Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build International flag

Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions

Resource Profile: PhenopacketsGenomicInterpretation - Detailed Descriptions

Draft as of 2021-10-18

Definitions for the phenopackets-genomic-interpretation resource profile.

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

0. DiagnosticReport
2. DiagnosticReport.modifierExtension
Control1..?
SlicingThis element introduces a set of slices on DiagnosticReport.modifierExtension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
  • value @ url
  • 4. DiagnosticReport.modifierExtension:interpretationStatus
    Slice NameinterpretationStatus
    ShortPhenopackets GenomicInterpretation.interpretation_status: status of the interpretation.
    Control1..1
    TypeExtension(Interpretation Status) (Extension Type: CodeableConcept)
    6. DiagnosticReport.status
    Pattern Valueunknown
    8. DiagnosticReport.subject
    ShortPhenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient or biosample that is the subject being interpreted. Check specimen element.
    Must Supporttrue
    Invariantsphenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present ()
    10. DiagnosticReport.specimen
    ShortPhenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient or biosample that is the subject being interpreted. Check subject element.
    Control0..1
    Invariantsphenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present ()
    12. DiagnosticReport.result
    Control1..?
    14. DiagnosticReport.result:variant
    Slice Namevariant
    ShortPhenopackets GenomicInterpretation.call: Represents the interpretation, i.e., oneof {GeneDescriptor|VariantInterpretation}.
    Control1..1
    TypeReference(Phenopackets Variant)
    Must Supporttrue

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

    0. DiagnosticReport
    Definition

    The findings and interpretation of diagnostic tests performed on patients, groups of patients, devices, and locations, and/or specimens derived from these. The report includes clinical context such as requesting and provider information, and some mix of atomic results, images, textual and coded interpretations, and formatted representation of diagnostic reports.

    ShortA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
    Comments

    This is intended to capture a single report and is not suitable for use in displaying summary information that covers multiple reports. For example, this resource has not been designed for laboratory cumulative reporting formats nor detailed structured reports for sequencing.

    Control0..*
    Is Modifierfalse
    Summaryfalse
    Alternate NamesReport, Test, Result, Results, Labs, Laboratory
    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())
    2. DiagnosticReport.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. DiagnosticReport.extension:genomics-artifact
    Slice Namegenomics-artifact
    Definition

    Captures citations, evidence and other supporting documentation for the observation or report.

    ShortGenomics Artifact
    Control0..*
    This element is affected by the following invariants: ele-1
    TypeExtension(Genomics Artifact) (Extension Type: RelatedArtifact)
    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())
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    6. DiagnosticReport.extension:genomics-file
    Slice Namegenomics-file
    Definition

    Used to transmit the contents of or links to files that were produced as part of the testing process. Examples are VCF, BAM, CRAM, and other similar files.

    ShortGenomics File
    Control0..*
    This element is affected by the following invariants: ele-1
    TypeExtension(Genomics File) (Extension Type: Reference(Genomics DocumentReference))
    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())
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    8. DiagnosticReport.extension:recommended-action
    Slice Namerecommended-action
    Definition

    References a proposed action that is recommended based on the results of the diagnostic report.

    ShortRecommended Action
    Control0..*
    This element is affected by the following invariants: ele-1
    TypeExtension(Recommended Action) (Extension Type: Reference(Medication Recommendation, Followup Recommendation))
    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())
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    10. DiagnosticReport.extension:genomics-risk-assessment
    Slice Namegenomics-risk-assessment
    Definition

    RiskAssessment delivered as part of a genomics report or observation

    ShortGenomics Risk Assessment
    Control0..*
    This element is affected by the following invariants: ele-1
    TypeExtension(Genomics Risk Assessment) (Extension Type: Reference(RiskAssessment))
    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())
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    12. DiagnosticReport.extension:coded-note
    Slice Namecoded-note
    Definition

    Adds codified notes to a report to capture additional content

    ShortComments about the report that also contain a coded type
    Comments

    May include general statements about the report, 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 results or conclusion or conclusionCode. 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
    TypeExtension(Genomic Report Note) (Extension Type: Annotation(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()))
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    14. DiagnosticReport.extension:supporting-info
    Slice Namesupporting-info
    Definition

    Other resources from the patient record that may be relevant to the event. The information from these resources was either used to create the instance or is provided to help with its interpretation. This extension should not be used if more specific inline elements or extensions are available. For example, use Observation.hasMember instead of supportingInformation for representing the members of an Observation panel.

    ShortOther information that may be relevant to this event.
    Control0..*
    This element is affected by the following invariants: ele-1
    TypeExtension(Supporting info) (Extension Type: Reference(Resource))
    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())
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    16. DiagnosticReport.modifierExtension
    Definition

    An Extension


    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).

    ShortExtensionExtensions 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.

    Control10..*
    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())
    SlicingThis element introduces a set of slices on DiagnosticReport.modifierExtension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
    • value @ url
    • 18. DiagnosticReport.modifierExtension:interpretationStatus
      Slice NameinterpretationStatus
      Definition

      Describes the conclusion made about the genomic interpretation.

      ShortPhenopackets GenomicInterpretation.interpretation_status: status of the interpretation.
      Control1..1
      This element is affected by the following invariants: ele-1
      TypeExtension(Interpretation Status) (Extension Type: CodeableConcept)
      Is Modifiertrue because The interpretation status could be REJECTED which may affect how the whole interpretation is interpreted.
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      20. DiagnosticReport.status
      Definition

      The status of the diagnostic report.

      Shortregistered | partial | preliminary | final +
      Control1..1
      BindingThe codes SHALL be taken from DiagnosticReportStatushttp://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1
      (required to http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1)

      The status of the diagnostic report.

      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

      Diagnostic services routinely issue provisional/incomplete reports, and sometimes withdraw previously released reports.

      Pattern Valueunknown
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      22. DiagnosticReport.category
      Definition

      A code that classifies the clinical discipline, department or diagnostic service that created the report (e.g. cardiology, biochemistry, hematology, MRI). This is used for searching, sorting and display purposes.

      ShortService category
      Comments

      Multiple categories are allowed using various categorization schemes. The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in DiagnosticReport.code.

      Control10..*
      BindingFor example codes, see DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sections
      (example to http://hl7.org/fhir/ValueSet/diagnostic-service-sections)

      Codes for diagnostic service sections.

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Alternate NamesDepartment, Sub-department, Service, Discipline
      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 DiagnosticReport.category. The slices areUnordered and Open, and can be differentiated using the following discriminators:
      • pattern @ coding
      • 24. DiagnosticReport.category:Genetics
        Slice NameGenetics
        Definition

        A code that classifies the clinical discipline, department or diagnostic service that created the report (e.g. cardiology, biochemistry, hematology, MRI). This is used for searching, sorting and display purposes.

        ShortService category
        Comments

        Multiple categories are allowed using various categorization schemes. The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in DiagnosticReport.code.

        Control10..1*
        BindingFor example codes, see DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sections
        (example to http://hl7.org/fhir/ValueSet/diagnostic-service-sections)

        Codes for diagnostic service sections.

        TypeCodeableConcept
        Is Modifierfalse
        Summarytrue
        Alternate NamesDepartment, Sub-department, Service, Discipline
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        26. DiagnosticReport.category:Genetics.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..*
        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()))
        28. DiagnosticReport.code
        Definition

        A code or name that describes this diagnostic report.

        ShortName/Code for this diagnostic report
        Control1..1
        BindingThe codes SHOULD be taken from LOINCDiagnosticReportCodeshttp://hl7.org/fhir/ValueSet/report-codes
        (preferred to http://hl7.org/fhir/ValueSet/report-codes)

        Codes that describe Diagnostic Reports.

        TypeCodeableConcept
        Is Modifierfalse
        Summarytrue
        Alternate NamesType
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        30. DiagnosticReport.subject
        Definition

        The subject of the report. Usually, but not always, this is a patient. However, diagnostic services also perform analyses on specimens collected from a variety of other sources.

        ShortPhenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient or biosample that is the subject being interpreted. Check specimen element.The subject of the report - usually, but not always, the patient
        Control0..1
        TypeReference(Patient, Group, Device, Location)
        Is Modifierfalse
        Must Supporttrue
        Must Support TypesNo must-support rules about the choice of types/profiles
        Summarytrue
        Requirements

        SHALL know the subject context.

        Alternate NamesPatient
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present ()
        32. DiagnosticReport.specimen
        Definition

        Details about the specimens on which this diagnostic report is based.

        ShortPhenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient or biosample that is the subject being interpreted. Check subject element.Specimens this report is based on
        Comments

        If the specimen is sufficiently specified with a code in the test result name, then this additional data may be redundant. If there are multiple specimens, these may be represented per observation or group.

        Control0..1*
        TypeReference(Specimen)
        Is Modifierfalse
        Summaryfalse
        Requirements

        Need to be able to report information about the collected specimens on which the report is based.

        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present ()
        34. DiagnosticReport.result
        Definition

        Observations that are part of this diagnostic report.

        ShortObservations
        Comments

        Observations can contain observations.

        Control10..*
        TypeReference(Observation)
        Is Modifierfalse
        Summaryfalse
        Requirements

        Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

        Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
        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 DiagnosticReport.result. The slices areUnordered and Open, and can be differentiated using the following discriminators:
        • profile @ resolve()
        • 36. DiagnosticReport.result:overall
          Slice Nameoverall
          Definition

          Observations that are part of this diagnostic report.

          ShortAssessment of overall resultsObservations
          Comments

          Observations can contain observations.

          Control0..1*
          TypeReference(Overall Interpretation, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          38. DiagnosticReport.result:diagnostic-implication
          Slice Namediagnostic-implication
          Definition

          Observations that are part of this diagnostic report.

          ShortDiagnostic ImplicationObservations
          Comments

          Observations can contain observations.

          Control0..*
          TypeReference(Diagnostic Implication, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          40. DiagnosticReport.result:therapeutic-implication
          Slice Nametherapeutic-implication
          Definition

          Observations that are part of this diagnostic report.

          ShortTherapeutic ImplicationObservations
          Comments

          Observations can contain observations.

          Control0..*
          TypeReference(Therapeutic Implication, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          42. DiagnosticReport.result:variant
          Slice Namevariant
          Definition

          Observations that are part of this diagnostic report.

          ShortPhenopackets GenomicInterpretation.call: Represents the interpretation, i.e., oneof {GeneDescriptor|VariantInterpretation}.Observations
          Comments

          Observations can contain observations.

          Control10..1*
          TypeReference(Phenopackets Variant, Observation)
          Is Modifierfalse
          Must Supporttrue
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          44. DiagnosticReport.result:sequence-phase-relation
          Slice Namesequence-phase-relation
          Definition

          Observations that are part of this diagnostic report.

          ShortSequence Phase RelationshipObservations
          Comments

          Observations can contain observations.

          Control0..*
          TypeReference(Sequence Phase Relationship, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          46. DiagnosticReport.result:region-studied
          Slice Nameregion-studied
          Definition

          Observations that are part of this diagnostic report.

          ShortRegion StudiedObservations
          Comments

          Observations can contain observations.

          Control0..*
          TypeReference(Region Studied, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          48. DiagnosticReport.result:genotype
          Slice Namegenotype
          Definition

          Observations that are part of this diagnostic report.

          ShortGenotypeObservations
          Comments

          Observations can contain observations.

          Control0..*
          TypeReference(Genotype, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          50. DiagnosticReport.result:haplotype
          Slice Namehaplotype
          Definition

          Observations that are part of this diagnostic report.

          ShortHaplotypeObservations
          Comments

          Observations can contain observations.

          Control0..*
          TypeReference(Haplotype, Observation)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

          Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
          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. DiagnosticReport
          Definition

          The findings and interpretation of diagnostic tests performed on patients, groups of patients, devices, and locations, and/or specimens derived from these. The report includes clinical context such as requesting and provider information, and some mix of atomic results, images, textual and coded interpretations, and formatted representation of diagnostic reports.

          ShortA Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports
          Comments

          This is intended to capture a single report and is not suitable for use in displaying summary information that covers multiple reports. For example, this resource has not been designed for laboratory cumulative reporting formats nor detailed structured reports for sequencing.

          Control0..*
          Is Modifierfalse
          Summaryfalse
          Alternate NamesReport, Test, Result, Results, Labs, Laboratory
          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())
          2. DiagnosticReport.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. DiagnosticReport.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. DiagnosticReport.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. DiagnosticReport.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. DiagnosticReport.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. DiagnosticReport.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. DiagnosticReport.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 DiagnosticReport.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
          • value @ url
          • 16. DiagnosticReport.extension:genomics-artifact
            Slice Namegenomics-artifact
            Definition

            Captures citations, evidence and other supporting documentation for the observation or report.

            ShortGenomics Artifact
            Control0..*
            This element is affected by the following invariants: ele-1
            TypeExtension(Genomics Artifact) (Extension Type: RelatedArtifact)
            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. DiagnosticReport.extension:genomics-file
            Slice Namegenomics-file
            Definition

            Used to transmit the contents of or links to files that were produced as part of the testing process. Examples are VCF, BAM, CRAM, and other similar files.

            ShortGenomics File
            Control0..*
            This element is affected by the following invariants: ele-1
            TypeExtension(Genomics File) (Extension Type: Reference(Genomics DocumentReference))
            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. DiagnosticReport.extension:recommended-action
            Slice Namerecommended-action
            Definition

            References a proposed action that is recommended based on the results of the diagnostic report.

            ShortRecommended Action
            Control0..*
            This element is affected by the following invariants: ele-1
            TypeExtension(Recommended Action) (Extension Type: Reference(Medication Recommendation, Followup Recommendation))
            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())
            22. DiagnosticReport.extension:genomics-risk-assessment
            Slice Namegenomics-risk-assessment
            Definition

            RiskAssessment delivered as part of a genomics report or observation

            ShortGenomics Risk Assessment
            Control0..*
            This element is affected by the following invariants: ele-1
            TypeExtension(Genomics Risk Assessment) (Extension Type: Reference(RiskAssessment))
            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())
            24. DiagnosticReport.extension:coded-note
            Slice Namecoded-note
            Definition

            Adds codified notes to a report to capture additional content

            ShortComments about the report that also contain a coded type
            Comments

            May include general statements about the report, 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 results or conclusion or conclusionCode. 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
            TypeExtension(Genomic Report Note) (Extension Type: Annotation(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()))
            ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
            26. DiagnosticReport.extension:supporting-info
            Slice Namesupporting-info
            Definition

            Other resources from the patient record that may be relevant to the event. The information from these resources was either used to create the instance or is provided to help with its interpretation. This extension should not be used if more specific inline elements or extensions are available. For example, use Observation.hasMember instead of supportingInformation for representing the members of an Observation panel.

            ShortOther information that may be relevant to this event.
            Control0..*
            This element is affected by the following invariants: ele-1
            TypeExtension(Supporting info) (Extension Type: Reference(Resource))
            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())
            28. DiagnosticReport.modifierExtension
            Definition

            An Extension

            ShortExtension
            Control1..*
            TypeExtension
            Is Modifiertrue because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
            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 DiagnosticReport.modifierExtension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
            • value @ url
            • 30. DiagnosticReport.modifierExtension:interpretationStatus
              Slice NameinterpretationStatus
              Definition

              Describes the conclusion made about the genomic interpretation.

              ShortPhenopackets GenomicInterpretation.interpretation_status: status of the interpretation.
              Control1..1
              This element is affected by the following invariants: ele-1
              TypeExtension(Interpretation Status) (Extension Type: CodeableConcept)
              Is Modifiertrue because The interpretation status could be REJECTED which may affect how the whole interpretation is interpreted.
              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())
              32. DiagnosticReport.identifier
              Definition

              Identifiers assigned to this report by the performer or other systems.

              ShortBusiness identifier for report
              Comments

              Usually assigned by the Information System of the diagnostic service provider (filler id).

              NoteThis is a business identifier, not a resource identifier (see discussion)
              Control0..*
              TypeIdentifier
              Is Modifierfalse
              Summarytrue
              Requirements

              Need to know what identifier to use when making queries about this report from the source laboratory, and for linking to the report outside FHIR context.

              Alternate NamesReportID, Filler ID, Placer ID
              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              34. DiagnosticReport.basedOn
              Definition

              Details concerning a service requested.

              ShortWhat was requested
              Comments

              Note: Usually there is one test request for each result, however in some circumstances multiple test requests may be represented using a single test result resource. Note that there are also cases where one request leads to multiple reports.

              Control0..*
              TypeReference(CarePlan, ImmunizationRecommendation, MedicationRequest, NutritionOrder, ServiceRequest)
              Is Modifierfalse
              Summaryfalse
              Requirements

              This allows tracing of authorization for the report and tracking whether proposals/recommendations were acted upon.

              Alternate NamesRequest
              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              36. DiagnosticReport.status
              Definition

              The status of the diagnostic report.

              Shortregistered | partial | preliminary | final +
              Control1..1
              BindingThe codes SHALL be taken from DiagnosticReportStatus
              (required to http://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1)

              The status of the diagnostic report.

              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

              Diagnostic services routinely issue provisional/incomplete reports, and sometimes withdraw previously released reports.

              Pattern Valueunknown
              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              38. DiagnosticReport.category
              Definition

              A code that classifies the clinical discipline, department or diagnostic service that created the report (e.g. cardiology, biochemistry, hematology, MRI). This is used for searching, sorting and display purposes.

              ShortService category
              Comments

              Multiple categories are allowed using various categorization schemes. The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in DiagnosticReport.code.

              Control1..*
              BindingFor example codes, see DiagnosticServiceSectionCodes
              (example to http://hl7.org/fhir/ValueSet/diagnostic-service-sections)

              Codes for diagnostic service sections.

              TypeCodeableConcept
              Is Modifierfalse
              Summarytrue
              Alternate NamesDepartment, Sub-department, Service, Discipline
              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 DiagnosticReport.category. The slices areUnordered and Open, and can be differentiated using the following discriminators:
              • pattern @ coding
              • 40. DiagnosticReport.category:Genetics
                Slice NameGenetics
                Definition

                A code that classifies the clinical discipline, department or diagnostic service that created the report (e.g. cardiology, biochemistry, hematology, MRI). This is used for searching, sorting and display purposes.

                ShortService category
                Comments

                Multiple categories are allowed using various categorization schemes. The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in DiagnosticReport.code.

                Control1..1
                BindingFor example codes, see DiagnosticServiceSectionCodes
                (example to http://hl7.org/fhir/ValueSet/diagnostic-service-sections)

                Codes for diagnostic service sections.

                TypeCodeableConcept
                Is Modifierfalse
                Summarytrue
                Alternate NamesDepartment, Sub-department, Service, Discipline
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                42. DiagnosticReport.category:Genetics.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
                44. DiagnosticReport.category:Genetics.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 DiagnosticReport.category.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                • value @ url
                • 46. DiagnosticReport.category:Genetics.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..*
                  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()))
                  48. DiagnosticReport.category:Genetics.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()))
                  50. DiagnosticReport.code
                  Definition

                  A code or name that describes this diagnostic report.

                  ShortName/Code for this diagnostic report
                  Control1..1
                  BindingThe codes SHOULD be taken from LOINCDiagnosticReportCodes
                  (preferred to http://hl7.org/fhir/ValueSet/report-codes)

                  Codes that describe Diagnostic Reports.

                  TypeCodeableConcept
                  Is Modifierfalse
                  Summarytrue
                  Alternate NamesType
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  52. DiagnosticReport.subject
                  Definition

                  The subject of the report. Usually, but not always, this is a patient. However, diagnostic services also perform analyses on specimens collected from a variety of other sources.

                  ShortPhenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient or biosample that is the subject being interpreted. Check specimen element.
                  Control0..1
                  TypeReference(Patient, Group, Device, Location)
                  Is Modifierfalse
                  Must Supporttrue
                  Must Support TypesNo must-support rules about the choice of types/profiles
                  Summarytrue
                  Requirements

                  SHALL know the subject context.

                  Alternate NamesPatient
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present ()
                  54. DiagnosticReport.encounter
                  Definition

                  The healthcare event (e.g. a patient and healthcare provider interaction) which this DiagnosticReport is about.

                  ShortHealth care event when test ordered
                  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

                  Links the request to the Encounter context.

                  Alternate NamesContext
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  56. DiagnosticReport.effective[x]
                  Definition

                  The time or time-period the observed values are related to. When the subject of the report is a patient, this is usually either the time of the procedure or of specimen collection(s), but very often the source of the date/time is not known, only the date/time itself.

                  ShortClinically relevant time/time-period for report
                  Comments

                  If the diagnostic procedure was performed on the patient, this is the time it was performed. If there are specimens, the diagnostically relevant time can be derived from the specimen collection times, but the specimen information is not always available, and the exact relationship between the specimens and the diagnostically relevant time is not always automatic.

                  Control0..1
                  TypedateTime
                  [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

                  Need to know where in the patient history to file/present this report.

                  Alternate NamesObservation time, Effective Time, Occurrence
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  58. DiagnosticReport.issued
                  Definition

                  The date and time that this version of the report was made available to providers, typically after the report was reviewed and verified.

                  ShortDateTime this version was made
                  Comments

                  May be different from the update time of the resource itself, because that is the status of the record (potentially a secondary copy), not the actual release time of the report.

                  Control0..1
                  Typeinstant
                  Is Modifierfalse
                  Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                  Summarytrue
                  Requirements

                  Clinicians need to be able to check the date that the report was released.

                  Alternate NamesDate published, Date Issued, Date Verified
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  60. DiagnosticReport.performer
                  Definition

                  The diagnostic service that is responsible for issuing the report.

                  ShortResponsible Diagnostic Service
                  Comments

                  This is not necessarily the source of the atomic data items or the entity that interpreted the results. It is the entity that takes responsibility for the clinical report.

                  Control0..*
                  TypeReference(Practitioner, PractitionerRole, Organization, CareTeam)
                  Is Modifierfalse
                  Summarytrue
                  Requirements

                  Need to know whom to contact if there are queries about the results. Also may need to track the source of reports for secondary data analysis.

                  Alternate NamesLaboratory, Service, Practitioner, Department, Company, Authorized by, Director
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  62. DiagnosticReport.resultsInterpreter
                  Definition

                  The practitioner or organization that is responsible for the report's conclusions and interpretations.

                  ShortPrimary result interpreter
                  Comments

                  Might not be the same entity that takes responsibility for the clinical report.

                  Control0..*
                  TypeReference(Practitioner, PractitionerRole, Organization, CareTeam)
                  Is Modifierfalse
                  Summarytrue
                  Requirements

                  Need to know whom to contact if there are queries about the results. Also may need to track the source of reports for secondary data analysis.

                  Alternate NamesAnalyzed by, Reported by
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  64. DiagnosticReport.specimen
                  Definition

                  Details about the specimens on which this diagnostic report is based.

                  ShortPhenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient or biosample that is the subject being interpreted. Check subject element.
                  Comments

                  If the specimen is sufficiently specified with a code in the test result name, then this additional data may be redundant. If there are multiple specimens, these may be represented per observation or group.

                  Control0..1
                  TypeReference(Specimen)
                  Is Modifierfalse
                  Summaryfalse
                  Requirements

                  Need to be able to report information about the collected specimens on which the report is based.

                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present ()
                  66. DiagnosticReport.result
                  Definition

                  Observations that are part of this diagnostic report.

                  ShortObservations
                  Comments

                  Observations can contain observations.

                  Control1..*
                  TypeReference(Observation)
                  Is Modifierfalse
                  Summaryfalse
                  Requirements

                  Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                  Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                  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 DiagnosticReport.result. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                  • profile @ resolve()
                  • 68. DiagnosticReport.result:overall
                    Slice Nameoverall
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortAssessment of overall results
                    Comments

                    Observations can contain observations.

                    Control0..1
                    TypeReference(Overall Interpretation)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    70. DiagnosticReport.result:diagnostic-implication
                    Slice Namediagnostic-implication
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortDiagnostic Implication
                    Comments

                    Observations can contain observations.

                    Control0..*
                    TypeReference(Diagnostic Implication)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    72. DiagnosticReport.result:therapeutic-implication
                    Slice Nametherapeutic-implication
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortTherapeutic Implication
                    Comments

                    Observations can contain observations.

                    Control0..*
                    TypeReference(Therapeutic Implication)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    74. DiagnosticReport.result:variant
                    Slice Namevariant
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortPhenopackets GenomicInterpretation.call: Represents the interpretation, i.e., oneof {GeneDescriptor|VariantInterpretation}.
                    Comments

                    Observations can contain observations.

                    Control1..1
                    TypeReference(Phenopackets Variant)
                    Is Modifierfalse
                    Must Supporttrue
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    76. DiagnosticReport.result:sequence-phase-relation
                    Slice Namesequence-phase-relation
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortSequence Phase Relationship
                    Comments

                    Observations can contain observations.

                    Control0..*
                    TypeReference(Sequence Phase Relationship)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    78. DiagnosticReport.result:region-studied
                    Slice Nameregion-studied
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortRegion Studied
                    Comments

                    Observations can contain observations.

                    Control0..*
                    TypeReference(Region Studied)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    80. DiagnosticReport.result:genotype
                    Slice Namegenotype
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortGenotype
                    Comments

                    Observations can contain observations.

                    Control0..*
                    TypeReference(Genotype)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    82. DiagnosticReport.result:haplotype
                    Slice Namehaplotype
                    Definition

                    Observations that are part of this diagnostic report.

                    ShortHaplotype
                    Comments

                    Observations can contain observations.

                    Control0..*
                    TypeReference(Haplotype)
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Need to support individual results, or groups of results, where the result grouping is arbitrary, but meaningful.

                    Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    84. DiagnosticReport.imagingStudy
                    Definition

                    One or more links to full details of any imaging performed during the diagnostic investigation. Typically, this is imaging performed by DICOM enabled modalities, but this is not required. A fully enabled PACS viewer can use this information to provide views of the source images.

                    ShortReference to full details of imaging associated with the diagnostic report
                    Comments

                    ImagingStudy and the image element are somewhat overlapping - typically, the list of image references in the image element will also be found in one of the imaging study resources. However, each caters to different types of displays for different types of purposes. Neither, either, or both may be provided.

                    Control0..*
                    TypeReference(ImagingStudy)
                    Is Modifierfalse
                    Summaryfalse
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    86. DiagnosticReport.media
                    Definition

                    A list of key images associated with this report. The images are generally created during the diagnostic process, and may be directly of the patient, or of treated specimens (i.e. slides of interest).

                    ShortKey images associated with this report
                    Control0..*
                    TypeBackboneElement
                    Is Modifierfalse
                    Summarytrue
                    Requirements

                    Many diagnostic services include images in the report as part of their service.

                    Alternate NamesDICOM, Slides, Scans
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    88. DiagnosticReport.media.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
                    90. DiagnosticReport.media.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())
                    92. DiagnosticReport.media.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())
                    94. DiagnosticReport.media.comment
                    Definition

                    A comment about the image. Typically, this is used to provide an explanation for why the image is included, or to draw the viewer's attention to important features.

                    ShortComment about the image (e.g. explanation)
                    Comments

                    The comment should be displayed with the image. It would be common for the report to include additional discussion of the image contents in other sections such as the conclusion.

                    Control0..1
                    Typestring
                    Is Modifierfalse
                    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                    Summaryfalse
                    Requirements

                    The provider of the report should make a comment about each image included in the report.

                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    96. DiagnosticReport.media.link
                    Definition

                    Reference to the image source.

                    ShortReference to the image source
                    Control1..1
                    TypeReference(Media)
                    Is Modifierfalse
                    Summarytrue
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    98. DiagnosticReport.conclusion
                    Definition

                    Concise and clinically contextualized summary conclusion (interpretation/impression) of the diagnostic report.

                    ShortClinical conclusion (interpretation) of test results
                    Control0..1
                    Typestring
                    Is Modifierfalse
                    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                    Summaryfalse
                    Requirements

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

                    Alternate NamesReport
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    100. DiagnosticReport.conclusionCode
                    Definition

                    One or more codes that represent the summary conclusion (interpretation/impression) of the diagnostic report.

                    ShortCodes for the clinical conclusion of test results
                    Control0..*
                    BindingFor example codes, see SNOMEDCTClinicalFindings
                    (example to http://hl7.org/fhir/ValueSet/clinical-findings)

                    Diagnosis codes provided as adjuncts to the report.

                    TypeCodeableConcept
                    Is Modifierfalse
                    Summaryfalse
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    102. DiagnosticReport.presentedForm
                    Definition

                    Rich text representation of the entire result as issued by the diagnostic service. Multiple formats are allowed but they SHALL be semantically equivalent.

                    ShortEntire report as issued
                    Comments

                    "application/pdf" is recommended as the most reliable and interoperable in this context.

                    Control0..*
                    TypeAttachment
                    Is Modifierfalse
                    Summaryfalse
                    Requirements

                    Gives laboratory the ability to provide its own fully formatted report for clinical fidelity.

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