Genomics Reporting Implementation Guide
3.0.0 - release 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 3.0.0 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 - Detailed Descriptions

Active as of 2024-11-24

Definitions for the variant resource profile.

Guidance on how to interpret the contents of this table can be found here

0. Observation
ShortVariant
2. Observation.code
Short69548-6
Pattern Value{
  "coding" : [{
    "system" : "http://loinc.org",
    "code" : "69548-6"
  }]
}
4. Observation.value[x]
[x] NoteSeeChoice of Data Typesfor further information about how to use [x]
SlicingThis element introduces a set of slices on Observation.value[x]. The slices areUnordered and Open, and can be differentiated using the following discriminators:
  • type @ $this
  • 6. Observation.value[x]:valueCodeableConcept
    Slice NamevalueCodeableConcept
    Definition

    The presence or absence of the variant described in the components. If not searching for specific variations and merely reporting what's found, the profile's value should be set to 'Present'.

    ShortIndeterminate | No call | Present | Absent.
    Comments

    See here for usage guidance.

    Control0..1
    BindingThe codes SHALL be taken from LOINC Answer List LL1971-2
    (required to http://loinc.org/vs/LL1971-2)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    8. Observation.method
    ShortSequencing | SNP array | PCR | Computational analysis | ...
    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL4048-6
    (extensible to http://loinc.org/vs/LL4048-6)
    10. Observation.component:representative-coding-hgvs
    Slice Namerepresentative-coding-hgvs
    Definition

    Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.

    ShortDNA change (c.HGVS)
    Control0..1
    12. Observation.component:representative-coding-hgvs.code
    Short48004-6
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48004-6"
      }]
    }
    14. Observation.component:representative-coding-hgvs.value[x]
    ShortA valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
    Control1..?
    BindingThe codes SHALL be taken from Human Genome Variation Society (HGVS) Nomenclature
    (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    16. Observation.component:genomic-hgvs
    Slice Namegenomic-hgvs
    Definition

    Description of the genomic (gDNA) sequence change using a valid HGVS-formatted string.

    ShortGenomic (gDNA) Change - gHGVS
    Control0..1
    18. Observation.component:genomic-hgvs.code
    Short81290-9
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81290-9"
      }]
    }
    20. Observation.component:genomic-hgvs.value[x]
    ShortA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
    Control1..?
    BindingThe codes SHALL be taken from Human Genome Variation Society (HGVS) Nomenclature
    (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    22. Observation.component:cytogenomic-nomenclature
    Slice Namecytogenomic-nomenclature
    Definition

    Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.

    ShortCytogenomic Nomenclature (ISCN)
    Control0..1
    24. Observation.component:cytogenomic-nomenclature.code
    Short81291-7
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81291-7"
      }]
    }
    26. Observation.component:cytogenomic-nomenclature.value[x]
    Control1..?
    Binding

    Binding not yet defined

    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    28. Observation.component:genomic-ref-seq
    Slice Namegenomic-ref-seq
    Definition

    ID of the genomic reference sequence, which includes transcribed and non transcribed stretches

    ShortGenomic Reference Sequence
    Control0..1
    30. Observation.component:genomic-ref-seq.code
    Short48013-7
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48013-7"
      }]
    }
    32. Observation.component:genomic-ref-seq.value[x]
    ShortVersioned genomic reference sequence identifier
    Control1..?
    Binding

    Multiple bindings acceptable (NCBI or LRG)

    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    34. Observation.component:representative-protein-ref-seq
    Slice Namerepresentative-protein-ref-seq
    Definition

    ID of the protein reference sequence, which includes transcribed and non transcribed stretches. It covers the entire protein described.

    ShortProtein Reference Sequence
    Control0..1
    36. Observation.component:representative-protein-ref-seq.code
    Shortprotein-ref-seq
    Pattern Value{
      "coding" : [{
        "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
        "code" : "protein-ref-seq"
      }]
    }
    38. Observation.component:representative-protein-ref-seq.value[x]
    ShortVersioned protein reference sequence identifier
    Control1..?
    Binding

    Multiple bindings acceptable (NCBI or LRG)

    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    40. Observation.component:representative-transcript-ref-seq
    Slice Namerepresentative-transcript-ref-seq
    Definition

    NCBI's RefSeq ('NM_...'), Ensembl ('ENST...'), and LRG ('LRG...' plus 't1' to indicate transcript)

    ShortReference Transcript
    Control0..1
    42. Observation.component:representative-transcript-ref-seq.code
    Short51958-7
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "51958-7"
      }]
    }
    44. Observation.component:representative-transcript-ref-seq.value[x]
    ShortVersioned transcript reference sequence identifier
    Control1..?
    Binding

    Multiple bindings acceptable (NCBI or LRG)

    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    46. Observation.component:exact-start-end
    Slice Nameexact-start-end
    Definition

    The exact integer-based genomic coordinates of the start and end of the variant region.

    ShortExact Start-End
    Control0..1
    48. Observation.component:exact-start-end.code
    Short81254-5
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81254-5"
      }]
    }
    50. Observation.component:exact-start-end.value[x]
    ShortRange in question. 'High' can be omitted for single nucleotide variants.
    TypeRange
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    52. Observation.component:inner-start-end
    Slice Nameinner-start-end
    Definition

    The genomic coordinates of the narrowest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.

    ShortInner Start-End
    Control0..1
    54. Observation.component:inner-start-end.code
    Short81302-2
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81302-2"
      }]
    }
    56. Observation.component:inner-start-end.value[x]
    ShortImprecise variant inner-bounding range
    TypeRange
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    58. Observation.component:outer-start-end
    Slice Nameouter-start-end
    Definition

    The genomic coordinates of the widest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.

    ShortOuter Start-End
    Control0..1
    60. Observation.component:outer-start-end.code
    Short81301-4
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81301-4"
      }]
    }
    62. Observation.component:outer-start-end.value[x]
    ShortImprecise variant outer-bounding range
    TypeRange
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    64. Observation.component:coordinate-system
    Slice Namecoordinate-system
    Definition

    These are different ways of identifying nucleotides or amino acids within a sequence. In the 1-based system, the first unit of the polymer (e.g. the first nucleotide) is counted as number 1. In the 0-based system, the number 0 designates the location before the first nucleotide. Different databases and file types may use different systems.

    ShortCoordinate System
    Control0..1
    66. Observation.component:coordinate-system.code
    Short92822-6
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "92822-6"
      }]
    }
    68. Observation.component:coordinate-system.value[x]
    Short0-based interval counting | 0-based character counting | 1-based character counting
    Control1..?
    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL5323-2
    (extensible to http://loinc.org/vs/LL5323-2)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    70. Observation.component:ref-allele
    Slice Nameref-allele
    Definition

    Reference values ('normal') examined within the Reference Sequence.

    ShortGenomic Ref Allele
    Control0..1
    72. Observation.component:ref-allele.code
    Short69547-8
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "69547-8"
      }]
    }
    74. Observation.component:ref-allele.value[x]
    ShortNormalized string per the VCF format.
    Typestring
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    76. Observation.component:alt-allele
    Slice Namealt-allele
    Definition

    The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant.

    ShortGenomic Alt Allele
    Control0..1
    78. Observation.component:alt-allele.code
    Short69551-0
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "69551-0"
      }]
    }
    80. Observation.component:alt-allele.value[x]
    ShortNormalized string per the VCF format.
    Typestring
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    82. Observation.component:coding-change-type
    Slice Namecoding-change-type
    Definition

    Type of DNA change observed. Convenience property for variants with exact breakpoints, required otherwise.

    ShortCoding DNA Change Type
    Control0..1
    84. Observation.component:coding-change-type.code
    Short48019-4
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48019-4"
      }]
    }
    86. Observation.component:coding-change-type.value[x]
    Shortdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
    Control1..?
    BindingUnless not suitable, these codes SHALL be taken from DNA Change Type
    (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs)

    Concepts in sequence ontology under SO:0002072

    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    88. Observation.component:genomic-source-class
    Slice Namegenomic-source-class
    Definition

    The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.

    ShortGenomic Source Class
    Control0..1
    90. Observation.component:genomic-source-class.code
    Short48002-0
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48002-0"
      }]
    }
    92. Observation.component:genomic-source-class.value[x]
    ShortGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
    Control1..?
    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL378-1
    (extensible to http://loinc.org/vs/LL378-1)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    94. Observation.component:sample-allelic-frequency
    Slice Namesample-allelic-frequency
    Definition

    The relative frequency of the allele at a given locus in the sample.

    ShortSample Allelic Frequency
    Control0..1
    96. Observation.component:sample-allelic-frequency.code
    Short81258-6
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81258-6"
      }]
    }
    98. Observation.component:sample-allelic-frequency.value[x]
    ShortRelative frequency in the sample
    TypeQuantity
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    100. Observation.component:sample-allelic-frequency.value[x].system
    Pattern Valuehttp://unitsofmeasure.org
    102. Observation.component:allelic-read-depth
    Slice Nameallelic-read-depth
    Definition

    Specifies the number of reads that identified the allele in question whether it consists of one or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads to be acceptable. Often >400, sometimes as few as 2-4.

    ShortAllelic Read Depth
    Comments

    See here for usage guidance.

    Control0..1
    104. Observation.component:allelic-read-depth.code
    Short82121-5
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "82121-5"
      }]
    }
    106. Observation.component:allelic-read-depth.value[x]
    ShortUnfiltered count of supporting reads
    TypeQuantity
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    108. Observation.component:allelic-state
    Slice Nameallelic-state
    Definition

    The observed level of occurrence of the variant in the set of chromosomes.

    ShortAllelic State
    Control0..1
    110. Observation.component:allelic-state.code
    Short53034-5
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "53034-5"
      }]
    }
    112. Observation.component:allelic-state.value[x]
    ShortHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
    Control1..?
    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL381-5
    (extensible to http://loinc.org/vs/LL381-5)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    114. Observation.component:variant-inheritance
    Slice Namevariant-inheritance
    Definition

    The source or inheritance of a specific germline variation found in an individual patient.

    ShortOrigin of germline genetic variant
    Control0..1
    116. Observation.component:variant-inheritance.code
    Short94186-4
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "94186-4"
      }]
    }
    118. Observation.component:variant-inheritance.value[x]
    ShortMaternal | Paternal | Unknown
    Control1..?
    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL5489-1
    (extensible to http://loinc.org/vs/LL5489-1)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    120. Observation.component:variant-inheritance-basis
    Slice Namevariant-inheritance-basis
    Definition

    The method by which the variant inheritance is determined.

    ShortEvidential basis for variant inheritance
    Control0..1
    122. Observation.component:variant-inheritance-basis.code
    ShortBasis for allelic phase
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "82309-6"
      }]
    }
    124. Observation.component:variant-inheritance-basis.value[x]
    ShortDirectly measured | Family DNA | Family history | Inferred from population data
    Control1..?
    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL4050-2
    (extensible to http://loinc.org/vs/LL4050-2)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    126. Observation.component:variation-code
    Slice Namevariation-code
    Definition

    Accession number in a variant database such as ClinVar, given for cross-reference.

    ShortVariation Code
    Control0..*
    128. Observation.component:variation-code.code
    Short81252-9
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81252-9"
      }]
    }
    130. Observation.component:variation-code.value[x]
    ShortClinVar ID or similar
    Control1..?
    Binding

    Multiple bindings acceptable

    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    132. Observation.component:representative-protein-hgvs
    Slice Namerepresentative-protein-hgvs
    Definition

    Description of the protein (amino acid) sequence change using a valid HGVS-formatted string. The description of the variant is surrounded in parentheses if it is calculated rather than directly observed.

    ShortProtein (Amino Acid) Change - pHGVS
    Control0..1
    134. Observation.component:representative-protein-hgvs.code
    Short48005-3
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48005-3"
      }]
    }
    136. Observation.component:representative-protein-hgvs.value[x]
    ShortA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
    Control1..?
    BindingThe codes SHALL be taken from Human Genome Variation Society (HGVS) Nomenclature
    (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    138. Observation.component:copy-number
    Slice Namecopy-number
    Definition

    The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. If the value determined by the assay is not a whole number, a range or decimal number can be specified. Note that a copy number of 1 can imply a deletion.

    ShortGenomic Structural Variant Copy Number
    Comments

    Copy number variants are often described with a single copy number value. However, due to the nature of assays, such as qPCR and microarray, it can be difficult to assign an exact copy number. Therefore, labs sometimes report a range instead of an exact copy number. They may alternatively choose to report decimal numbers, even if whole numbers are biologically correct.

    In general, it can be difficult to estimate a copy number from measurements taken on a heterogenous population of cells, such as a tumor. As indicated in the ISCN 2020 specifications, it is appropriate to express the measurements using a range. Furthermore, regardless of cell population, many assays use fluorescent probes to detect copy number. These testing methodologies do not always provide an exact, discrete value for this data point.

    Control0..1
    Requirements

    There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM.

    140. Observation.component:copy-number.code
    Short82155-3
    Pattern Value{
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "82155-3"
      }]
    }
    142. Observation.component:copy-number.value[x]
    TypeChoice of: Quantity, Range
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    144. Observation.component:variant-confidence-status
    Slice Namevariant-confidence-status
    Definition

    A code that represents the confidence of a true positive variant call.

    ShortVariant Confidence Status
    Comments

    See here for usage guidance.

    Control0..1
    146. Observation.component:variant-confidence-status.code
    Shortvariant-confidence-status
    Pattern Value{
      "coding" : [{
        "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
        "code" : "variant-confidence-status"
      }]
    }
    148. Observation.component:variant-confidence-status.value[x]
    ShortHigh | Intermediate | Low
    Control1..?
    BindingThe codes SHALL be taken from Variant Confidence Status
    (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs)
    TypeCodeableConcept
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    150. Observation.component:repeat-motif
    Slice Namerepeat-motif
    Definition

    Nucleotides of a repeat expansion motif.

    ShortRepeat Motif
    Control0..*
    152. Observation.component:repeat-motif.extension
    SlicingThis element introduces a set of slices on Observation.component.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
    • value @ url
    • 154. Observation.component:repeat-motif.extension:repeat-motif-order
      Slice Namerepeat-motif-order
      Comments

      If there are multiple repeat expansion pairs, this must be used both to indicate the sequence position of a given repeat-motif and repeat-number pair and to group the related components together. Components with the same extension value describe the same motif.

      Control0..1
      TypeExtension(Repeat Motif Order) (Extension Type: positiveInt)
      Requirements

      The value must be a natural number starting from 1 and increasing sequentially

      156. Observation.component:repeat-motif.code
      Shortrepeat-motif
      Pattern Value{
        "coding" : [{
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
          "code" : "repeat-motif"
        }]
      }
      158. Observation.component:repeat-motif.value[x]
      ShortCAG
      Control1..?
      Typestring
      [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
      Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
      160. Observation.component:repeat-number
      Slice Namerepeat-number
      Definition

      Number of repeats of a repeat expansion.

      ShortRepeat Number
      Control0..*
      162. Observation.component:repeat-number.extension
      SlicingThis element introduces a set of slices on Observation.component.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
      • value @ url
      • 164. Observation.component:repeat-number.extension:repeat-motif-order
        Slice Namerepeat-motif-order
        Comments

        If there are multiple repeat expansion pairs, this must be used both to indicate the sequence position of a given repeat-motif and repeat-number pair and to group the related components together. Components with the same extension value describe the same motif.

        Control0..1
        TypeExtension(Repeat Motif Order) (Extension Type: positiveInt)
        Requirements

        The value must be a natural number starting from 1 and increasing sequentially

        166. Observation.component:repeat-number.code
        Shortrepeat-number
        Pattern Value{
          "coding" : [{
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "repeat-number"
          }]
        }
        168. Observation.component:repeat-number.value[x]
        Short40
        Control1..?
        TypeQuantity
        [x] NoteSeeChoice of Data Typesfor further information about how to use [x]

        Guidance on how to interpret the contents of this table can be found here

        0. Observation
        Definition

        Measurements and simple assertions made about a patient, device or other subject.

        ShortVariantMeasurements and simple assertions
        Comments

        Used for simple observations such as device measurements, laboratory atomic results, vital signs, height, weight, smoking status, comments, etc. Other resources are used to provide context for observations such as laboratory reports, etc.

        Control0..*
        Is Modifierfalse
        Summaryfalse
        Alternate NamesVital Signs, Measurement, Results, Tests
        Invariantsdom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (contained.contained.empty())
        dom-3: 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: 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: If a resource is contained in another resource, it SHALL NOT have a security label (contained.meta.security.empty())
        dom-6: A resource should have narrative for robust management (text.`div`.exists())
        obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present (dataAbsentReason.empty() or value.empty())
        obs-7: 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())
        obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present (dataAbsentReason.empty() or value.empty())
        obs-7: 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())
        2. Observation.implicitRules
        Definition

        A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

        ShortA set of rules under which this content was created
        Comments

        Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.

        Control0..1
        Typeuri
        Is Modifiertrue because This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation
        Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        4. Observation.extension:secondary-finding
        Slice Namesecondary-finding
        Definition

        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) or Whole Genome Sequencing (WGS) 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.

        ShortSecondary 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
        Control0..1
        TypeExtension(Observation Secondary Finding) (Extension Type: CodeableConcept)
        Is Modifierfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        6. Observation.extension:body-structure
        Slice Namebody-structure
        Definition

        Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.

        ShortTarget anatomic location or structure
        Control0..1
        TypeExtension(BodyStructure Reference) (Extension Type: Reference(BodyStructure))
        Is Modifierfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        8. Observation.modifierExtension
        Definition

        May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

        Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

        ShortExtensions that cannot be ignored
        Comments

        There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

        Control0..*
        TypeExtension
        Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
        Summaryfalse
        Requirements

        Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

        Alternate Namesextensions, user content
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        10. Observation.status
        Definition

        The status of the result value.

        Shortregistered | preliminary | final | amended +
        Comments

        This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.

        Control1..1
        BindingThe codes SHALL be taken from ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1
        (required to http://hl7.org/fhir/ValueSet/observation-status|4.0.1)

        Codes providing the status of an observation.

        Typecode
        Is Modifiertrue because This element is labeled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid
        Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
        Summarytrue
        Requirements

        Need to track the status of individual results. Some results are finalized before the whole report is finalized.

        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        12. Observation.category
        Definition

        A code that classifies the general type of observation being made.

        ShortClassification of type of observation
        Comments

        In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

        Control20..*
        BindingThe codes SHOULD be taken from ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category
        (preferred to http://hl7.org/fhir/ValueSet/observation-category)

        Codes for high level observation categories.

        TypeCodeableConcept
        Is Modifierfalse
        Summaryfalse
        Requirements

        Used for filtering what observations are retrieved and displayed.

        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        SlicingThis element introduces a set of slices on Observation.category. The slices areUnordered and Open, and can be differentiated using the following discriminators:
        • value @ coding
        • 14. Observation.category:labCategory
          Slice NamelabCategory
          Definition

          A code that classifies the general type of observation being made.

          ShortClassification of type of observation
          Comments

          In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

          Control10..1*
          BindingThe codes SHOULD be taken from ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category
          (preferred to http://hl7.org/fhir/ValueSet/observation-category)

          Codes for high level observation categories.

          TypeCodeableConcept
          Is Modifierfalse
          Summaryfalse
          Requirements

          Used for filtering what observations are retrieved and displayed.

          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          16. Observation.category:labCategory.coding
          Definition

          A reference to a code defined by a terminology system.

          ShortCode defined by a terminology system
          Comments

          Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

          Control10..1*
          TypeCoding
          Is Modifierfalse
          Summarytrue
          Requirements

          Allows for alternative encodings within a code system, and translations to other code systems.

          Pattern Value{
            "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
            "code" : "laboratory"
          }
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          18. Observation.category:geCategory
          Slice NamegeCategory
          Definition

          A code that classifies the general type of observation being made.

          ShortClassification of type of observation
          Comments

          In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

          Control10..1*
          BindingThe codes SHOULD be taken from ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category
          (preferred to http://hl7.org/fhir/ValueSet/observation-category)

          Codes for high level observation categories.

          TypeCodeableConcept
          Is Modifierfalse
          Summaryfalse
          Requirements

          Used for filtering what observations are retrieved and displayed.

          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          20. Observation.category:geCategory.coding
          Definition

          A reference to a code defined by a terminology system.

          ShortCode defined by a terminology system
          Comments

          Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

          Control10..1*
          TypeCoding
          Is Modifierfalse
          Summarytrue
          Requirements

          Allows for alternative encodings within a code system, and translations to other code systems.

          Pattern Value{
            "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
            "code" : "GE"
          }
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          22. Observation.code
          Definition

          Describes what was observed. Sometimes this is called the observation "name".

          Short69548-6Type of observation (code / type)
          Comments

          All code-value and, if present, component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

          Control1..1
          BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
          (example to http://hl7.org/fhir/ValueSet/observation-codes)

          Codes identifying names of simple observations.

          TypeCodeableConcept
          Is Modifierfalse
          Summarytrue
          Requirements

          Knowing what kind of observation is being made is essential to understanding the observation.

          Alternate NamesName
          Pattern Value{
            "coding" : [{
              "system" : "http://loinc.org",
              "code" : "69548-6"
            }]
          }
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          24. Observation.value[x]
          Definition

          The information determined as a result of making the observation, if the information has a simple value.

          ShortActual result
          Comments

          An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

          Control0..1
          This element is affected by the following invariants: obs-7
          TypeChoice of: Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
          [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
          Is Modifierfalse
          Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
          Summarytrue
          Requirements

          An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          SlicingThis element introduces a set of slices on Observation.value[x]. The slices areUnordered and Open, and can be differentiated using the following discriminators:
          • type @ $this
          • 26. Observation.value[x]:valueCodeableConcept
            Slice NamevalueCodeableConcept
            Definition

            The presence or absence of the variant described in the components. If not searching for specific variations and merely reporting what's found, the profile's value should be set to 'Present'.


            The information determined as a result of making the observation, if the information has a simple value.

            ShortIndeterminate | No call | Present | Absent.Actual result
            Comments

            See here for usage guidance.


            An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

            Control0..1
            This element is affected by the following invariants: obs-7
            BindingThe codes SHALL be taken from For codes, see LOINC Answer List LL1971-2
            (required to http://loinc.org/vs/LL1971-2)
            TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
            [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
            Is Modifierfalse
            Summarytrue
            Requirements

            An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
            28. Observation.method
            Definition

            Indicates the mechanism used to perform the observation.

            ShortSequencing | SNP array | PCR | Computational analysis | ...How it was done
            Comments

            Only used if not implicit in code for Observation.code.

            Control0..1
            BindingUnless not suitable, these codes SHALL be taken from For example codes, see LOINC Answer List LL4048-6http://hl7.org/fhir/ValueSet/observation-methods
            (extensible to http://loinc.org/vs/LL4048-6)
            TypeCodeableConcept
            Is Modifierfalse
            Summaryfalse
            Requirements

            In some cases, method can impact results and is thus used for determining whether results can be compared or determining significance of results.

            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
            30. Observation.derivedFrom
            Definition

            The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

            ShortRelated measurements the observation is made from
            Comments

            All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

            Control0..*
            TypeReference(DocumentReference, ImagingStudy, Media, QuestionnaireResponse, Observation, MolecularSequence)
            Is Modifierfalse
            Summarytrue
            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
            SlicingThis element introduces a set of slices on Observation.derivedFrom. The slices areUnordered and Open, and can be differentiated using the following discriminators:
            • profile @ resolve()
            • 32. Observation.component
              Definition

              Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

              ShortComponent results
              Comments

              For a discussion on the ways Observations can be assembled in groups together see Notes below.

              Control0..*
              TypeBackboneElement
              Is Modifierfalse
              Summarytrue
              Requirements

              Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              SlicingThis element introduces a set of slices on Observation.component. The slices areUnordered and Open, and can be differentiated using the following discriminators:
              • value @ code
              • 34. Observation.component.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                36. Observation.component.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                ShortType of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                38. Observation.component:conclusion-string
                Slice Nameconclusion-string
                Definition

                Concise and clinically contextualized summary conclusion (interpretation/impression) of the observation


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortClinical ConclusionComponent results
                Comments

                An example would be the interpretative information, typically canned, about a variant identified in the patient.


                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Need to be able to provide a conclusion that is not lost among the basic result data.


                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                40. Observation.component:conclusion-string.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                42. Observation.component:conclusion-string.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Shortconclusion-stringType of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                    "code" : "conclusion-string"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                44. Observation.component:gene-studied
                Slice Namegene-studied
                Definition

                The gene(s) on which the variant is located.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGene StudiedComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                46. Observation.component:gene-studied.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                48. Observation.component:gene-studied.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48018-6Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48018-6"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                50. Observation.component:gene-studied.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortThe 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.Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see HUGO Gene Nomenclature Committee Gene Names (HGNC)
                (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                52. Observation.component:cytogenetic-location
                Slice Namecytogenetic-location
                Definition

                The relevant chromosomal region. The combination of numbers and letters provide a genetic 'address'.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortCytogenetic (Chromosome) LocationComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                54. Observation.component:cytogenetic-location.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                56. Observation.component:cytogenetic-location.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48001-2Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48001-2"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                58. Observation.component:cytogenetic-location.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortExample: 1q21.1Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                60. Observation.component:reference-sequence-assembly
                Slice Namereference-sequence-assembly
                Definition

                The reference genome/assembly used in this analysis.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortHuman Reference Sequence AssemblyComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                62. Observation.component:reference-sequence-assembly.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                64. Observation.component:reference-sequence-assembly.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short62374-4Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "62374-4"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                66. Observation.component:reference-sequence-assembly.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortGRCh37 | GRCh38 | ...Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see LOINC Answer List LL1040-6
                (extensible to http://loinc.org/vs/LL1040-6)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                68. Observation.component:chromosome-identifier
                Slice Namechromosome-identifier
                Definition

                An indicator, enumerated in humans by numbers 1-22, X, and Y, representing the chromosome on which the finding is located.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortChromosome IdentifierComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                70. Observation.component:chromosome-identifier.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                72. Observation.component:chromosome-identifier.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48000-4Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48000-4"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                74. Observation.component:chromosome-identifier.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortChromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome YActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingThe codes SHALL be taken from For codes, see LOINC Answer List LL2938-0
                (required to http://loinc.org/vs/LL2938-0)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                76. Observation.component:representative-coding-hgvs
                Slice Namerepresentative-coding-hgvs
                Definition

                Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. The use of the nomenclature must be extended to describe non-variations (aka. wild types) see samples for wild type examples.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortDNA change (c.HGVS)Component results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                78. Observation.component:representative-coding-hgvs.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                80. Observation.component:representative-coding-hgvs.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48004-6Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48004-6"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                82. Observation.component:representative-coding-hgvs.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortA valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingThe codes SHALL be taken from For codes, see Human Genome Variation Society (HGVS) Nomenclature
                (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                84. Observation.component:genomic-hgvs
                Slice Namegenomic-hgvs
                Definition

                Description of the genomic (gDNA) sequence change using a valid HGVS-formatted string.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGenomic (gDNA) Change - gHGVSComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                86. Observation.component:genomic-hgvs.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                88. Observation.component:genomic-hgvs.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81290-9Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81290-9"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                90. Observation.component:genomic-hgvs.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dupActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingThe codes SHALL be taken from For codes, see Human Genome Variation Society (HGVS) Nomenclature
                (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                92. Observation.component:cytogenomic-nomenclature
                Slice Namecytogenomic-nomenclature
                Definition

                Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortCytogenomic Nomenclature (ISCN)Component results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                94. Observation.component:cytogenomic-nomenclature.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                96. Observation.component:cytogenomic-nomenclature.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81291-7Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81291-7"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                98. Observation.component:cytogenomic-nomenclature.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                Binding

                Binding not yet defined

                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                100. Observation.component:genomic-ref-seq
                Slice Namegenomic-ref-seq
                Definition

                ID of the genomic reference sequence, which includes transcribed and non transcribed stretches


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGenomic Reference SequenceComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                102. Observation.component:genomic-ref-seq.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                104. Observation.component:genomic-ref-seq.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48013-7Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48013-7"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                106. Observation.component:genomic-ref-seq.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortVersioned genomic reference sequence identifierActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                Binding

                Multiple bindings acceptable (NCBI or LRG)

                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                108. Observation.component:representative-protein-ref-seq
                Slice Namerepresentative-protein-ref-seq
                Definition

                ID of the protein reference sequence, which includes transcribed and non transcribed stretches. It covers the entire protein described.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortProtein Reference SequenceComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                110. Observation.component:representative-protein-ref-seq.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                112. Observation.component:representative-protein-ref-seq.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Shortprotein-ref-seqType of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                    "code" : "protein-ref-seq"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                114. Observation.component:representative-protein-ref-seq.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortVersioned protein reference sequence identifierActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                Binding

                Multiple bindings acceptable (NCBI or LRG)

                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                116. Observation.component:representative-transcript-ref-seq
                Slice Namerepresentative-transcript-ref-seq
                Definition

                NCBI's RefSeq ('NM_...'), Ensembl ('ENST...'), and LRG ('LRG...' plus 't1' to indicate transcript)


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortReference TranscriptComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                118. Observation.component:representative-transcript-ref-seq.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                120. Observation.component:representative-transcript-ref-seq.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short51958-7Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "51958-7"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                122. Observation.component:representative-transcript-ref-seq.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortVersioned transcript reference sequence identifierActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                Binding

                Multiple bindings acceptable (NCBI or LRG)

                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                124. Observation.component:exact-start-end
                Slice Nameexact-start-end
                Definition

                The exact integer-based genomic coordinates of the start and end of the variant region.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortExact Start-EndComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                126. Observation.component:exact-start-end.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                128. Observation.component:exact-start-end.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81254-5Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81254-5"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                130. Observation.component:exact-start-end.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortRange in question. 'High' can be omitted for single nucleotide variants.Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                TypeRange, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                132. Observation.component:inner-start-end
                Slice Nameinner-start-end
                Definition

                The genomic coordinates of the narrowest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortInner Start-EndComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                134. Observation.component:inner-start-end.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                136. Observation.component:inner-start-end.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81302-2Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81302-2"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                138. Observation.component:inner-start-end.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortImprecise variant inner-bounding rangeActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                TypeRange, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                140. Observation.component:outer-start-end
                Slice Nameouter-start-end
                Definition

                The genomic coordinates of the widest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortOuter Start-EndComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                142. Observation.component:outer-start-end.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                144. Observation.component:outer-start-end.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81301-4Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81301-4"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                146. Observation.component:outer-start-end.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortImprecise variant outer-bounding rangeActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                TypeRange, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                148. Observation.component:coordinate-system
                Slice Namecoordinate-system
                Definition

                These are different ways of identifying nucleotides or amino acids within a sequence. In the 1-based system, the first unit of the polymer (e.g. the first nucleotide) is counted as number 1. In the 0-based system, the number 0 designates the location before the first nucleotide. Different databases and file types may use different systems.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortCoordinate SystemComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                150. Observation.component:coordinate-system.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                152. Observation.component:coordinate-system.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short92822-6Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "92822-6"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                154. Observation.component:coordinate-system.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                Short0-based interval counting | 0-based character counting | 1-based character countingActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see LOINC Answer List LL5323-2
                (extensible to http://loinc.org/vs/LL5323-2)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                156. Observation.component:ref-allele
                Slice Nameref-allele
                Definition

                Reference values ('normal') examined within the Reference Sequence.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGenomic Ref AlleleComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                158. Observation.component:ref-allele.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                160. Observation.component:ref-allele.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short69547-8Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "69547-8"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                162. Observation.component:ref-allele.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortNormalized string per the VCF format.Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                Typestring, dateTime, boolean, SampledData, Quantity, Period, Ratio, integer, time, Range, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                164. Observation.component:alt-allele
                Slice Namealt-allele
                Definition

                The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGenomic Alt AlleleComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                166. Observation.component:alt-allele.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                168. Observation.component:alt-allele.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short69551-0Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "69551-0"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                170. Observation.component:alt-allele.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortNormalized string per the VCF format.Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                Typestring, dateTime, boolean, SampledData, Quantity, Period, Ratio, integer, time, Range, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                172. Observation.component:coding-change-type
                Slice Namecoding-change-type
                Definition

                Type of DNA change observed. Convenience property for variants with exact breakpoints, required otherwise.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortCoding DNA Change TypeComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                174. Observation.component:coding-change-type.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                176. Observation.component:coding-change-type.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48019-4Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48019-4"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                178. Observation.component:coding-change-type.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                Shortdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see DNA Change Type
                (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs)

                Concepts in sequence ontology under SO:0002072

                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                180. Observation.component:genomic-source-class
                Slice Namegenomic-source-class
                Definition

                The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGenomic Source ClassComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                182. Observation.component:genomic-source-class.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                184. Observation.component:genomic-source-class.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48002-0Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48002-0"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                186. Observation.component:genomic-source-class.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novoActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see LOINC Answer List LL378-1
                (extensible to http://loinc.org/vs/LL378-1)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                188. Observation.component:sample-allelic-frequency
                Slice Namesample-allelic-frequency
                Definition

                The relative frequency of the allele at a given locus in the sample.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortSample Allelic FrequencyComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                190. Observation.component:sample-allelic-frequency.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                192. Observation.component:sample-allelic-frequency.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81258-6Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81258-6"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                194. Observation.component:sample-allelic-frequency.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortRelative frequency in the sampleActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                TypeQuantity, dateTime, boolean, string, SampledData, Period, Ratio, integer, time, Range, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                196. Observation.component:sample-allelic-frequency.value[x].comparator
                Definition

                How the value should be understood and represented - whether the actual value is greater or less than the stated value due to measurement issues; e.g. if the comparator is "<" , then the real value is < stated value.

                Short< | <= | >= | > - how to understand the value
                Control0..1
                BindingThe codes SHALL be taken from QuantityComparatorhttp://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1
                (required to http://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1)

                How the Quantity should be understood and represented.

                Typecode
                Is Modifiertrue because This is labeled as "Is Modifier" because the comparator modifies the interpretation of the value significantly. If there is no comparator, then there is no modification of the value
                Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                Summarytrue
                Requirements

                Need a framework for handling measures where the value is <5ug/L or >400mg/L due to the limitations of measuring methodology.

                Meaning if MissingIf there is no comparator, then there is no modification of the value
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                198. Observation.component:sample-allelic-frequency.value[x].system
                Definition

                The identification of the system that provides the coded form of the unit.

                ShortSystem that defines coded unit form
                Control0..1
                This element is affected by the following invariants: qty-3
                Typeuri
                Is Modifierfalse
                Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                Summarytrue
                Requirements

                Need to know the system that defines the coded form of the unit.

                Pattern Valuehttp://unitsofmeasure.org
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                200. Observation.component:allelic-read-depth
                Slice Nameallelic-read-depth
                Definition

                Specifies the number of reads that identified the allele in question whether it consists of one or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads to be acceptable. Often >400, sometimes as few as 2-4.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortAllelic Read DepthComponent results
                Comments

                See here for usage guidance.


                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                202. Observation.component:allelic-read-depth.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                204. Observation.component:allelic-read-depth.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short82121-5Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "82121-5"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                206. Observation.component:allelic-read-depth.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortUnfiltered count of supporting readsActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                TypeQuantity, dateTime, boolean, string, SampledData, Period, Ratio, integer, time, Range, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                208. Observation.component:allelic-state
                Slice Nameallelic-state
                Definition

                The observed level of occurrence of the variant in the set of chromosomes.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortAllelic StateComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                210. Observation.component:allelic-state.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                212. Observation.component:allelic-state.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short53034-5Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "53034-5"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                214. Observation.component:allelic-state.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | HemizygousActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see LOINC Answer List LL381-5
                (extensible to http://loinc.org/vs/LL381-5)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                216. Observation.component:variant-inheritance
                Slice Namevariant-inheritance
                Definition

                The source or inheritance of a specific germline variation found in an individual patient.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortOrigin of germline genetic variantComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                218. Observation.component:variant-inheritance.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                220. Observation.component:variant-inheritance.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short94186-4Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "94186-4"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                222. Observation.component:variant-inheritance.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortMaternal | Paternal | UnknownActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see LOINC Answer List LL5489-1
                (extensible to http://loinc.org/vs/LL5489-1)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                224. Observation.component:variant-inheritance-basis
                Slice Namevariant-inheritance-basis
                Definition

                The method by which the variant inheritance is determined.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortEvidential basis for variant inheritanceComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                226. Observation.component:variant-inheritance-basis.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                228. Observation.component:variant-inheritance-basis.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                ShortBasis for allelic phaseType of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "82309-6"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                230. Observation.component:variant-inheritance-basis.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortDirectly measured | Family DNA | Family history | Inferred from population dataActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingUnless not suitable, these codes SHALL be taken from For codes, see LOINC Answer List LL4050-2
                (extensible to http://loinc.org/vs/LL4050-2)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                232. Observation.component:variation-code
                Slice Namevariation-code
                Definition

                Accession number in a variant database such as ClinVar, given for cross-reference.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortVariation CodeComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                234. Observation.component:variation-code.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                236. Observation.component:variation-code.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short81252-9Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "81252-9"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                238. Observation.component:variation-code.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortClinVar ID or similarActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                Binding

                Multiple bindings acceptable

                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                240. Observation.component:representative-protein-hgvs
                Slice Namerepresentative-protein-hgvs
                Definition

                Description of the protein (amino acid) sequence change using a valid HGVS-formatted string. The description of the variant is surrounded in parentheses if it is calculated rather than directly observed.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortProtein (Amino Acid) Change - pHGVSComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                242. Observation.component:representative-protein-hgvs.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                244. Observation.component:representative-protein-hgvs.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short48005-3Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "48005-3"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                246. Observation.component:representative-protein-hgvs.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)Actual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingThe codes SHALL be taken from For codes, see Human Genome Variation Society (HGVS) Nomenclature
                (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                248. Observation.component:copy-number
                Slice Namecopy-number
                Definition

                The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. If the value determined by the assay is not a whole number, a range or decimal number can be specified. Note that a copy number of 1 can imply a deletion.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortGenomic Structural Variant Copy NumberComponent results
                Comments

                Copy number variants are often described with a single copy number value. However, due to the nature of assays, such as qPCR and microarray, it can be difficult to assign an exact copy number. Therefore, labs sometimes report a range instead of an exact copy number. They may alternatively choose to report decimal numbers, even if whole numbers are biologically correct.

                In general, it can be difficult to estimate a copy number from measurements taken on a heterogenous population of cells, such as a tumor. As indicated in the ISCN 2020 specifications, it is appropriate to express the measurements using a range. Furthermore, regardless of cell population, many assays use fluorescent probes to detect copy number. These testing methodologies do not always provide an exact, discrete value for this data point.


                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM.


                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                250. Observation.component:copy-number.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                252. Observation.component:copy-number.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Short82155-3Type of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://loinc.org",
                    "code" : "82155-3"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                254. Observation.component:copy-number.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control0..1
                TypeChoice of: Quantity, Range, dateTime, boolean, string, SampledData, Period, Ratio, integer, time, CodeableConcept
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                256. Observation.component:variant-confidence-status
                Slice Namevariant-confidence-status
                Definition

                A code that represents the confidence of a true positive variant call.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortVariant Confidence StatusComponent results
                Comments

                See here for usage guidance.


                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..1*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                258. Observation.component:variant-confidence-status.modifierExtension
                Definition

                May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                ShortExtensions that cannot be ignored even if unrecognized
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                Summarytrue
                Requirements

                Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                Alternate Namesextensions, user content, modifiers
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                260. Observation.component:variant-confidence-status.code
                Definition

                Describes what was observed. Sometimes this is called the observation "code".

                Shortvariant-confidence-statusType of component observation (code / type)
                Comments

                All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                Control1..1
                BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                (example to http://hl7.org/fhir/ValueSet/observation-codes)

                Codes identifying names of simple observations.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Requirements

                Knowing what kind of observation is being made is essential to understanding the observation.

                Pattern Value{
                  "coding" : [{
                    "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                    "code" : "variant-confidence-status"
                  }]
                }
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                262. Observation.component:variant-confidence-status.value[x]
                Definition

                The information determined as a result of making the observation, if the information has a simple value.

                ShortHigh | Intermediate | LowActual component result
                Comments

                Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                Control10..1
                BindingThe codes SHALL be taken from For codes, see Variant Confidence Status
                (required to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs)
                TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summarytrue
                Requirements

                An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                264. Observation.component:repeat-motif
                Slice Namerepeat-motif
                Definition

                Nucleotides of a repeat expansion motif.


                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                ShortRepeat MotifComponent results
                Comments

                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                Control0..*
                TypeBackboneElement
                Is Modifierfalse
                Summarytrue
                Requirements

                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                266. Observation.component:repeat-motif.extension
                Definition

                An Extension


                May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                ShortExtensionAdditional content defined by implementations
                Comments

                There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                Control0..*
                TypeExtension
                Is Modifierfalse
                Summaryfalse
                Alternate Namesextensions, user content
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                SlicingThis element introduces a set of slices on Observation.component.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                • value @ url
                • 268. Observation.component:repeat-motif.extension:repeat-motif-order
                  Slice Namerepeat-motif-order
                  Definition

                  Use to group and order repeat expansion motifs.

                  ShortRepeat Motif Order
                  Comments

                  If there are multiple repeat expansion pairs, this must be used both to indicate the sequence position of a given repeat-motif and repeat-number pair and to group the related components together. Components with the same extension value describe the same motif.

                  Control0..1
                  This element is affected by the following invariants: ele-1
                  TypeExtension(Repeat Motif Order) (Extension Type: positiveInt)
                  Is Modifierfalse
                  Requirements

                  The value must be a natural number starting from 1 and increasing sequentially

                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                  270. Observation.component:repeat-motif.modifierExtension
                  Definition

                  May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                  Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                  ShortExtensions that cannot be ignored even if unrecognized
                  Comments

                  There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                  Control0..*
                  TypeExtension
                  Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                  Summarytrue
                  Requirements

                  Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                  Alternate Namesextensions, user content, modifiers
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                  272. Observation.component:repeat-motif.code
                  Definition

                  Describes what was observed. Sometimes this is called the observation "code".

                  Shortrepeat-motifType of component observation (code / type)
                  Comments

                  All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                  Control1..1
                  BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                  (example to http://hl7.org/fhir/ValueSet/observation-codes)

                  Codes identifying names of simple observations.

                  TypeCodeableConcept
                  Is Modifierfalse
                  Summarytrue
                  Requirements

                  Knowing what kind of observation is being made is essential to understanding the observation.

                  Pattern Value{
                    "coding" : [{
                      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                      "code" : "repeat-motif"
                    }]
                  }
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  274. Observation.component:repeat-motif.value[x]
                  Definition

                  The information determined as a result of making the observation, if the information has a simple value.

                  ShortCAGActual component result
                  Comments

                  Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                  Control10..1
                  Typestring, dateTime, boolean, SampledData, Quantity, Period, Ratio, integer, time, Range, CodeableConcept
                  [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                  Is Modifierfalse
                  Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                  Summarytrue
                  Requirements

                  An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  276. Observation.component:repeat-number
                  Slice Namerepeat-number
                  Definition

                  Number of repeats of a repeat expansion.


                  Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                  ShortRepeat NumberComponent results
                  Comments

                  For a discussion on the ways Observations can be assembled in groups together see Notes below.

                  Control0..*
                  TypeBackboneElement
                  Is Modifierfalse
                  Summarytrue
                  Requirements

                  Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  278. Observation.component:repeat-number.extension
                  Definition

                  An Extension


                  May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                  ShortExtensionAdditional content defined by implementations
                  Comments

                  There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                  Control0..*
                  TypeExtension
                  Is Modifierfalse
                  Summaryfalse
                  Alternate Namesextensions, user content
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                  SlicingThis element introduces a set of slices on Observation.component.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                  • value @ url
                  • 280. Observation.component:repeat-number.extension:repeat-motif-order
                    Slice Namerepeat-motif-order
                    Definition

                    Use to group and order repeat expansion motifs.

                    ShortRepeat Motif Order
                    Comments

                    If there are multiple repeat expansion pairs, this must be used both to indicate the sequence position of a given repeat-motif and repeat-number pair and to group the related components together. Components with the same extension value describe the same motif.

                    Control0..1
                    This element is affected by the following invariants: ele-1
                    TypeExtension(Repeat Motif Order) (Extension Type: positiveInt)
                    Is Modifierfalse
                    Requirements

                    The value must be a natural number starting from 1 and increasing sequentially

                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                    282. Observation.component:repeat-number.modifierExtension
                    Definition

                    May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                    Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                    ShortExtensions that cannot be ignored even if unrecognized
                    Comments

                    There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                    Control0..*
                    TypeExtension
                    Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                    Summarytrue
                    Requirements

                    Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                    Alternate Namesextensions, user content, modifiers
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                    284. Observation.component:repeat-number.code
                    Definition

                    Describes what was observed. Sometimes this is called the observation "code".

                    Shortrepeat-numberType of component observation (code / type)
                    Comments

                    All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                    Control1..1
                    BindingFor example codes, see LOINCCodeshttp://hl7.org/fhir/ValueSet/observation-codes
                    (example to http://hl7.org/fhir/ValueSet/observation-codes)

                    Codes identifying names of simple observations.

                    TypeCodeableConcept
                    Is Modifierfalse
                    Summarytrue
                    Requirements

                    Knowing what kind of observation is being made is essential to understanding the observation.

                    Pattern Value{
                      "coding" : [{
                        "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                        "code" : "repeat-number"
                      }]
                    }
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    286. Observation.component:repeat-number.value[x]
                    Definition

                    The information determined as a result of making the observation, if the information has a simple value.

                    Short40Actual component result
                    Comments

                    Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                    Control10..1
                    TypeQuantity, dateTime, boolean, string, SampledData, Period, Ratio, integer, time, Range, CodeableConcept
                    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                    Is Modifierfalse
                    Summarytrue
                    Requirements

                    An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))

                    Guidance on how to interpret the contents of this table can be found here

                    0. Observation
                    Definition

                    Measurements and simple assertions made about a patient, device or other subject.

                    ShortVariant
                    Comments

                    Used for simple observations such as device measurements, laboratory atomic results, vital signs, height, weight, smoking status, comments, etc. Other resources are used to provide context for observations such as laboratory reports, etc.

                    Control0..*
                    Is Modifierfalse
                    Summaryfalse
                    Alternate NamesVital Signs, Measurement, Results, Tests
                    Invariantsdom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (contained.contained.empty())
                    dom-3: 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: 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: If a resource is contained in another resource, it SHALL NOT have a security label (contained.meta.security.empty())
                    dom-6: A resource should have narrative for robust management (text.`div`.exists())
                    obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present (dataAbsentReason.empty() or value.empty())
                    obs-7: 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())
                    2. Observation.id
                    Definition

                    The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

                    ShortLogical id of this artifact
                    Comments

                    The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

                    Control0..1
                    Typeid
                    Is Modifierfalse
                    Summarytrue
                    4. Observation.meta
                    Definition

                    The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.

                    ShortMetadata about the resource
                    Control0..1
                    TypeMeta
                    Is Modifierfalse
                    Summarytrue
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    6. Observation.implicitRules
                    Definition

                    A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

                    ShortA set of rules under which this content was created
                    Comments

                    Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc.

                    Control0..1
                    Typeuri
                    Is Modifiertrue because This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation
                    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                    Summarytrue
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    8. Observation.language
                    Definition

                    The base language in which the resource is written.

                    ShortLanguage of the resource content
                    Comments

                    Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).

                    Control0..1
                    BindingThe codes SHOULD be taken from CommonLanguages
                    (preferred to http://hl7.org/fhir/ValueSet/languages)

                    A human language.

                    Additional BindingsPurpose
                    AllLanguagesMax Binding
                    Typecode
                    Is Modifierfalse
                    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                    Summaryfalse
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    10. Observation.text
                    Definition

                    A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.

                    ShortText summary of the resource, for human interpretation
                    Comments

                    Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.

                    Control0..1
                    TypeNarrative
                    Is Modifierfalse
                    Summaryfalse
                    Alternate Namesnarrative, html, xhtml, display
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    12. Observation.contained
                    Definition

                    These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

                    ShortContained, inline Resources
                    Comments

                    This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.

                    Control0..*
                    TypeResource
                    Is Modifierfalse
                    Summaryfalse
                    Alternate Namesinline resources, anonymous resources, contained resources
                    14. Observation.extension
                    Definition

                    An Extension

                    ShortExtension
                    Control0..*
                    TypeExtension
                    Is Modifierfalse
                    Summaryfalse
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                    SlicingThis element introduces a set of slices on Observation.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                    • value @ url
                    • 16. Observation.extension:secondary-finding
                      Slice Namesecondary-finding
                      Definition

                      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) or Whole Genome Sequencing (WGS) 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.

                      ShortSecondary 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
                      Control0..1
                      TypeExtension(Observation Secondary Finding) (Extension Type: CodeableConcept)
                      Is Modifierfalse
                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                      18. Observation.extension:body-structure
                      Slice Namebody-structure
                      Definition

                      Record details about the anatomical location of a specimen or body part. This resource may be used when a coded concept does not provide the necessary detail needed for the use case.

                      ShortTarget anatomic location or structure
                      Control0..1
                      TypeExtension(BodyStructure Reference) (Extension Type: Reference(BodyStructure))
                      Is Modifierfalse
                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                      20. Observation.modifierExtension
                      Definition

                      May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                      Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                      ShortExtensions that cannot be ignored
                      Comments

                      There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                      Control0..*
                      TypeExtension
                      Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
                      Summaryfalse
                      Requirements

                      Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                      Alternate Namesextensions, user content
                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                      22. Observation.identifier
                      Definition

                      A unique identifier assigned to this observation.

                      ShortBusiness Identifier for observation
                      NoteThis is a business identifier, not a resource identifier (see discussion)
                      Control0..*
                      TypeIdentifier
                      Is Modifierfalse
                      Summarytrue
                      Requirements

                      Allows observations to be distinguished and referenced.

                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      24. Observation.basedOn
                      Definition

                      A plan, proposal or order that is fulfilled in whole or in part by this event. For example, a MedicationRequest may require a patient to have laboratory test performed before it is dispensed.

                      ShortFulfills plan, proposal or order
                      Control0..*
                      TypeReference(CarePlan, DeviceRequest, ImmunizationRecommendation, MedicationRequest, NutritionOrder, ServiceRequest)
                      Is Modifierfalse
                      Summarytrue
                      Requirements

                      Allows tracing of authorization for the event and tracking whether proposals/recommendations were acted upon.

                      Alternate NamesFulfills
                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      26. Observation.partOf
                      Definition

                      A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.

                      ShortPart of referenced event
                      Comments

                      To link an Observation to an Encounter use encounter. See the Notes below for guidance on referencing another Observation.

                      Control0..*
                      TypeReference(MedicationAdministration, MedicationDispense, MedicationStatement, Procedure, Immunization, ImagingStudy, Genomic Study)
                      Is Modifierfalse
                      Summarytrue
                      Alternate NamesContainer
                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      28. Observation.status
                      Definition

                      The status of the result value.

                      Shortregistered | preliminary | final | amended +
                      Comments

                      This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.

                      Control1..1
                      BindingThe codes SHALL be taken from ObservationStatus
                      (required to http://hl7.org/fhir/ValueSet/observation-status|4.0.1)

                      Codes providing the status of an observation.

                      Typecode
                      Is Modifiertrue because This element is labeled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid
                      Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                      Summarytrue
                      Requirements

                      Need to track the status of individual results. Some results are finalized before the whole report is finalized.

                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      30. Observation.category
                      Definition

                      A code that classifies the general type of observation being made.

                      ShortClassification of type of observation
                      Comments

                      In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

                      Control2..*
                      BindingThe codes SHOULD be taken from ObservationCategoryCodes
                      (preferred to http://hl7.org/fhir/ValueSet/observation-category)

                      Codes for high level observation categories.

                      TypeCodeableConcept
                      Is Modifierfalse
                      Summaryfalse
                      Requirements

                      Used for filtering what observations are retrieved and displayed.

                      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                      SlicingThis element introduces a set of slices on Observation.category. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                      • value @ coding
                      • 32. Observation.category:labCategory
                        Slice NamelabCategory
                        Definition

                        A code that classifies the general type of observation being made.

                        ShortClassification of type of observation
                        Comments

                        In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

                        Control1..1
                        BindingThe codes SHOULD be taken from ObservationCategoryCodes
                        (preferred to http://hl7.org/fhir/ValueSet/observation-category)

                        Codes for high level observation categories.

                        TypeCodeableConcept
                        Is Modifierfalse
                        Summaryfalse
                        Requirements

                        Used for filtering what observations are retrieved and displayed.

                        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                        34. Observation.category:labCategory.id
                        Definition

                        Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                        ShortUnique id for inter-element referencing
                        Control0..1
                        Typestring
                        Is Modifierfalse
                        XML FormatIn the XML format, this property is represented as an attribute.
                        Summaryfalse
                        36. Observation.category:labCategory.extension
                        Definition

                        May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                        ShortAdditional content defined by implementations
                        Comments

                        There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                        Control0..*
                        TypeExtension
                        Is Modifierfalse
                        Summaryfalse
                        Alternate Namesextensions, user content
                        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                        SlicingThis element introduces a set of slices on Observation.category.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                        • value @ url
                        • 38. Observation.category:labCategory.coding
                          Definition

                          A reference to a code defined by a terminology system.

                          ShortCode defined by a terminology system
                          Comments

                          Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

                          Control1..1
                          TypeCoding
                          Is Modifierfalse
                          Summarytrue
                          Requirements

                          Allows for alternative encodings within a code system, and translations to other code systems.

                          Pattern Value{
                            "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
                            "code" : "laboratory"
                          }
                          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                          40. Observation.category:labCategory.text
                          Definition

                          A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

                          ShortPlain text representation of the concept
                          Comments

                          Very often the text is the same as a displayName of one of the codings.

                          Control0..1
                          Typestring
                          Is Modifierfalse
                          Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                          Summarytrue
                          Requirements

                          The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.

                          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                          42. Observation.category:geCategory
                          Slice NamegeCategory
                          Definition

                          A code that classifies the general type of observation being made.

                          ShortClassification of type of observation
                          Comments

                          In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

                          Control1..1
                          BindingThe codes SHOULD be taken from ObservationCategoryCodes
                          (preferred to http://hl7.org/fhir/ValueSet/observation-category)

                          Codes for high level observation categories.

                          TypeCodeableConcept
                          Is Modifierfalse
                          Summaryfalse
                          Requirements

                          Used for filtering what observations are retrieved and displayed.

                          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                          44. Observation.category:geCategory.id
                          Definition

                          Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                          ShortUnique id for inter-element referencing
                          Control0..1
                          Typestring
                          Is Modifierfalse
                          XML FormatIn the XML format, this property is represented as an attribute.
                          Summaryfalse
                          46. Observation.category:geCategory.extension
                          Definition

                          May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                          ShortAdditional content defined by implementations
                          Comments

                          There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                          Control0..*
                          TypeExtension
                          Is Modifierfalse
                          Summaryfalse
                          Alternate Namesextensions, user content
                          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                          ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                          SlicingThis element introduces a set of slices on Observation.category.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                          • value @ url
                          • 48. Observation.category:geCategory.coding
                            Definition

                            A reference to a code defined by a terminology system.

                            ShortCode defined by a terminology system
                            Comments

                            Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

                            Control1..1
                            TypeCoding
                            Is Modifierfalse
                            Summarytrue
                            Requirements

                            Allows for alternative encodings within a code system, and translations to other code systems.

                            Pattern Value{
                              "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
                              "code" : "GE"
                            }
                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            50. Observation.category:geCategory.text
                            Definition

                            A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

                            ShortPlain text representation of the concept
                            Comments

                            Very often the text is the same as a displayName of one of the codings.

                            Control0..1
                            Typestring
                            Is Modifierfalse
                            Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                            Summarytrue
                            Requirements

                            The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.

                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            52. Observation.code
                            Definition

                            Describes what was observed. Sometimes this is called the observation "name".

                            Short69548-6
                            Comments

                            All code-value and, if present, component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                            Control1..1
                            BindingFor example codes, see LOINCCodes
                            (example to http://hl7.org/fhir/ValueSet/observation-codes)

                            Codes identifying names of simple observations.

                            TypeCodeableConcept
                            Is Modifierfalse
                            Summarytrue
                            Requirements

                            Knowing what kind of observation is being made is essential to understanding the observation.

                            Alternate NamesName
                            Pattern Value{
                              "coding" : [{
                                "system" : "http://loinc.org",
                                "code" : "69548-6"
                              }]
                            }
                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            54. Observation.subject
                            Definition

                            The patient, or group of patients, location, or device this observation is about and into whose record the observation is placed. If the actual focus of the observation is different from the subject (or a sample of, part, or region of the subject), the focus element or the code itself specifies the actual focus of the observation.

                            ShortWho and/or what the observation is about
                            Comments

                            One would expect this element to be a cardinality of 1..1. The only circumstance in which the subject can be missing is when the observation is made by a device that does not know the patient. In this case, the observation SHALL be matched to a patient through some context/channel matching technique, and at this point, the observation should be updated.

                            Control0..1
                            TypeReference(Patient, Group, Device, Location)
                            Is Modifierfalse
                            Summarytrue
                            Requirements

                            Observations have no value if you don't know who or what they're about.

                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            56. Observation.focus
                            Definition

                            The actual focus of an observation when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, fetus, or donor. For example, fetus observations in a mother's record. The focus of an observation could also be an existing condition, an intervention, the subject's diet, another observation of the subject, or a body structure such as tumor or implanted device. An example use case would be using the Observation resource to capture whether the mother is trained to change her child's tracheostomy tube. In this example, the child is the patient of record and the mother is the focus.

                            ShortWhat the observation is about, when it is not about the subject of record
                            Comments

                            Typically, an observation is made about the subject - a patient, or group of patients, location, or device - and the distinction between the subject and what is directly measured for an observation is specified in the observation code itself ( e.g., "Blood Glucose") and does not need to be represented separately using this element. Use specimen if a reference to a specimen is required. If a code is required instead of a resource use either bodysite for bodysites or the standard extension focusCode.

                            Control0..*
                            TypeReference(Resource)
                            Is Modifierfalse
                            Summarytrue
                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            58. Observation.encounter
                            Definition

                            The healthcare event (e.g. a patient and healthcare provider interaction) during which this observation is made.

                            ShortHealthcare event during which this observation is made
                            Comments

                            This will typically be the encounter the event occurred within, but some events may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter (e.g. pre-admission laboratory tests).

                            Control0..1
                            TypeReference(Encounter)
                            Is Modifierfalse
                            Summarytrue
                            Requirements

                            For some observations it may be important to know the link between an observation and a particular encounter.

                            Alternate NamesContext
                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            60. Observation.effective[x]
                            Definition

                            The time or time-period the observed value is asserted as being true. For biological subjects - e.g. human patients - this is usually called the "physiologically relevant time". This is usually either the time of the procedure or of specimen collection, but very often the source of the date/time is not known, only the date/time itself.

                            ShortClinically relevant time/time-period for observation
                            Comments

                            At least a date should be present unless this observation is a historical report. For recording imprecise or "fuzzy" times (For example, a blood glucose measurement taken "after breakfast") use the Timing datatype which allow the measurement to be tied to regular life events.

                            Control0..1
                            TypeChoice of: dateTime, Period, Timing, instant
                            [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                            Is Modifierfalse
                            Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                            Summarytrue
                            Requirements

                            Knowing when an observation was deemed true is important to its relevance as well as determining trends.

                            Alternate NamesOccurrence
                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            62. Observation.issued
                            Definition

                            The date and time this version of the observation was made available to providers, typically after the results have been reviewed and verified.

                            ShortDate/Time this version was made available
                            Comments

                            For Observations that don’t require review and verification, it may be the same as the lastUpdated time of the resource itself. For Observations that do require review and verification for certain updates, it might not be the same as the lastUpdated time of the resource itself due to a non-clinically significant update that doesn’t require the new version to be reviewed and verified again.

                            Control0..1
                            Typeinstant
                            Is Modifierfalse
                            Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                            Summarytrue
                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            64. Observation.performer
                            Definition

                            Who was responsible for asserting the observed value as "true".

                            ShortWho is responsible for the observation
                            Control0..*
                            TypeReference(Practitioner, PractitionerRole, Organization, CareTeam, Patient, RelatedPerson)
                            Is Modifierfalse
                            Summarytrue
                            Requirements

                            May give a degree of confidence in the observation and also indicates where follow-up questions should be directed.

                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            66. Observation.value[x]
                            Definition

                            The information determined as a result of making the observation, if the information has a simple value.

                            ShortActual result
                            Comments

                            An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                            Control0..1
                            This element is affected by the following invariants: obs-7
                            TypeChoice of: Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
                            [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                            Is Modifierfalse
                            Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                            Summarytrue
                            Requirements

                            An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                            SlicingThis element introduces a set of slices on Observation.value[x]. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                            • type @ $this
                            • 68. Observation.value[x]:valueCodeableConcept
                              Slice NamevalueCodeableConcept
                              Definition

                              The presence or absence of the variant described in the components. If not searching for specific variations and merely reporting what's found, the profile's value should be set to 'Present'.

                              ShortIndeterminate | No call | Present | Absent.
                              Comments

                              See here for usage guidance.

                              Control0..1
                              This element is affected by the following invariants: obs-7
                              BindingThe codes SHALL be taken from LOINC Answer List LL1971-2
                              (required to http://loinc.org/vs/LL1971-2)
                              TypeCodeableConcept
                              [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                              Is Modifierfalse
                              Summarytrue
                              Requirements

                              An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              70. Observation.dataAbsentReason
                              Definition

                              Provides a reason why the expected value in the element Observation.value[x] is missing.

                              ShortWhy the result is missing
                              Comments

                              Null or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be "detected", "not detected", "inconclusive", or "specimen unsatisfactory".

                              The alternate way is to use the value element for actual observations and use the explicit dataAbsentReason element to record exceptional values. For example, the dataAbsentReason code "error" could be used when the measurement was not completed. Note that an observation may only be reported if there are values to report. For example differential cell counts values may be reported only when > 0. Because of these options, use-case agreements are required to interpret general observations for null or exceptional values.

                              Control0..1
                              This element is affected by the following invariants: obs-6
                              BindingUnless not suitable, these codes SHALL be taken from DataAbsentReason
                              (extensible to http://hl7.org/fhir/ValueSet/data-absent-reason)

                              Codes specifying why the result (Observation.value[x]) is missing.

                              TypeCodeableConcept
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              For many results it is necessary to handle exceptional values in measurements.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              72. Observation.interpretation
                              Definition

                              A categorical assessment of an observation value. For example, high, low, normal.

                              ShortHigh, low, normal, etc.
                              Comments

                              Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.

                              Control0..*
                              BindingUnless not suitable, these codes SHALL be taken from ObservationInterpretationCodes
                              (extensible to http://hl7.org/fhir/ValueSet/observation-interpretation)

                              Codes identifying interpretations of observations.

                              TypeCodeableConcept
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

                              Alternate NamesAbnormal Flag
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              74. Observation.note
                              Definition

                              A text note which also contains information about who made the statement and when.

                              ShortComments about the Observation that also contain a coded type
                              Comments

                              May include general statements about the observation, or statements about significant, unexpected or unreliable results values, or information about its source when relevant to its interpretation. The CodedAnnotation data type, while not allowing for or intending to make the content computable, does allow the author to indicate the type of note. This does not replace the use of interpretation, value, or component values. One important note is that Annotation is a FHIR data type, this is NOT about annotations in the genomic context.

                              Control0..*
                              This element is affected by the following invariants: ele-1
                              TypeAnnotation(Coded Annotation)
                              Is Modifierfalse
                              Requirements

                              Need to be able to provide free text additional information. Notes SHALL NOT contain information which can be captured in a structured way.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              76. Observation.bodySite
                              Definition

                              Indicates the site on the subject's body where the observation was made (i.e. the target site).

                              ShortObserved body part
                              Comments

                              Only used if not implicit in code found in Observation.code. In many systems, this may be represented as a related observation instead of an inline component.

                              If the use case requires BodySite to be handled as a separate resource (e.g. to identify and track separately) then use the standard extension bodySite.

                              Control0..1
                              BindingFor example codes, see SNOMEDCTBodyStructures
                              (example to http://hl7.org/fhir/ValueSet/body-site)

                              Codes describing anatomical locations. May include laterality.

                              TypeCodeableConcept
                              Is Modifierfalse
                              Summaryfalse
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              78. Observation.method
                              Definition

                              Indicates the mechanism used to perform the observation.

                              ShortSequencing | SNP array | PCR | Computational analysis | ...
                              Comments

                              Only used if not implicit in code for Observation.code.

                              Control0..1
                              BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL4048-6
                              (extensible to http://loinc.org/vs/LL4048-6)
                              TypeCodeableConcept
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              In some cases, method can impact results and is thus used for determining whether results can be compared or determining significance of results.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              80. Observation.specimen
                              Definition

                              The specimen that was used when this observation was made.

                              ShortSpecimen used for this observation
                              Comments

                              Should only be used if not implicit in code found in Observation.code. Observations are not made on specimens themselves; they are made on a subject, but in many cases by the means of a specimen. Note that although specimens are often involved, they are not always tracked and reported explicitly. Also note that observation resources may be used in contexts that track the specimen explicitly (e.g. Diagnostic Report).

                              Control0..1
                              TypeReference(Specimen)
                              Is Modifierfalse
                              Summaryfalse
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              82. Observation.device
                              Definition

                              The device used to generate the observation data.

                              Short(Measurement) Device
                              Comments

                              Note that this is not meant to represent a device involved in the transmission of the result, e.g., a gateway. Such devices may be documented using the Provenance resource where relevant.

                              Control0..1
                              TypeReference(Device, DeviceMetric)
                              Is Modifierfalse
                              Summaryfalse
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              84. Observation.referenceRange
                              Definition

                              Guidance on how to interpret the value by comparison to a normal or recommended range. Multiple reference ranges are interpreted as an "OR". In other words, to represent two distinct target populations, two referenceRange elements would be used.

                              ShortProvides guide for interpretation
                              Comments

                              Most observations only have one generic reference range. Systems MAY choose to restrict to only supplying the relevant reference range based on knowledge about the patient (e.g., specific to the patient's age, gender, weight and other factors), but this might not be possible or appropriate. Whenever more than one reference range is supplied, the differences between them SHOULD be provided in the reference range and/or age properties.

                              Control0..*
                              TypeBackboneElement
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              obs-3: Must have at least a low or a high or text (low.exists() or high.exists() or text.exists())
                              86. Observation.referenceRange.id
                              Definition

                              Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                              ShortUnique id for inter-element referencing
                              Control0..1
                              Typestring
                              Is Modifierfalse
                              XML FormatIn the XML format, this property is represented as an attribute.
                              Summaryfalse
                              88. Observation.referenceRange.extension
                              Definition

                              May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                              ShortAdditional content defined by implementations
                              Comments

                              There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                              Control0..*
                              TypeExtension
                              Is Modifierfalse
                              Summaryfalse
                              Alternate Namesextensions, user content
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                              90. Observation.referenceRange.modifierExtension
                              Definition

                              May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                              Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                              ShortExtensions that cannot be ignored even if unrecognized
                              Comments

                              There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                              Control0..*
                              TypeExtension
                              Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                              Summarytrue
                              Requirements

                              Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                              Alternate Namesextensions, user content, modifiers
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                              92. Observation.referenceRange.low
                              Definition

                              The value of the low bound of the reference range. The low bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the low bound is omitted, it is assumed to be meaningless (e.g. reference range is <=2.3).

                              ShortLow Range, if relevant
                              Control0..1
                              This element is affected by the following invariants: obs-3
                              TypeQuantity(SimpleQuantity)
                              Is Modifierfalse
                              Summaryfalse
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              94. Observation.referenceRange.high
                              Definition

                              The value of the high bound of the reference range. The high bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the high bound is omitted, it is assumed to be meaningless (e.g. reference range is >= 2.3).

                              ShortHigh Range, if relevant
                              Control0..1
                              This element is affected by the following invariants: obs-3
                              TypeQuantity(SimpleQuantity)
                              Is Modifierfalse
                              Summaryfalse
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              96. Observation.referenceRange.type
                              Definition

                              Codes to indicate the what part of the targeted reference population it applies to. For example, the normal or therapeutic range.

                              ShortReference range qualifier
                              Comments

                              This SHOULD be populated if there is more than one range. If this element is not present then the normal range is assumed.

                              Control0..1
                              BindingThe codes SHOULD be taken from ObservationReferenceRangeMeaningCodes
                              (preferred to http://hl7.org/fhir/ValueSet/referencerange-meaning)

                              Code for the meaning of a reference range.

                              TypeCodeableConcept
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              Need to be able to say what kind of reference range this is - normal, recommended, therapeutic, etc., - for proper interpretation.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              98. Observation.referenceRange.appliesTo
                              Definition

                              Codes to indicate the target population this reference range applies to. For example, a reference range may be based on the normal population or a particular sex or race. Multiple appliesTo are interpreted as an "AND" of the target populations. For example, to represent a target population of African American females, both a code of female and a code for African American would be used.

                              ShortReference range population
                              Comments

                              This SHOULD be populated if there is more than one range. If this element is not present then the normal population is assumed.

                              Control0..*
                              BindingFor example codes, see ObservationReferenceRangeAppliesToCodes
                              (example to http://hl7.org/fhir/ValueSet/referencerange-appliesto)

                              Codes identifying the population the reference range applies to.

                              TypeCodeableConcept
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              Need to be able to identify the target population for proper interpretation.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              100. Observation.referenceRange.age
                              Definition

                              The age at which this reference range is applicable. This is a neonatal age (e.g. number of weeks at term) if the meaning says so.

                              ShortApplicable age range, if relevant
                              Control0..1
                              TypeRange
                              Is Modifierfalse
                              Summaryfalse
                              Requirements

                              Some analytes vary greatly over age.

                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              102. Observation.referenceRange.text
                              Definition

                              Text based reference range in an observation which may be used when a quantitative range is not appropriate for an observation. An example would be a reference value of "Negative" or a list or table of "normals".

                              ShortText based reference range in an observation
                              Control0..1
                              Typestring
                              Is Modifierfalse
                              Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                              Summaryfalse
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              104. Observation.hasMember
                              Definition

                              This observation is a group observation (e.g. a battery, a panel of tests, a set of vital sign measurements) that includes the target as a member of the group.

                              ShortRelated resource that belongs to the Observation group
                              Comments

                              When using this element, an observation will typically have either a value or a set of related resources, although both may be present in some cases. For a discussion on the ways Observations can assembled in groups together, see Notes below. Note that a system may calculate results from QuestionnaireResponse into a final score and represent the score as an Observation.

                              Control0..*
                              TypeReference(Observation, QuestionnaireResponse, MolecularSequence)
                              Is Modifierfalse
                              Summarytrue
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              106. Observation.derivedFrom
                              Definition

                              The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

                              ShortRelated measurements the observation is made from
                              Comments

                              All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

                              Control0..*
                              TypeReference(DocumentReference, ImagingStudy, Media, QuestionnaireResponse, Observation, MolecularSequence)
                              Is Modifierfalse
                              Summarytrue
                              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                              SlicingThis element introduces a set of slices on Observation.derivedFrom. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                              • profile @ resolve()
                              • 108. Observation.component
                                Definition

                                Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

                                ShortComponent results
                                Comments

                                For a discussion on the ways Observations can be assembled in groups together see Notes below.

                                Control0..*
                                TypeBackboneElement
                                Is Modifierfalse
                                Summarytrue
                                Requirements

                                Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

                                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                SlicingThis element introduces a set of slices on Observation.component. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                                • value @ code
                                • 110. Observation.component.id
                                  Definition

                                  Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                                  ShortUnique id for inter-element referencing
                                  Control0..1
                                  Typestring
                                  Is Modifierfalse
                                  XML FormatIn the XML format, this property is represented as an attribute.
                                  Summaryfalse
                                  112. Observation.component.extension
                                  Definition

                                  May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                                  ShortAdditional content defined by implementations
                                  Comments

                                  There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                                  Control0..*
                                  TypeExtension
                                  Is Modifierfalse
                                  Summaryfalse
                                  Alternate Namesextensions, user content
                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                                  114. Observation.component.modifierExtension
                                  Definition

                                  May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                                  Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                                  ShortExtensions that cannot be ignored even if unrecognized
                                  Comments

                                  There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                                  Control0..*
                                  TypeExtension
                                  Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                                  Summarytrue
                                  Requirements

                                  Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                                  Alternate Namesextensions, user content, modifiers
                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                                  116. Observation.component.code
                                  Definition

                                  Describes what was observed. Sometimes this is called the observation "code".

                                  ShortType of component observation (code / type)
                                  Comments

                                  All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                                  Control1..1
                                  BindingFor example codes, see LOINCCodes
                                  (example to http://hl7.org/fhir/ValueSet/observation-codes)

                                  Codes identifying names of simple observations.

                                  TypeCodeableConcept
                                  Is Modifierfalse
                                  Summarytrue
                                  Requirements

                                  Knowing what kind of observation is being made is essential to understanding the observation.

                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  118. Observation.component.value[x]
                                  Definition

                                  The information determined as a result of making the observation, if the information has a simple value.

                                  ShortActual component result
                                  Comments

                                  Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

                                  Control0..1
                                  TypeChoice of: Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period
                                  [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                                  Is Modifierfalse
                                  Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                                  Summarytrue
                                  Requirements

                                  An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  120. Observation.component.dataAbsentReason
                                  Definition

                                  Provides a reason why the expected value in the element Observation.component.value[x] is missing.

                                  ShortWhy the component result is missing
                                  Comments

                                  "Null" or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be "detected", "not detected", "inconclusive", or "test not done".

                                  The alternate way is to use the value element for actual observations and use the explicit dataAbsentReason element to record exceptional values. For example, the dataAbsentReason code "error" could be used when the measurement was not completed. Because of these options, use-case agreements are required to interpret general observations for exceptional values.

                                  Control0..1
                                  This element is affected by the following invariants: obs-6
                                  BindingUnless not suitable, these codes SHALL be taken from DataAbsentReason
                                  (extensible to http://hl7.org/fhir/ValueSet/data-absent-reason)

                                  Codes specifying why the result (Observation.value[x]) is missing.

                                  TypeCodeableConcept
                                  Is Modifierfalse
                                  Summaryfalse
                                  Requirements

                                  For many results it is necessary to handle exceptional values in measurements.

                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  122. Observation.component.interpretation
                                  Definition

                                  A categorical assessment of an observation value. For example, high, low, normal.

                                  ShortHigh, low, normal, etc.
                                  Comments

                                  Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.

                                  Control0..*
                                  BindingUnless not suitable, these codes SHALL be taken from ObservationInterpretationCodes
                                  (extensible to http://hl7.org/fhir/ValueSet/observation-interpretation)

                                  Codes identifying interpretations of observations.

                                  TypeCodeableConcept
                                  Is Modifierfalse
                                  Summaryfalse
                                  Requirements

                                  For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

                                  Alternate NamesAbnormal Flag
                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  124. Observation.component.referenceRange
                                  Definition

                                  Guidance on how to interpret the value by comparison to a normal or recommended range.

                                  ShortProvides guide for interpretation of component result
                                  Comments

                                  Most observations only have one generic reference range. Systems MAY choose to restrict to only supplying the relevant reference range based on knowledge about the patient (e.g., specific to the patient's age, gender, weight and other factors), but this might not be possible or appropriate. Whenever more than one reference range is supplied, the differences between them SHOULD be provided in the reference range and/or age properties.

                                  Control0..*
                                  TypeSeettp://hl7.org/fhir/StructureDefinition/Observation#Observation.referenceRange
                                  Is Modifierfalse
                                  Summaryfalse
                                  Requirements

                                  Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  126. Observation.component:conclusion-string
                                  Slice Nameconclusion-string
                                  Definition

                                  Concise and clinically contextualized summary conclusion (interpretation/impression) of the observation

                                  ShortClinical Conclusion
                                  Comments

                                  An example would be the interpretative information, typically canned, about a variant identified in the patient.

                                  Control0..1
                                  TypeBackboneElement
                                  Is Modifierfalse
                                  Summarytrue
                                  Requirements

                                  Need to be able to provide a conclusion that is not lost among the basic result data.

                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  128. Observation.component:conclusion-string.id
                                  Definition

                                  Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                                  ShortUnique id for inter-element referencing
                                  Control0..1
                                  Typestring
                                  Is Modifierfalse
                                  XML FormatIn the XML format, this property is represented as an attribute.
                                  Summaryfalse
                                  130. Observation.component:conclusion-string.extension
                                  Definition

                                  May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

                                  ShortAdditional content defined by implementations
                                  Comments

                                  There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                                  Control0..*
                                  TypeExtension
                                  Is Modifierfalse
                                  Summaryfalse
                                  Alternate Namesextensions, user content
                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                                  132. Observation.component:conclusion-string.modifierExtension
                                  Definition

                                  May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

                                  Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

                                  ShortExtensions that cannot be ignored even if unrecognized
                                  Comments

                                  There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

                                  Control0..*
                                  TypeExtension
                                  Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
                                  Summarytrue
                                  Requirements

                                  Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions.

                                  Alternate Namesextensions, user content, modifiers
                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                                  134. Observation.component:conclusion-string.code
                                  Definition

                                  Describes what was observed. Sometimes this is called the observation "code".

                                  Shortconclusion-string
                                  Comments

                                  All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

                                  Control1..1
                                  BindingFor example codes, see LOINCCodes
                                  (example to http://hl7.org/fhir/ValueSet/observation-codes)

                                  Codes identifying names of simple observations.

                                  TypeCodeableConcept
                                  Is Modifierfalse
                                  Summarytrue
                                  Requirements

                                  Knowing what kind of observation is being made is essential to understanding the observation.

                                  Pattern Value{
                                    "coding" : [{
                                      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
                                      "code" : "conclusion-string"
                                    }]
                                  }
                                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                                  136. Observation.component:conclusion-string.value[x]