Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot 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 3.0.1-SNAPSHOT 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: Haplotype - Detailed Descriptions

Active as of 2024-07-08

Definitions for the haplotype resource profile.

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

0. Observation
ShortHaplotype
2. Observation.code
Short84414-2
Pattern Value{
  "coding" : [{
    "system" : "http://loinc.org",
    "code" : "84414-2"
  }]
}
4. Observation.value[x]
ShortHaplotype name
Control1..?
Binding

Binding not yet standardized

TypeCodeableConcept, dateTime, boolean, string, SampledData, Quantity, Period, Ratio, integer, time, Range
[x] NoteSeeChoice of Data Typesfor further information about how to use [x]
6. Observation.method
ShortDirectly measured | Family DNA | Family history | Inferred from population data
BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL4050-2
(extensible to http://loinc.org/vs/LL4050-2)
8. Observation.derivedFrom:haplotype
Slice Namehaplotype
ShortHaplotype this haplotype is derived from
Control0..*
TypeReference(Haplotype)
10. Observation.derivedFrom:variant
Slice Namevariant
ShortVariant this haplotype is derived from
Control0..*
TypeReference(Variant)
12. Observation.derivedFrom:molecular-sequence
Slice Namemolecular-sequence
ShortMolecularSequence this haplotype is derived from
Control0..*
TypeReference(MolecularSequence)

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.

ShortHaplotypeMeasurements 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".

    Short84414-2Type 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" : "84414-2"
      }]
    }
    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.

    ShortHaplotype nameActual 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.

    Control10..1
    This element is affected by the following invariants: obs-7
    Binding

    Binding not yet standardized

    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()))
    26. Observation.method
    Definition

    Indicates the mechanism used to perform the observation.

    ShortDirectly measured | Family DNA | Family history | Inferred from population dataHow 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 LL4050-2http://hl7.org/fhir/ValueSet/observation-methods
    (extensible to http://loinc.org/vs/LL4050-2)
    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()))
    28. 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()
    • 30. Observation.derivedFrom:haplotype
      Slice Namehaplotype
      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.

      ShortHaplotype this haplotype is derived fromRelated 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(Haplotype, 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()))
      32. Observation.derivedFrom:variant
      Slice Namevariant
      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.

      ShortVariant this haplotype is derived fromRelated 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(Variant, 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()))
      34. Observation.derivedFrom:molecular-sequence
      Slice Namemolecular-sequence
      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.

      ShortMolecularSequence this haplotype is derived fromRelated 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(MolecularSequence, DocumentReference, ImagingStudy, Media, QuestionnaireResponse, Observation)
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      36. 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:
      • pattern @ code
      • 38. 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())
        40. 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()))
        42. 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()))
        44. 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())
        46. 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()))
        48. 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()))
        50. 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())
        52. 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()))
        54. 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()))
        56. 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()))
        58. 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())
        60. 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()))
        62. 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()))
        64. 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()))
        66. 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())
        68. 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()))
        70. 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()))

        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.

        ShortHaplotype
        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:
        • pattern @ 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".

                Short84414-2
                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" : "84414-2"
                  }]
                }
                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.

                ShortHaplotype name
                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.

                Control1..1
                This element is affected by the following invariants: obs-7
                Binding

                Binding not yet standardized

                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()))
                68. 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()))
                70. 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()))
                72. 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()))
                74. 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()))
                76. Observation.method
                Definition

                Indicates the mechanism used to perform the observation.

                ShortDirectly measured | Family DNA | Family history | Inferred from population data
                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 LL4050-2
                (extensible to http://loinc.org/vs/LL4050-2)
                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()))
                78. 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()))
                80. 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()))
                82. 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())
                84. 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
                86. 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())
                88. 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())
                90. 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()))
                92. 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()))
                94. 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()))
                96. 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()))
                98. 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()))
                100. 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()))
                102. 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()))
                104. 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()
                • 106. Observation.derivedFrom:haplotype
                  Slice Namehaplotype
                  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.

                  ShortHaplotype this haplotype is derived 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(Haplotype)
                  Is Modifierfalse
                  Summarytrue
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  108. Observation.derivedFrom:variant
                  Slice Namevariant
                  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.

                  ShortVariant this haplotype is derived 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(Variant)
                  Is Modifierfalse
                  Summarytrue
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  110. Observation.derivedFrom:molecular-sequence
                  Slice Namemolecular-sequence
                  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.

                  ShortMolecularSequence this haplotype is derived 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(MolecularSequence)
                  Is Modifierfalse
                  Summarytrue
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  112. 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:
                  • pattern @ code
                  • 114. 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
                    116. Observation.component.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())
                    118. 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())
                    120. 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()))
                    122. 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()))
                    124. 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()))
                    126. 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()))
                    128. 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()))
                    130. 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()))
                    132. 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
                    134. 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())
                    136. 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())
                    138. 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()))
                    140. Observation.component:conclusion-string.value[x]
                    Definition

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

                    ShortSummary conclusion (interpretation/impression)
                    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
                    [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()))
                    142. Observation.component:conclusion-string.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()))
                    144. Observation.component:conclusion-string.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()))
                    146. Observation.component:conclusion-string.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()))
                    148. Observation.component:gene-studied
                    Slice Namegene-studied
                    Definition

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

                    ShortGene Studied
                    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()))
                    150. Observation.component:gene-studied.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
                    152. Observation.component:gene-studied.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())
                    154. 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())
                    156. Observation.component:gene-studied.code
                    Definition

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

                    Short48018-6
                    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://loinc.org",
                        "code" : "48018-6"
                      }]
                    }
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    158. 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.
                    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.

                    Control1..1
                    BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
                    (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
                    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()))
                    160. Observation.component:gene-studied.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()))
                    162. Observation.component:gene-studied.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()))
                    164. Observation.component:gene-studied.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()))
                    166. Observation.component:cytogenetic-location
                    Slice Namecytogenetic-location
                    Definition

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

                    ShortCytogenetic (Chromosome) Location
                    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()))
                    168. Observation.component:cytogenetic-location.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
                    170. Observation.component:cytogenetic-location.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())
                    172. 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())
                    174. Observation.component:cytogenetic-location.code
                    Definition

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

                    Short48001-2
                    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://loinc.org",
                        "code" : "48001-2"
                      }]
                    }
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    176. 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: 1q21.1
                    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.

                    Control1..1
                    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()))
                    178. Observation.component:cytogenetic-location.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()))
                    180. Observation.component:cytogenetic-location.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()))
                    182. Observation.component:cytogenetic-location.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()))
                    184. Observation.component:reference-sequence-assembly
                    Slice Namereference-sequence-assembly
                    Definition

                    The reference genome/assembly used in this analysis.

                    ShortHuman Reference Sequence Assembly
                    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()))
                    186. Observation.component:reference-sequence-assembly.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
                    188. Observation.component:reference-sequence-assembly.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())
                    190. 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())
                    192. Observation.component:reference-sequence-assembly.code
                    Definition

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

                    Short62374-4
                    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://loinc.org",
                        "code" : "62374-4"
                      }]
                    }
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    194. 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 | ...
                    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.

                    Control1..1
                    BindingUnless not suitable, these codes SHALL be taken from LOINC Answer List LL1040-6
                    (extensible to http://loinc.org/vs/LL1040-6)
                    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()))
                    196. Observation.component:reference-sequence-assembly.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()))
                    198. Observation.component:reference-sequence-assembly.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()))
                    200. Observation.component:reference-sequence-assembly.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()))