valueTime time
Observation.Slices for value[x].valueDateTime dateTime
Observation.Slices for value[x].valuePeriod Period
Observation.Slices for value[x].value[x]:valueCodeableConcept This element is included in summaries. C 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
Observation.dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
Observation.bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
Observation.method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
Observation.specimen 0..1 Reference(Specimen) Specimen used for this observation
Observation.device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
Observation.referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3
Observation.referenceRange.id 0..1 string Unique id for inter-element referencing
Observation.referenceRange.extension 0..* Extension Additional content defined by implementations
Observation.referenceRange.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.referenceRange.low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
Constraints: sqty-1
Observation.referenceRange.high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
Constraints: sqty-1
Observation.referenceRange.type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
Observation.referenceRange.appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
Observation.referenceRange.age 0..1 Range Applicable age range, if relevant
Observation.referenceRange.text 0..1 string Text based reference range in an observation
Observation.hasMember This element is included in summaries. 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:All Slices.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:All Slices.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:All Slices.value[x].valueQuantity Quantity
Observation.Slices for component.component:All Slices.value[x].valueCodeableConcept CodeableConcept
Observation.Slices for component.component:All Slices.value[x].valueString string
Observation.Slices for component.component:All Slices.value[x].valueBoolean boolean
Observation.Slices for component.component:All Slices.value[x].valueInteger integer
Observation.Slices for component.component:All Slices.value[x].valueRange Range
Observation.Slices for component.component:All Slices.value[x].valueRatio Ratio
Observation.Slices for component.component:All Slices.value[x].valueSampledData SampledData
Observation.Slices for component.component:All Slices.value[x].valueTime time
Observation.Slices for component.component:All Slices.value[x].valueDateTime dateTime
Observation.Slices for component.component:All Slices.value[x].valuePeriod Period
Observation.Slices for component.component:All Slices.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:All Slices.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:All Slices.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:conclusion-string.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:conclusion-string.value[x] This element is included in summaries. 0..1 string Summary conclusion (interpretation/impression)
Observation.Slices for component.component:conclusion-string.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:conclusion-string.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:conclusion-string.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:gene-studied.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:gene-studied.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:gene-studied.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:gene-studied.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:cytogenetic-location.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:cytogenetic-location.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:cytogenetic-location.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:cytogenetic-location.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:reference-sequence-assembly.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:reference-sequence-assembly.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:reference-sequence-assembly.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:reference-sequence-assembly.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:chromosome-identifier.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
Observation.Slices for component.component:chromosome-identifier.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:chromosome-identifier.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:chromosome-identifier.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:representative-coding-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-coding-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-coding-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:representative-coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:representative-coding-hgvs.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-coding-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-coding-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:genomic-hgvs This element is included in summaries. 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
Observation.Slices for component.component:genomic-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:genomic-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:genomic-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-hgvs.code This element is included in summaries. 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81290-9"
    }
  ]
}
Observation.Slices for component.component:genomic-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:genomic-hgvs.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:genomic-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:genomic-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:cytogenomic-nomenclature This element is included in summaries. 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
Observation.Slices for component.component:cytogenomic-nomenclature.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:cytogenomic-nomenclature.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:cytogenomic-nomenclature.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenomic-nomenclature.code This element is included in summaries. 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81291-7"
    }
  ]
}
Observation.Slices for component.component:cytogenomic-nomenclature.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:cytogenomic-nomenclature.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:cytogenomic-nomenclature.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:cytogenomic-nomenclature.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:genomic-ref-seq This element is included in summaries. 0..1 BackboneElement Genomic Reference Sequence
Observation.Slices for component.component:genomic-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:genomic-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:genomic-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48013-7"
    }
  ]
}
Observation.Slices for component.component:genomic-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:genomic-ref-seq.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:genomic-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:genomic-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:representative-protein-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-protein-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-protein-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:representative-protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-protein-ref-seq.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-protein-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-protein-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:representative-transcript-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-transcript-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-transcript-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:representative-transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-transcript-ref-seq.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-transcript-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-transcript-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:exact-start-end This element is included in summaries. 0..1 BackboneElement Exact Start-End
Observation.Slices for component.component:exact-start-end.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:exact-start-end.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:exact-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:exact-start-end.code This element is included in summaries. 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81254-5"
    }
  ]
}
Observation.Slices for component.component:exact-start-end.value[x] This element is included in summaries. 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
Observation.Slices for component.component:exact-start-end.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:exact-start-end.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:exact-start-end.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:inner-start-end This element is included in summaries. 0..1 BackboneElement Inner Start-End
Observation.Slices for component.component:inner-start-end.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:inner-start-end.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:inner-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:inner-start-end.code This element is included in summaries. 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81302-2"
    }
  ]
}
Observation.Slices for component.component:inner-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant inner-bounding range
Observation.Slices for component.component:inner-start-end.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:inner-start-end.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:inner-start-end.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:outer-start-end This element is included in summaries. 0..1 BackboneElement Outer Start-End
Observation.Slices for component.component:outer-start-end.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:outer-start-end.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:outer-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:outer-start-end.code This element is included in summaries. 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81301-4"
    }
  ]
}
Observation.Slices for component.component:outer-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant outer-bounding range
Observation.Slices for component.component:outer-start-end.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:outer-start-end.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:outer-start-end.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:coordinate-system This element is included in summaries. 0..1 BackboneElement Coordinate System
Observation.Slices for component.component:coordinate-system.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:coordinate-system.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:coordinate-system.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coordinate-system.code This element is included in summaries. 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92822-6"
    }
  ]
}
Observation.Slices for component.component:coordinate-system.value[x] This element is included in summaries. 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
Observation.Slices for component.component:coordinate-system.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:coordinate-system.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:coordinate-system.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:ref-allele This element is included in summaries. 0..1 BackboneElement Genomic Ref Allele
Observation.Slices for component.component:ref-allele.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:ref-allele.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:ref-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:ref-allele.code This element is included in summaries. 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69547-8"
    }
  ]
}
Observation.Slices for component.component:ref-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:ref-allele.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:ref-allele.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:ref-allele.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:alt-allele This element is included in summaries. 0..1 BackboneElement Genomic Alt Allele
Observation.Slices for component.component:alt-allele.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:alt-allele.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:alt-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:alt-allele.code This element is included in summaries. 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69551-0"
    }
  ]
}
Observation.Slices for component.component:alt-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:alt-allele.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:alt-allele.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:alt-allele.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:coding-change-type This element is included in summaries. 0..1 BackboneElement Coding DNA Change Type
Observation.Slices for component.component:coding-change-type.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:coding-change-type.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:coding-change-type.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coding-change-type.code This element is included in summaries. 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48019-4"
    }
  ]
}
Observation.Slices for component.component:coding-change-type.value[x] This element is included in summaries. 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
Observation.Slices for component.component:coding-change-type.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:coding-change-type.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:coding-change-type.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:genomic-source-class This element is included in summaries. 0..1 BackboneElement Genomic Source Class
Observation.Slices for component.component:genomic-source-class.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:genomic-source-class.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:genomic-source-class.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-source-class.code This element is included in summaries. 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48002-0"
    }
  ]
}
Observation.Slices for component.component:genomic-source-class.value[x] This element is included in summaries. 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
Observation.Slices for component.component:genomic-source-class.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:genomic-source-class.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:genomic-source-class.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:sample-allelic-frequency This element is included in summaries. 0..1 BackboneElement Sample Allelic Frequency
Observation.Slices for component.component:sample-allelic-frequency.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:sample-allelic-frequency.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:sample-allelic-frequency.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:sample-allelic-frequency.code This element is included in summaries. 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81258-6"
    }
  ]
}
Observation.Slices for component.component:sample-allelic-frequency.value[x] This element is included in summaries. 0..1 Quantity Relative frequency in the sample
Observation.Slices for component.component:sample-allelic-frequency.value[x].id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:sample-allelic-frequency.value[x].extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for component.component:sample-allelic-frequency.value[x].value This element is included in summaries. 0..1 decimal Numerical value (with implicit precision)
Observation.Slices for component.component:sample-allelic-frequency.value[x].comparator This element is a modifier element. This element is included in summaries. 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
Observation.Slices for component.component:sample-allelic-frequency.value[x].unit This element is included in summaries. 0..1 string Unit representation
Observation.Slices for component.component:sample-allelic-frequency.value[x].system This element is included in summaries. C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org (extensions allowed)
Observation.Slices for component.component:sample-allelic-frequency.value[x].code This element is included in summaries. 0..1 code Coded form of the unit
Observation.Slices for component.component:sample-allelic-frequency.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:sample-allelic-frequency.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:sample-allelic-frequency.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:allelic-read-depth This element is included in summaries. 0..1 BackboneElement Allelic Read Depth
Observation.Slices for component.component:allelic-read-depth.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:allelic-read-depth.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:allelic-read-depth.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-read-depth.code This element is included in summaries. 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82121-5"
    }
  ]
}
Observation.Slices for component.component:allelic-read-depth.value[x] This element is included in summaries. 0..1 Quantity Unfiltered count of supporting reads
Observation.Slices for component.component:allelic-read-depth.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:allelic-read-depth.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:allelic-read-depth.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:allelic-state This element is included in summaries. 0..1 BackboneElement Allelic State
Observation.Slices for component.component:allelic-state.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:allelic-state.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:allelic-state.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-state.code This element is included in summaries. 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53034-5"
    }
  ]
}
Observation.Slices for component.component:allelic-state.value[x] This element is included in summaries. 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
Observation.Slices for component.component:allelic-state.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:allelic-state.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:allelic-state.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variant-inheritance This element is included in summaries. 0..1 BackboneElement Origin of germline genetic variant
Observation.Slices for component.component:variant-inheritance.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variant-inheritance.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variant-inheritance.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance.code This element is included in summaries. 1..1 CodeableConcept 94186-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "94186-4"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance.value[x] This element is included in summaries. 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
Observation.Slices for component.component:variant-inheritance.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variant-inheritance.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variant-inheritance.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variant-inheritance-basis This element is included in summaries. 0..1 BackboneElement Evidential basis for variant inheritance
Observation.Slices for component.component:variant-inheritance-basis.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variant-inheritance-basis.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variant-inheritance-basis.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance-basis.code This element is included in summaries. 1..1 CodeableConcept Basis for allelic phase
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82309-6"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance-basis.value[x] This element is included in summaries. 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
Observation.Slices for component.component:variant-inheritance-basis.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variant-inheritance-basis.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variant-inheritance-basis.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variation-code This element is included in summaries. 0..* BackboneElement Variation Code
Observation.Slices for component.component:variation-code.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variation-code.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variation-code.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variation-code.code This element is included in summaries. 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81252-9"
    }
  ]
}
Observation.Slices for component.component:variation-code.value[x] This element is included in summaries. 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
Observation.Slices for component.component:variation-code.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variation-code.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variation-code.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:representative-protein-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-protein-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-protein-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:representative-protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:representative-protein-hgvs.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-protein-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-protein-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:copy-number This element is included in summaries. 0..1 BackboneElement Genomic Structural Variant Copy Number
Observation.Slices for component.component:copy-number.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:copy-number.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:copy-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:copy-number.code This element is included in summaries. 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82155-3"
    }
  ]
}
Observation.Slices for component.component:copy-number.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:copy-number.value[x].valueQuantity Quantity
Observation.Slices for component.component:copy-number.value[x].valueRange Range
Observation.Slices for component.component:copy-number.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:copy-number.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:copy-number.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variant-confidence-status This element is included in summaries. 0..1 BackboneElement Variant Confidence Status
Observation.Slices for component.component:variant-confidence-status.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variant-confidence-status.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variant-confidence-status.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-confidence-status.code This element is included in summaries. 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "variant-confidence-status"
    }
  ]
}
Observation.Slices for component.component:variant-confidence-status.value[x] This element is included in summaries. 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
Observation.Slices for component.component:variant-confidence-status.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variant-confidence-status.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variant-confidence-status.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:repeat-motif This element is included in summaries. 0..* BackboneElement Repeat Motif
Observation.Slices for component.component:repeat-motif.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:repeat-motif.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-motif.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-motif.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-motif.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-motif.code This element is included in summaries. 1..1 CodeableConcept repeat-motif
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-motif"
    }
  ]
}
Observation.Slices for component.component:repeat-motif.value[x] This element is included in summaries. 1..1 string CAG
Observation.Slices for component.component:repeat-motif.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:repeat-motif.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:repeat-motif.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:repeat-number This element is included in summaries. 0..* BackboneElement Repeat Number
Observation.Slices for component.component:repeat-number.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:repeat-number.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-number.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-number.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-number.code This element is included in summaries. 1..1 CodeableConcept repeat-number
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-number"
    }
  ]
}
Observation.Slices for component.component:repeat-number.value[x] This element is included in summaries. 1..1 Quantity 40
Observation.Slices for component.component:repeat-number.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:repeat-number.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:repeat-number.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Observation.method Base extensible LOINC Answer Codes for LL4048-6 ∅ unknown?
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:representative-coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-cibuild This IG
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variant-inheritance-basis.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:representative-protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-cibuild This IG
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-motif.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-motif.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:repeat-motif.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If 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-4 error Observation If 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-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
obs-3 error Observation.referenceRange Must have at least a low or a high or text low.exists() or high.exists() or text.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If 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.intersect(%resource.code.coding).exists()).empty()
sqty-1 error Observation.referenceRange.low, Observation.referenceRange.high The comparator is not used on a SimpleQuantity comparator.empty()

This structure is derived from GenomicFinding

Summary

Mandatory: 0 element(17 nested mandatory elements)

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of Observation.value[x]

Maturity: 2

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.Slices for extension Content/Rules for all slices
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary 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): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.code This element is included in summaries. 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69548-6"
    }
  ]
}
Observation.Slices for value[x] This element is included in summaries. C 0..1 Actual result
Slice: Unordered, Closed by type:$this
Slicing Note: Other type slices that contain no new information are not shown in this view
Observation.Slices for value[x].valueQuantity Quantity
Observation.Slices for value[x].valueCodeableConcept CodeableConcept
Observation.Slices for value[x].valueString string
Observation.Slices for value[x].valueBoolean boolean
Observation.Slices for value[x].valueInteger integer
Observation.Slices for value[x].valueRange Range
Observation.Slices for value[x].valueRatio Ratio
Observation.Slices for value[x].valueSampledData SampledData
Observation.Slices for value[x].valueTime time
Observation.Slices for value[x].valueDateTime dateTime
Observation.Slices for value[x].valuePeriod Period
Observation.Slices for value[x].value[x]:valueCodeableConcept This element is included in summaries. C 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
Observation.method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
Observation.Slices for component.component:representative-coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:representative-coding-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:representative-coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:genomic-hgvs This element is included in summaries. 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
Observation.Slices for component.component:genomic-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-hgvs.code This element is included in summaries. 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81290-9"
    }
  ]
}
Observation.Slices for component.component:genomic-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:cytogenomic-nomenclature This element is included in summaries. 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
Observation.Slices for component.component:cytogenomic-nomenclature.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenomic-nomenclature.code This element is included in summaries. 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81291-7"
    }
  ]
}
Observation.Slices for component.component:cytogenomic-nomenclature.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:genomic-ref-seq This element is included in summaries. 0..1 BackboneElement Genomic Reference Sequence
Observation.Slices for component.component:genomic-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48013-7"
    }
  ]
}
Observation.Slices for component.component:genomic-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:representative-protein-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:representative-protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:representative-transcript-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:representative-transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:exact-start-end This element is included in summaries. 0..1 BackboneElement Exact Start-End
Observation.Slices for component.component:exact-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:exact-start-end.code This element is included in summaries. 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81254-5"
    }
  ]
}
Observation.Slices for component.component:exact-start-end.value[x] This element is included in summaries. 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
Observation.Slices for component.component:inner-start-end This element is included in summaries. 0..1 BackboneElement Inner Start-End
Observation.Slices for component.component:inner-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:inner-start-end.code This element is included in summaries. 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81302-2"
    }
  ]
}
Observation.Slices for component.component:inner-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant inner-bounding range
Observation.Slices for component.component:outer-start-end This element is included in summaries. 0..1 BackboneElement Outer Start-End
Observation.Slices for component.component:outer-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:outer-start-end.code This element is included in summaries. 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81301-4"
    }
  ]
}
Observation.Slices for component.component:outer-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant outer-bounding range
Observation.Slices for component.component:coordinate-system This element is included in summaries. 0..1 BackboneElement Coordinate System
Observation.Slices for component.component:coordinate-system.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coordinate-system.code This element is included in summaries. 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92822-6"
    }
  ]
}
Observation.Slices for component.component:coordinate-system.value[x] This element is included in summaries. 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
Observation.Slices for component.component:ref-allele This element is included in summaries. 0..1 BackboneElement Genomic Ref Allele
Observation.Slices for component.component:ref-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:ref-allele.code This element is included in summaries. 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69547-8"
    }
  ]
}
Observation.Slices for component.component:ref-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:alt-allele This element is included in summaries. 0..1 BackboneElement Genomic Alt Allele
Observation.Slices for component.component:alt-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:alt-allele.code This element is included in summaries. 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69551-0"
    }
  ]
}
Observation.Slices for component.component:alt-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:coding-change-type This element is included in summaries. 0..1 BackboneElement Coding DNA Change Type
Observation.Slices for component.component:coding-change-type.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coding-change-type.code This element is included in summaries. 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48019-4"
    }
  ]
}
Observation.Slices for component.component:coding-change-type.value[x] This element is included in summaries. 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
Observation.Slices for component.component:genomic-source-class This element is included in summaries. 0..1 BackboneElement Genomic Source Class
Observation.Slices for component.component:genomic-source-class.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-source-class.code This element is included in summaries. 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48002-0"
    }
  ]
}
Observation.Slices for component.component:genomic-source-class.value[x] This element is included in summaries. 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
Observation.Slices for component.component:sample-allelic-frequency This element is included in summaries. 0..1 BackboneElement Sample Allelic Frequency
Observation.Slices for component.component:sample-allelic-frequency.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:sample-allelic-frequency.code This element is included in summaries. 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81258-6"
    }
  ]
}
Observation.Slices for component.component:sample-allelic-frequency.value[x] This element is included in summaries. 0..1 Quantity Relative frequency in the sample
Observation.Slices for component.component:sample-allelic-frequency.value[x].comparator This element is a modifier element. This element is included in summaries. 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
Observation.Slices for component.component:sample-allelic-frequency.value[x].system This element is included in summaries. C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org (extensions allowed)
Observation.Slices for component.component:allelic-read-depth This element is included in summaries. 0..1 BackboneElement Allelic Read Depth
Observation.Slices for component.component:allelic-read-depth.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-read-depth.code This element is included in summaries. 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82121-5"
    }
  ]
}
Observation.Slices for component.component:allelic-read-depth.value[x] This element is included in summaries. 0..1 Quantity Unfiltered count of supporting reads
Observation.Slices for component.component:allelic-state This element is included in summaries. 0..1 BackboneElement Allelic State
Observation.Slices for component.component:allelic-state.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-state.code This element is included in summaries. 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53034-5"
    }
  ]
}
Observation.Slices for component.component:allelic-state.value[x] This element is included in summaries. 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
Observation.Slices for component.component:variant-inheritance This element is included in summaries. 0..1 BackboneElement Origin of germline genetic variant
Observation.Slices for component.component:variant-inheritance.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance.code This element is included in summaries. 1..1 CodeableConcept 94186-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "94186-4"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance.value[x] This element is included in summaries. 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
Observation.Slices for component.component:variant-inheritance-basis This element is included in summaries. 0..1 BackboneElement Evidential basis for variant inheritance
Observation.Slices for component.component:variant-inheritance-basis.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance-basis.code This element is included in summaries. 1..1 CodeableConcept Basis for allelic phase
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82309-6"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance-basis.value[x] This element is included in summaries. 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
Observation.Slices for component.component:variation-code This element is included in summaries. 0..* BackboneElement Variation Code
Observation.Slices for component.component:variation-code.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variation-code.code This element is included in summaries. 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81252-9"
    }
  ]
}
Observation.Slices for component.component:variation-code.value[x] This element is included in summaries. 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
Observation.Slices for component.component:representative-protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:representative-protein-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:representative-protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:copy-number This element is included in summaries. 0..1 BackboneElement Genomic Structural Variant Copy Number
Observation.Slices for component.component:copy-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:copy-number.code This element is included in summaries. 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82155-3"
    }
  ]
}
Observation.Slices for component.component:copy-number.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:copy-number.value[x].valueQuantity Quantity
Observation.Slices for component.component:copy-number.value[x].valueRange Range
Observation.Slices for component.component:variant-confidence-status This element is included in summaries. 0..1 BackboneElement Variant Confidence Status
Observation.Slices for component.component:variant-confidence-status.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-confidence-status.code This element is included in summaries. 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "variant-confidence-status"
    }
  ]
}
Observation.Slices for component.component:variant-confidence-status.value[x] This element is included in summaries. 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
Observation.Slices for component.component:repeat-motif This element is included in summaries. 0..* BackboneElement Repeat Motif
Observation.Slices for component.component:repeat-motif.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-motif.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-motif.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-motif.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-motif.code This element is included in summaries. 1..1 CodeableConcept repeat-motif
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-motif"
    }
  ]
}
Observation.Slices for component.component:repeat-motif.value[x] This element is included in summaries. 1..1 string CAG
Observation.Slices for component.component:repeat-number This element is included in summaries. 0..* BackboneElement Repeat Number
Observation.Slices for component.component:repeat-number.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-number.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-number.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-number.code This element is included in summaries. 1..1 CodeableConcept repeat-number
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-number"
    }
  ]
}
Observation.Slices for component.component:repeat-number.value[x] This element is included in summaries. 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.method Base extensible LOINC Answer Codes for LL4048-6 ∅ unknown?
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-cibuild This IG
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-cibuild This IG
Observation.component:repeat-motif.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If 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-4 error Observation If 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-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If 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.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation 0..* GenomicFinding Variant
Observation.code 1..1 CodeableConcept 69548-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69548-6"
    }
  ]
}
Observation.Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual result
Slice: Unordered, Open by type:$this
Slicing Note: Other type slices that contain no new information are not shown in this view
Observation.Slices for value[x].value[x]:valueCodeableConcept 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
Observation.method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
Observation.Slices for component Content/Rules for all slices
Observation.Slices for component.component:representative-coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:representative-coding-hgvs.code 1..1 CodeableConcept 48004-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:representative-coding-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:genomic-hgvs 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
Observation.Slices for component.component:genomic-hgvs.code 1..1 CodeableConcept 81290-9
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81290-9"
    }
  ]
}
Observation.Slices for component.component:genomic-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:cytogenomic-nomenclature 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
Observation.Slices for component.component:cytogenomic-nomenclature.code 1..1 CodeableConcept 81291-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81291-7"
    }
  ]
}
Observation.Slices for component.component:cytogenomic-nomenclature.value[x] 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:genomic-ref-seq 0..1 BackboneElement Genomic Reference Sequence
Observation.Slices for component.component:genomic-ref-seq.code 1..1 CodeableConcept 48013-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48013-7"
    }
  ]
}
Observation.Slices for component.component:genomic-ref-seq.value[x] 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:representative-protein-ref-seq.code 1..1 CodeableConcept protein-ref-seq
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:representative-protein-ref-seq.value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-transcript-ref-seq 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:representative-transcript-ref-seq.code 1..1 CodeableConcept 51958-7
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:representative-transcript-ref-seq.value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:exact-start-end 0..1 BackboneElement Exact Start-End
Observation.Slices for component.component:exact-start-end.code 1..1 CodeableConcept 81254-5
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81254-5"
    }
  ]
}
Observation.Slices for component.component:exact-start-end.value[x] 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
Observation.Slices for component.component:inner-start-end 0..1 BackboneElement Inner Start-End
Observation.Slices for component.component:inner-start-end.code 1..1 CodeableConcept 81302-2
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81302-2"
    }
  ]
}
Observation.Slices for component.component:inner-start-end.value[x] 0..1 Range Imprecise variant inner-bounding range
Observation.Slices for component.component:outer-start-end 0..1 BackboneElement Outer Start-End
Observation.Slices for component.component:outer-start-end.code 1..1 CodeableConcept 81301-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81301-4"
    }
  ]
}
Observation.Slices for component.component:outer-start-end.value[x] 0..1 Range Imprecise variant outer-bounding range
Observation.Slices for component.component:coordinate-system 0..1 BackboneElement Coordinate System
Observation.Slices for component.component:coordinate-system.code 1..1 CodeableConcept 92822-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92822-6"
    }
  ]
}
Observation.Slices for component.component:coordinate-system.value[x] 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
Observation.Slices for component.component:ref-allele 0..1 BackboneElement Genomic Ref Allele
Observation.Slices for component.component:ref-allele.code 1..1 CodeableConcept 69547-8
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69547-8"
    }
  ]
}
Observation.Slices for component.component:ref-allele.value[x] 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:alt-allele 0..1 BackboneElement Genomic Alt Allele
Observation.Slices for component.component:alt-allele.code 1..1 CodeableConcept 69551-0
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69551-0"
    }
  ]
}
Observation.Slices for component.component:alt-allele.value[x] 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:coding-change-type 0..1 BackboneElement Coding DNA Change Type
Observation.Slices for component.component:coding-change-type.code 1..1 CodeableConcept 48019-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48019-4"
    }
  ]
}
Observation.Slices for component.component:coding-change-type.value[x] 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
Observation.Slices for component.component:genomic-source-class 0..1 BackboneElement Genomic Source Class
Observation.Slices for component.component:genomic-source-class.code 1..1 CodeableConcept 48002-0
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48002-0"
    }
  ]
}
Observation.Slices for component.component:genomic-source-class.value[x] 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
Observation.Slices for component.component:sample-allelic-frequency 0..1 BackboneElement Sample Allelic Frequency
Observation.Slices for component.component:sample-allelic-frequency.code 1..1 CodeableConcept 81258-6
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81258-6"
    }
  ]
}
Observation.Slices for component.component:sample-allelic-frequency.value[x] 0..1 Quantity Relative frequency in the sample
Observation.Slices for component.component:sample-allelic-frequency.value[x].system 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org (extensions allowed)
Observation.Slices for component.component:allelic-read-depth 0..1 BackboneElement Allelic Read Depth
Observation.Slices for component.component:allelic-read-depth.code 1..1 CodeableConcept 82121-5
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82121-5"
    }
  ]
}
Observation.Slices for component.component:allelic-read-depth.value[x] 0..1 Quantity Unfiltered count of supporting reads
Observation.Slices for component.component:allelic-state 0..1 BackboneElement Allelic State
Observation.Slices for component.component:allelic-state.code 1..1 CodeableConcept 53034-5
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53034-5"
    }
  ]
}
Observation.Slices for component.component:allelic-state.value[x] 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
Observation.Slices for component.component:variant-inheritance 0..1 BackboneElement Origin of germline genetic variant
Observation.Slices for component.component:variant-inheritance.code 1..1 CodeableConcept 94186-4
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "94186-4"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance.value[x] 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
Observation.Slices for component.component:variant-inheritance-basis 0..1 BackboneElement Evidential basis for variant inheritance
Observation.Slices for component.component:variant-inheritance-basis.code 1..1 CodeableConcept Basis for allelic phase
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82309-6"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance-basis.value[x] 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
Observation.Slices for component.component:variation-code 0..* BackboneElement Variation Code
Observation.Slices for component.component:variation-code.code 1..1 CodeableConcept 81252-9
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81252-9"
    }
  ]
}
Observation.Slices for component.component:variation-code.value[x] 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
Observation.Slices for component.component:representative-protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:representative-protein-hgvs.code 1..1 CodeableConcept 48005-3
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:representative-protein-hgvs.value[x] 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:copy-number 0..1 BackboneElement Genomic Structural Variant Copy Number
Observation.Slices for component.component:copy-number.code 1..1 CodeableConcept 82155-3
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82155-3"
    }
  ]
}
Observation.Slices for component.component:copy-number.value[x] 0..1 Actual component result
Observation.Slices for component.component:copy-number.value[x].valueQuantity Quantity
Observation.Slices for component.component:copy-number.value[x].valueRange Range
Observation.Slices for component.component:variant-confidence-status 0..1 BackboneElement Variant Confidence Status
Observation.Slices for component.component:variant-confidence-status.code 1..1 CodeableConcept variant-confidence-status
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "variant-confidence-status"
    }
  ]
}
Observation.Slices for component.component:variant-confidence-status.value[x] 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
Observation.Slices for component.component:repeat-motif 0..* BackboneElement Repeat Motif
Observation.Slices for component.component:repeat-motif.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-motif.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-motif.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-motif.code 1..1 CodeableConcept repeat-motif
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-motif"
    }
  ]
}
Observation.Slices for component.component:repeat-motif.value[x] 1..1 string CAG
Observation.Slices for component.component:repeat-number 0..* BackboneElement Repeat Number
Observation.Slices for component.component:repeat-number.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-number.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-number.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-number.code 1..1 CodeableConcept repeat-number
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-number"
    }
  ]
}
Observation.Slices for component.component:repeat-number.value[x] 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.method Base extensible LOINC Answer Codes for LL4048-6 ∅ unknown?
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-cibuild This IG
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-cibuild This IG

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7
Observation.id This element is included in summaries. 0..1 id Logical id of this artifact
Observation.meta This element is included in summaries. 0..1 Meta Metadata about the resource
Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created
Observation.language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
Observation.text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
Observation.contained 0..* Resource Contained, inline Resources
Observation.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for extension.extension:secondary-finding 0..1 CodeableConcept Secondary 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): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored
Observation.identifier This element is included in summaries. 0..* Identifier Business Identifier for observation
Observation.basedOn This element is included in summaries. 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
Observation.partOf This element is included in summaries. 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Observation.Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:labCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:labCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}
Observation.Slices for category.category:labCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.id 0..1 string Unique id for inter-element referencing
Observation.Slices for category.category:geCategory.extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for category.category:geCategory.coding This element is included in summaries. 1..1 Coding Code defined by a terminology system

Required Pattern: 
{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}
Observation.Slices for category.category:geCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept
Observation.code This element is included in summaries. 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69548-6"
    }
  ]
}
Observation.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) Who and/or what the observation is about
Observation.focus This element is included in summaries. 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
Observation.encounter This element is included in summaries. 0..1 Reference(Encounter) Healthcare event during which this observation is made
Observation.effective[x] This element is included in summaries. 0..1 Clinically relevant time/time-period for observation
Observation.effective[x].effectiveDateTime dateTime
Observation.effective[x].effectivePeriod Period
Observation.effective[x].effectiveTiming Timing
Observation.effective[x].effectiveInstant instant
Observation.issued This element is included in summaries. 0..1 instant Date/Time this version was made available
Observation.performer This element is included in summaries. 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
Observation.Slices for value[x] This element is included in summaries. C 0..1 Actual result
Slice: Unordered, Closed by type:$this
Slicing Note: Other type slices that contain no new information are not shown in this view
Observation.Slices for value[x].valueQuantity Quantity
Observation.Slices for value[x].valueCodeableConcept CodeableConcept
Observation.Slices for value[x].valueString string
Observation.Slices for value[x].valueBoolean boolean
Observation.Slices for value[x].valueInteger integer
Observation.Slices for value[x].valueRange Range
Observation.Slices for value[x].valueRatio Ratio
Observation.Slices for value[x].valueSampledData SampledData
Observation.Slices for value[x].valueTime time
Observation.Slices for value[x].valueDateTime dateTime
Observation.Slices for value[x].valuePeriod Period
Observation.Slices for value[x].value[x]:valueCodeableConcept This element is included in summaries. C 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
Observation.dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.note 0..* CodedAnnotation Comments about the Observation that also contain a coded type
Observation.bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
Observation.method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
Observation.specimen 0..1 Reference(Specimen) Specimen used for this observation
Observation.device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
Observation.referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3
Observation.referenceRange.id 0..1 string Unique id for inter-element referencing
Observation.referenceRange.extension 0..* Extension Additional content defined by implementations
Observation.referenceRange.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.referenceRange.low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
Constraints: sqty-1
Observation.referenceRange.high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
Constraints: sqty-1
Observation.referenceRange.type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
Observation.referenceRange.appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
Observation.referenceRange.age 0..1 Range Applicable age range, if relevant
Observation.referenceRange.text 0..1 string Text based reference range in an observation
Observation.hasMember This element is included in summaries. 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices Content/Rules for all slices
Observation.Slices for component.component:All Slices.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:All Slices.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:All Slices.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:All Slices.value[x].valueQuantity Quantity
Observation.Slices for component.component:All Slices.value[x].valueCodeableConcept CodeableConcept
Observation.Slices for component.component:All Slices.value[x].valueString string
Observation.Slices for component.component:All Slices.value[x].valueBoolean boolean
Observation.Slices for component.component:All Slices.value[x].valueInteger integer
Observation.Slices for component.component:All Slices.value[x].valueRange Range
Observation.Slices for component.component:All Slices.value[x].valueRatio Ratio
Observation.Slices for component.component:All Slices.value[x].valueSampledData SampledData
Observation.Slices for component.component:All Slices.value[x].valueTime time
Observation.Slices for component.component:All Slices.value[x].valueDateTime dateTime
Observation.Slices for component.component:All Slices.value[x].valuePeriod Period
Observation.Slices for component.component:All Slices.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:All Slices.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:All Slices.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion
Observation.Slices for component.component:conclusion-string.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:conclusion-string.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code This element is included in summaries. 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}
Observation.Slices for component.component:conclusion-string.value[x] This element is included in summaries. 0..1 string Summary conclusion (interpretation/impression)
Observation.Slices for component.component:conclusion-string.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:conclusion-string.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:conclusion-string.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:gene-studied This element is included in summaries. 0..* BackboneElement Gene Studied
Observation.Slices for component.component:gene-studied.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:gene-studied.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:gene-studied.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:gene-studied.code This element is included in summaries. 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48018-6"
    }
  ]
}
Observation.Slices for component.component:gene-studied.value[x] This element is included in summaries. 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
Observation.Slices for component.component:gene-studied.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:gene-studied.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:gene-studied.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:cytogenetic-location This element is included in summaries. 0..* BackboneElement Cytogenetic (Chromosome) Location
Observation.Slices for component.component:cytogenetic-location.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:cytogenetic-location.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:cytogenetic-location.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenetic-location.code This element is included in summaries. 1..1 CodeableConcept 48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48001-2"
    }
  ]
}
Observation.Slices for component.component:cytogenetic-location.value[x] This element is included in summaries. 1..1 CodeableConcept Example: 1q21.1
Observation.Slices for component.component:cytogenetic-location.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:cytogenetic-location.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:cytogenetic-location.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:reference-sequence-assembly This element is included in summaries. 0..* BackboneElement Human Reference Sequence Assembly
Observation.Slices for component.component:reference-sequence-assembly.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:reference-sequence-assembly.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:reference-sequence-assembly.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:reference-sequence-assembly.code This element is included in summaries. 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "62374-4"
    }
  ]
}
Observation.Slices for component.component:reference-sequence-assembly.value[x] This element is included in summaries. 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
Observation.Slices for component.component:reference-sequence-assembly.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:reference-sequence-assembly.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:reference-sequence-assembly.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:chromosome-identifier This element is included in summaries. 0..* BackboneElement Chromosome Identifier
Observation.Slices for component.component:chromosome-identifier.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:chromosome-identifier.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:chromosome-identifier.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:chromosome-identifier.code This element is included in summaries. 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48000-4"
    }
  ]
}
Observation.Slices for component.component:chromosome-identifier.value[x] This element is included in summaries. 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
Observation.Slices for component.component:chromosome-identifier.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:chromosome-identifier.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:chromosome-identifier.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-coding-hgvs This element is included in summaries. 0..1 BackboneElement DNA change (c.HGVS)
Observation.Slices for component.component:representative-coding-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-coding-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-coding-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-coding-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48004-6"
    }
  ]
}
Observation.Slices for component.component:representative-coding-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:representative-coding-hgvs.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-coding-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-coding-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:genomic-hgvs This element is included in summaries. 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
Observation.Slices for component.component:genomic-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:genomic-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:genomic-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-hgvs.code This element is included in summaries. 1..1 CodeableConcept 81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81290-9"
    }
  ]
}
Observation.Slices for component.component:genomic-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:genomic-hgvs.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:genomic-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:genomic-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:cytogenomic-nomenclature This element is included in summaries. 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
Observation.Slices for component.component:cytogenomic-nomenclature.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:cytogenomic-nomenclature.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:cytogenomic-nomenclature.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:cytogenomic-nomenclature.code This element is included in summaries. 1..1 CodeableConcept 81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81291-7"
    }
  ]
}
Observation.Slices for component.component:cytogenomic-nomenclature.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
Observation.Slices for component.component:cytogenomic-nomenclature.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:cytogenomic-nomenclature.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:cytogenomic-nomenclature.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:genomic-ref-seq This element is included in summaries. 0..1 BackboneElement Genomic Reference Sequence
Observation.Slices for component.component:genomic-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:genomic-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:genomic-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48013-7"
    }
  ]
}
Observation.Slices for component.component:genomic-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:genomic-ref-seq.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:genomic-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:genomic-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-protein-ref-seq This element is included in summaries. 0..1 BackboneElement Protein Reference Sequence
Observation.Slices for component.component:representative-protein-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-protein-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-protein-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-ref-seq.code This element is included in summaries. 1..1 CodeableConcept protein-ref-seq
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "protein-ref-seq"
    }
  ]
}
Observation.Slices for component.component:representative-protein-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-protein-ref-seq.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-protein-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-protein-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-transcript-ref-seq This element is included in summaries. 0..1 BackboneElement Reference Transcript
Observation.Slices for component.component:representative-transcript-ref-seq.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-transcript-ref-seq.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-transcript-ref-seq.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-transcript-ref-seq.code This element is included in summaries. 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "51958-7"
    }
  ]
}
Observation.Slices for component.component:representative-transcript-ref-seq.value[x] This element is included in summaries. 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
Observation.Slices for component.component:representative-transcript-ref-seq.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-transcript-ref-seq.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-transcript-ref-seq.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:exact-start-end This element is included in summaries. 0..1 BackboneElement Exact Start-End
Observation.Slices for component.component:exact-start-end.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:exact-start-end.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:exact-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:exact-start-end.code This element is included in summaries. 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81254-5"
    }
  ]
}
Observation.Slices for component.component:exact-start-end.value[x] This element is included in summaries. 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
Observation.Slices for component.component:exact-start-end.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:exact-start-end.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:exact-start-end.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:inner-start-end This element is included in summaries. 0..1 BackboneElement Inner Start-End
Observation.Slices for component.component:inner-start-end.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:inner-start-end.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:inner-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:inner-start-end.code This element is included in summaries. 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81302-2"
    }
  ]
}
Observation.Slices for component.component:inner-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant inner-bounding range
Observation.Slices for component.component:inner-start-end.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:inner-start-end.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:inner-start-end.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:outer-start-end This element is included in summaries. 0..1 BackboneElement Outer Start-End
Observation.Slices for component.component:outer-start-end.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:outer-start-end.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:outer-start-end.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:outer-start-end.code This element is included in summaries. 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81301-4"
    }
  ]
}
Observation.Slices for component.component:outer-start-end.value[x] This element is included in summaries. 0..1 Range Imprecise variant outer-bounding range
Observation.Slices for component.component:outer-start-end.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:outer-start-end.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:outer-start-end.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:coordinate-system This element is included in summaries. 0..1 BackboneElement Coordinate System
Observation.Slices for component.component:coordinate-system.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:coordinate-system.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:coordinate-system.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coordinate-system.code This element is included in summaries. 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92822-6"
    }
  ]
}
Observation.Slices for component.component:coordinate-system.value[x] This element is included in summaries. 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
Observation.Slices for component.component:coordinate-system.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:coordinate-system.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:coordinate-system.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:ref-allele This element is included in summaries. 0..1 BackboneElement Genomic Ref Allele
Observation.Slices for component.component:ref-allele.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:ref-allele.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:ref-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:ref-allele.code This element is included in summaries. 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69547-8"
    }
  ]
}
Observation.Slices for component.component:ref-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:ref-allele.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:ref-allele.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:ref-allele.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:alt-allele This element is included in summaries. 0..1 BackboneElement Genomic Alt Allele
Observation.Slices for component.component:alt-allele.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:alt-allele.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:alt-allele.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:alt-allele.code This element is included in summaries. 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "69551-0"
    }
  ]
}
Observation.Slices for component.component:alt-allele.value[x] This element is included in summaries. 0..1 string Normalized string per the VCF format.
Observation.Slices for component.component:alt-allele.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:alt-allele.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:alt-allele.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:coding-change-type This element is included in summaries. 0..1 BackboneElement Coding DNA Change Type
Observation.Slices for component.component:coding-change-type.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:coding-change-type.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:coding-change-type.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:coding-change-type.code This element is included in summaries. 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48019-4"
    }
  ]
}
Observation.Slices for component.component:coding-change-type.value[x] This element is included in summaries. 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
Observation.Slices for component.component:coding-change-type.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:coding-change-type.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:coding-change-type.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:genomic-source-class This element is included in summaries. 0..1 BackboneElement Genomic Source Class
Observation.Slices for component.component:genomic-source-class.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:genomic-source-class.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:genomic-source-class.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:genomic-source-class.code This element is included in summaries. 1..1 CodeableConcept 48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48002-0"
    }
  ]
}
Observation.Slices for component.component:genomic-source-class.value[x] This element is included in summaries. 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
Observation.Slices for component.component:genomic-source-class.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:genomic-source-class.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:genomic-source-class.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:sample-allelic-frequency This element is included in summaries. 0..1 BackboneElement Sample Allelic Frequency
Observation.Slices for component.component:sample-allelic-frequency.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:sample-allelic-frequency.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:sample-allelic-frequency.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:sample-allelic-frequency.code This element is included in summaries. 1..1 CodeableConcept 81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81258-6"
    }
  ]
}
Observation.Slices for component.component:sample-allelic-frequency.value[x] This element is included in summaries. 0..1 Quantity Relative frequency in the sample
Observation.Slices for component.component:sample-allelic-frequency.value[x].id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:sample-allelic-frequency.value[x].extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Observation.Slices for component.component:sample-allelic-frequency.value[x].value This element is included in summaries. 0..1 decimal Numerical value (with implicit precision)
Observation.Slices for component.component:sample-allelic-frequency.value[x].comparator This element is a modifier element. This element is included in summaries. 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
Observation.Slices for component.component:sample-allelic-frequency.value[x].unit This element is included in summaries. 0..1 string Unit representation
Observation.Slices for component.component:sample-allelic-frequency.value[x].system This element is included in summaries. C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org (extensions allowed)
Observation.Slices for component.component:sample-allelic-frequency.value[x].code This element is included in summaries. 0..1 code Coded form of the unit
Observation.Slices for component.component:sample-allelic-frequency.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:sample-allelic-frequency.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:sample-allelic-frequency.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:allelic-read-depth This element is included in summaries. 0..1 BackboneElement Allelic Read Depth
Observation.Slices for component.component:allelic-read-depth.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:allelic-read-depth.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:allelic-read-depth.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-read-depth.code This element is included in summaries. 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82121-5"
    }
  ]
}
Observation.Slices for component.component:allelic-read-depth.value[x] This element is included in summaries. 0..1 Quantity Unfiltered count of supporting reads
Observation.Slices for component.component:allelic-read-depth.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:allelic-read-depth.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:allelic-read-depth.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:allelic-state This element is included in summaries. 0..1 BackboneElement Allelic State
Observation.Slices for component.component:allelic-state.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:allelic-state.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:allelic-state.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:allelic-state.code This element is included in summaries. 1..1 CodeableConcept 53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53034-5"
    }
  ]
}
Observation.Slices for component.component:allelic-state.value[x] This element is included in summaries. 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
Observation.Slices for component.component:allelic-state.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:allelic-state.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:allelic-state.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variant-inheritance This element is included in summaries. 0..1 BackboneElement Origin of germline genetic variant
Observation.Slices for component.component:variant-inheritance.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variant-inheritance.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variant-inheritance.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance.code This element is included in summaries. 1..1 CodeableConcept 94186-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "94186-4"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance.value[x] This element is included in summaries. 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
Observation.Slices for component.component:variant-inheritance.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variant-inheritance.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variant-inheritance.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variant-inheritance-basis This element is included in summaries. 0..1 BackboneElement Evidential basis for variant inheritance
Observation.Slices for component.component:variant-inheritance-basis.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variant-inheritance-basis.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variant-inheritance-basis.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-inheritance-basis.code This element is included in summaries. 1..1 CodeableConcept Basis for allelic phase
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82309-6"
    }
  ]
}
Observation.Slices for component.component:variant-inheritance-basis.value[x] This element is included in summaries. 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
Observation.Slices for component.component:variant-inheritance-basis.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variant-inheritance-basis.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variant-inheritance-basis.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variation-code This element is included in summaries. 0..* BackboneElement Variation Code
Observation.Slices for component.component:variation-code.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variation-code.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variation-code.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variation-code.code This element is included in summaries. 1..1 CodeableConcept 81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "81252-9"
    }
  ]
}
Observation.Slices for component.component:variation-code.value[x] This element is included in summaries. 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
Observation.Slices for component.component:variation-code.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variation-code.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variation-code.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:representative-protein-hgvs This element is included in summaries. 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
Observation.Slices for component.component:representative-protein-hgvs.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:representative-protein-hgvs.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:representative-protein-hgvs.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:representative-protein-hgvs.code This element is included in summaries. 1..1 CodeableConcept 48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "48005-3"
    }
  ]
}
Observation.Slices for component.component:representative-protein-hgvs.value[x] This element is included in summaries. 1..1 CodeableConcept A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
Observation.Slices for component.component:representative-protein-hgvs.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:representative-protein-hgvs.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:representative-protein-hgvs.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:copy-number This element is included in summaries. 0..1 BackboneElement Genomic Structural Variant Copy Number
Observation.Slices for component.component:copy-number.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:copy-number.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:copy-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:copy-number.code This element is included in summaries. 1..1 CodeableConcept 82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "82155-3"
    }
  ]
}
Observation.Slices for component.component:copy-number.value[x] This element is included in summaries. 0..1 Actual component result
Observation.Slices for component.component:copy-number.value[x].valueQuantity Quantity
Observation.Slices for component.component:copy-number.value[x].valueRange Range
Observation.Slices for component.component:copy-number.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:copy-number.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:copy-number.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:variant-confidence-status This element is included in summaries. 0..1 BackboneElement Variant Confidence Status
Observation.Slices for component.component:variant-confidence-status.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:variant-confidence-status.extension 0..* Extension Additional content defined by implementations
Observation.Slices for component.component:variant-confidence-status.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:variant-confidence-status.code This element is included in summaries. 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "variant-confidence-status"
    }
  ]
}
Observation.Slices for component.component:variant-confidence-status.value[x] This element is included in summaries. 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
Observation.Slices for component.component:variant-confidence-status.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:variant-confidence-status.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:variant-confidence-status.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:repeat-motif This element is included in summaries. 0..* BackboneElement Repeat Motif
Observation.Slices for component.component:repeat-motif.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:repeat-motif.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-motif.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-motif.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-motif.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-motif.code This element is included in summaries. 1..1 CodeableConcept repeat-motif
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-motif"
    }
  ]
}
Observation.Slices for component.component:repeat-motif.value[x] This element is included in summaries. 1..1 string CAG
Observation.Slices for component.component:repeat-motif.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:repeat-motif.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:repeat-motif.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
Observation.Slices for component.component:repeat-number This element is included in summaries. 0..* BackboneElement Repeat Number
Observation.Slices for component.component:repeat-number.id 0..1 string Unique id for inter-element referencing
Observation.Slices for component.component:repeat-number.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
Observation.Slices for component.component:repeat-number.Slices for extension Content/Rules for all slices
Observation.Slices for component.component:repeat-number.Slices for extension.extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
Observation.Slices for component.component:repeat-number.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:repeat-number.code This element is included in summaries. 1..1 CodeableConcept repeat-number
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: 
{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "repeat-number"
    }
  ]
}
Observation.Slices for component.component:repeat-number.value[x] This element is included in summaries. 1..1 Quantity 40
Observation.Slices for component.component:repeat-number.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
Observation.Slices for component.component:repeat-number.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
Observation.Slices for component.component:repeat-number.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Observation.method Base extensible LOINC Answer Codes for LL4048-6 ∅ unknown?
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-cibuild This IG
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible LOINC Answer Codes for LL1040-6 ∅ unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required LOINC Answer Codes for LL2938-0 ∅ unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:representative-coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-cibuild This IG
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variant-inheritance-basis.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-cibuild This IG
Observation.component:representative-protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-cibuild This IG
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-motif.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-motif.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:repeat-motif.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:repeat-number.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If 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-4 error Observation If 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-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()
obs-3 error Observation.referenceRange Must have at least a low or a high or text low.exists() or high.exists() or text.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If 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.intersect(%resource.code.coding).exists()).empty()
sqty-1 error Observation.referenceRange.low, Observation.referenceRange.high The comparator is not used on a SimpleQuantity comparator.empty()

This structure is derived from GenomicFinding

Summary

Mandatory: 0 element(17 nested mandatory elements)

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of Observation.value[x]

Maturity: 2

 

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