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: GenomicStudyAnalysis - Detailed Descriptions

Active as of 2024-04-09

Definitions for the genomic-study-analysis resource profile.

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

0. Procedure
2. Procedure.extension
SlicingThis element introduces a set of slices on Procedure.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • value @ url
  • 4. Procedure.extension:method-type
    Slice Namemethod-type
    ShortGenomicStudy.analysis.methodType
    Control0..*
    TypeExtension(Genomic Study Analysis Method Type) (Extension Type: CodeableConcept)
    6. Procedure.extension:change-type
    Slice Namechange-type
    ShortGenomicStudy.analysis.changeType
    Control0..*
    TypeExtension(Genomic Study Analysis Change Type) (Extension Type: CodeableConcept)
    8. Procedure.extension:genome-build
    Slice Namegenome-build
    ShortGenomicStudy.analysis.genomeBuild
    Control0..1
    TypeExtension(Genomic Study Analysis Genome Build) (Extension Type: CodeableConcept)
    10. Procedure.extension:title
    Slice Nametitle
    ShortGenomicStudy.analysis.title
    Control0..1
    TypeExtension(Genomic Study Analysis Title) (Extension Type: string)
    12. Procedure.extension:focus
    Slice Namefocus
    ShortGenomicStudy.analysis.focus
    Control0..*
    TypeExtension(Genomic Study Analysis Focus) (Extension Type: Reference(Resource))
    14. Procedure.extension:specimen
    Slice Namespecimen
    ShortGenomicStudy.analysis.specimen
    Control0..*
    TypeExtension(Genomic Study Analysis Specimen) (Extension Type: Reference(Specimen))
    16. Procedure.extension:metrics
    Slice Namemetrics
    ShortGenomic Study Analysis Metrics
    Control0..1
    TypeExtension(Genomic Study Analysis Metrics) (Complex Extension)
    18. Procedure.extension:regions
    Slice Nameregions
    ShortGenomic Study Analysis Regions
    Control0..1
    TypeExtension(Genomic Study Analysis Regions) (Complex Extension)
    20. Procedure.extension:device
    Slice Namedevice
    ShortGenomicStudy.analysis.device
    Control0..*
    TypeExtension(Genomic Study Analysis Device) (Complex Extension)
    22. Procedure.extension:protocol-performed
    Slice Nameprotocol-performed
    ShortGenomicStudy.protocolPerformed
    Control0..1
    TypeExtension(Genomic Study Analysis Protocol Performed) (Extension Type: Reference(Procedure, Task))
    24. Procedure.extension:input
    Slice Nameinput
    ShortGenomicStudy.analysis.input
    Control0..*
    TypeExtension(Genomic Study Analysis Input) (Complex Extension)
    26. Procedure.extension:output
    Slice Nameoutput
    ShortGenomicStudy.analysis.output
    Control0..*
    TypeExtension(Genomic Study Analysis Output) (Complex Extension)
    28. Procedure.identifier
    ShortGenomicStudy.analysis.identifier
    NoteThis is a business identifier, not a resource identifier (see discussion)
    30. Procedure.instantiatesCanonical
    ShortGenomicStudy.analysis.instantiatesCanonical
    Typecanonical(PlanDefinition, ActivityDefinition)
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    32. Procedure.instantiatesUri
    ShortGenomicStudy.analysis.instantiatesUri
    34. Procedure.basedOn
    Control0..0
    36. Procedure.partOf
    Control0..0
    38. Procedure.status
    Pattern Valuecompleted
    40. Procedure.statusReason
    Control0..0
    42. Procedure.category
    Control1..?
    44. Procedure.category.coding
    Control1..1
    Pattern Value{
      "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
      "code" : "laboratory"
    }
    46. Procedure.code
    Control0..0
    48. Procedure.encounter
    Control0..0
    50. Procedure.performed[x]
    ShortGenomicStudy.analysis.date
    TypedateTime, string, Period, Range, Age
    [x] NoteSee Choice of Data Types for further information about how to use [x]
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    52. Procedure.recorder
    Control0..0
    54. Procedure.asserter
    Control0..0
    56. Procedure.performer
    58. Procedure.performer.function
    ShortGenomicStudy.analysis.performer.role
    60. Procedure.performer.actor
    ShortGenomicStudy.analysis.performer.actor
    TypeReference(Practitioner, PractitionerRole, Organization, Device)
    62. Procedure.location
    Control0..0
    64. Procedure.reasonCode
    Control0..0
    66. Procedure.reasonReference
    Control0..0
    68. Procedure.bodySite
    Control0..0
    70. Procedure.outcome
    Control0..0
    72. Procedure.report
    Control0..0
    74. Procedure.complication
    Control0..0
    76. Procedure.complicationDetail
    Control0..0
    78. Procedure.followUp
    Control0..0
    80. Procedure.note
    ShortGenomicStudy.analysis.note
    82. Procedure.focalDevice
    Control0..0
    84. Procedure.usedReference
    Control0..0
    86. Procedure.usedCode
    Control0..0

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

    0. Procedure
    Definition

    An action that is or was performed on or for a patient. This can be a physical intervention like an operation, or less invasive like long term services, counseling, or hypnotherapy.

    ShortAn action that is being or was performed on a patient
    Control0..*
    Is Modifierfalse
    Summaryfalse
    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. Procedure.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. Procedure.extension
    Definition

    An Extension


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

    ShortExtensionAdditional content defined by implementations
    Comments

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

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

      Defines a method type for a genomic analysis

      ShortGenomicStudy.analysis.methodType
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Method Type) (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())
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      8. Procedure.extension:change-type
      Slice Namechange-type
      Definition

      Defines the change type for a genomic analysis

      ShortGenomicStudy.analysis.changeType
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Change Type) (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())
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      10. Procedure.extension:genome-build
      Slice Namegenome-build
      Definition

      Defines the genome build for a genomic analysis

      ShortGenomicStudy.analysis.genomeBuild
      Control0..1
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Genome Build) (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())
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      12. Procedure.extension:title
      Slice Nametitle
      Definition

      Defines a title for a genomic analysis

      ShortGenomicStudy.analysis.title
      Control0..1
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Title) (Extension Type: string)
      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())
      14. Procedure.extension:focus
      Slice Namefocus
      Definition

      Defines a focus for a genomic analysis

      ShortGenomicStudy.analysis.focus
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Focus) (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. Procedure.extension:specimen
      Slice Namespecimen
      Definition

      Defines a specimen for a genomic analysis

      ShortGenomicStudy.analysis.specimen
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Specimen) (Extension Type: Reference(Specimen))
      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())
      18. Procedure.extension:metrics
      Slice Namemetrics
      Definition

      Metrics about the sequencing analysis that was performed

      ShortGenomic Study Analysis Metrics
      Control0..1
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Metrics) (Complex Extension)
      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. Procedure.extension:regions
      Slice Nameregions
      Definition

      Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

      ShortGenomic Study Analysis Regions
      Control0..1
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Regions) (Complex Extension)
      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. Procedure.extension:device
      Slice Namedevice
      Definition

      Genomic Study Analysis Device

      ShortGenomicStudy.analysis.device
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Device) (Complex Extension)
      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. Procedure.extension:protocol-performed
      Slice Nameprotocol-performed
      Definition

      Defines a protocol that was performed for a genomic analysis

      ShortGenomicStudy.protocolPerformed
      Control0..1
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Protocol Performed) (Extension Type: Reference(Procedure, Task))
      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())
      26. Procedure.extension:input
      Slice Nameinput
      Definition

      Genomic Study Analysis Input

      ShortGenomicStudy.analysis.input
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Input) (Complex Extension)
      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. Procedure.extension:output
      Slice Nameoutput
      Definition

      Genomic Study Analysis Output

      ShortGenomicStudy.analysis.output
      Control0..*
      This element is affected by the following invariants: ele-1
      TypeExtension(Genomic Study Analysis Output) (Complex Extension)
      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())
      30. Procedure.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())
      32. Procedure.identifier
      Definition

      Business identifiers assigned to this procedure by the performer or other systems which remain constant as the resource is updated and is propagated from server to server.

      ShortGenomicStudy.analysis.identifierExternal Identifiers for this procedure
      Comments

      This is a business identifier, not a resource identifier (see discussion). It is best practice for the identifier to only appear on a single resource instance, however business practices may occasionally dictate that multiple resource instances with the same identifier can exist - possibly even with different resource types. For example, multiple Patient and Person resource instances might share the same social insurance number.

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

      Allows identification of the procedure as it is known by various participating systems and in a way that remains consistent across servers.

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

      The URL pointing to a FHIR-defined protocol, guideline, order set or other definition that is adhered to in whole or in part by this Procedure.

      ShortGenomicStudy.analysis.instantiatesCanonicalInstantiates FHIR protocol or definition
      Control0..*
      Typecanonical(PlanDefinition, ActivityDefinition, Measure, OperationDefinition, Questionnaire)
      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()))
      36. Procedure.instantiatesUri
      Definition

      The URL pointing to an externally maintained protocol, guideline, order set or other definition that is adhered to in whole or in part by this Procedure.

      ShortGenomicStudy.analysis.instantiatesUriInstantiates external protocol or definition
      Comments

      This might be an HTML page, PDF, etc. or could just be a non-resolvable URI identifier.

      Control0..*
      Typeuri
      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()))
      38. Procedure.basedOn
      Definition

      A reference to a resource that contains details of the request for this procedure.

      ShortA request for this procedure
      Control0..0*
      TypeReference(CarePlan, ServiceRequest)
      Is Modifierfalse
      Summarytrue
      Alternate Namesfulfills
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      40. Procedure.partOf
      Definition

      A larger event of which this particular procedure is a component or step.

      ShortPart of referenced event
      Comments

      The MedicationAdministration resource has a partOf reference to Procedure, but this is not a circular reference. For example, the anesthesia MedicationAdministration is part of the surgical Procedure (MedicationAdministration.partOf = Procedure). For example, the procedure to insert the IV port for an IV medication administration is part of the medication administration (Procedure.partOf = MedicationAdministration).

      Control0..0*
      TypeReference(Procedure, Observation, MedicationAdministration)
      Is Modifierfalse
      Summarytrue
      Alternate Namescontainer
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      42. Procedure.status
      Definition

      A code specifying the state of the procedure. Generally, this will be the in-progress or completed state.

      Shortpreparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown
      Comments

      The "unknown" code is not to be used to convey other statuses. The "unknown" code should be used when one of the statuses applies, but the authoring system doesn't know the current state of the procedure.

      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 EventStatushttp://hl7.org/fhir/ValueSet/event-status|4.0.1
      (required to http://hl7.org/fhir/ValueSet/event-status|4.0.1)

      A code specifying the state of the procedure.

      Typecode
      Is Modifiertrue because This element is labelled 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
      Pattern Valuecompleted
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      44. Procedure.statusReason
      Definition

      Captures the reason for the current state of the procedure.

      ShortReason for current status
      Comments

      This is generally only used for "exception" statuses such as "not-done", "suspended" or "aborted". The reason for performing the event at all is captured in reasonCode, not here.

      Control0..01
      BindingFor example codes, see ProcedureNotPerformedReason(SNOMED-CT)http://hl7.org/fhir/ValueSet/procedure-not-performed-reason
      (example to http://hl7.org/fhir/ValueSet/procedure-not-performed-reason)

      A code that identifies the reason a procedure was not performed.

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Alternate NamesSuspended Reason, Cancelled Reason
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      46. Procedure.category
      Definition

      A code that classifies the procedure for searching, sorting and display purposes (e.g. "Surgical Procedure").

      ShortClassification of the procedure
      Control10..1
      BindingFor example codes, see ProcedureCategoryCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-category
      (example to http://hl7.org/fhir/ValueSet/procedure-category)

      A code that classifies a procedure for searching, sorting and display purposes.

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      48. Procedure.category.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()))
      50. Procedure.code
      Definition

      The specific procedure that is performed. Use text if the exact nature of the procedure cannot be coded (e.g. "Laparoscopic Appendectomy").

      ShortIdentification of the procedure
      Control0..01
      BindingFor example codes, see ProcedureCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-code
      (example to http://hl7.org/fhir/ValueSet/procedure-code)

      A code to identify a specific procedure .

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Requirements

      0..1 to account for primarily narrative only resources.

      Alternate Namestype
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      52. Procedure.subject
      Definition

      The person, animal or group on which the procedure was performed.

      ShortWho the procedure was performed on
      Control1..1
      TypeReference(Patient, Group)
      Is Modifierfalse
      Summarytrue
      Alternate Namespatient
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      54. Procedure.encounter
      Definition

      The Encounter during which this Procedure was created or performed or to which the creation of this record is tightly associated.

      ShortEncounter created as part of
      Comments

      This will typically be the encounter the event occurred within, but some activities may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter.

      Control0..01
      TypeReference(Encounter)
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      56. Procedure.performed[x]
      Definition

      Estimated or actual date, date-time, period, or age when the procedure was performed. Allows a period to support complex procedures that span more than one date, and also allows for the length of the procedure to be captured.

      ShortGenomicStudy.analysis.dateWhen the procedure was performed
      Comments

      Age is generally used when the patient reports an age at which the procedure was performed. Range is generally used when the patient reports an age range when the procedure was performed, such as sometime between 20-25 years old. dateTime supports a range of precision due to some procedures being reported as past procedures that might not have millisecond precision while other procedures performed and documented during the encounter might have more precise UTC timestamps with timezone.

      Control0..1
      TypedateTime, string, Period, Range, Age
      [x] NoteSee Choice of Data Types for further information about how to use [x]
      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()))
      58. Procedure.recorder
      Definition

      Individual who recorded the record and takes responsibility for its content.

      ShortWho recorded the procedure
      Control0..01
      TypeReference(Patient, RelatedPerson, Practitioner, PractitionerRole)
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      60. Procedure.asserter
      Definition

      Individual who is making the procedure statement.

      ShortPerson who asserts this procedure
      Control0..01
      TypeReference(Patient, RelatedPerson, Practitioner, PractitionerRole)
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      62. Procedure.location
      Definition

      The location where the procedure actually happened. E.g. a newborn at home, a tracheostomy at a restaurant.

      ShortWhere the procedure happened
      Control0..01
      TypeReference(Location)
      Is Modifierfalse
      Summarytrue
      Requirements

      Ties a procedure to where the records are likely kept.

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

      The coded reason why the procedure was performed. This may be a coded entity of some type, or may simply be present as text.

      ShortCoded reason procedure performed
      Comments

      Use Procedure.reasonCode when a code sufficiently describes the reason. Use Procedure.reasonReference when referencing a resource, which allows more information to be conveyed, such as onset date. Procedure.reasonCode and Procedure.reasonReference are not meant to be duplicative. For a single reason, either Procedure.reasonCode or Procedure.reasonReference can be used. Procedure.reasonCode may be a summary code, or Procedure.reasonReference may be used to reference a very precise definition of the reason using Condition | Observation | Procedure | DiagnosticReport | DocumentReference. Both Procedure.reasonCode and Procedure.reasonReference can be used if they are describing different reasons for the procedure.

      Control0..0*
      BindingFor example codes, see ProcedureReasonCodeshttp://hl7.org/fhir/ValueSet/procedure-reason
      (example to http://hl7.org/fhir/ValueSet/procedure-reason)

      A code that identifies the reason a procedure is required.

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      66. Procedure.reasonReference
      Definition

      The justification of why the procedure was performed.

      ShortThe justification that the procedure was performed
      Comments

      It is possible for a procedure to be a reason (such as C-Section) for another procedure (such as an epidural). Other examples include endoscopy for dilatation and biopsy (a combination of diagnostic and therapeutic use). Use Procedure.reasonCode when a code sufficiently describes the reason. Use Procedure.reasonReference when referencing a resource, which allows more information to be conveyed, such as onset date. Procedure.reasonCode and Procedure.reasonReference are not meant to be duplicative. For a single reason, either Procedure.reasonCode or Procedure.reasonReference can be used. Procedure.reasonCode may be a summary code, or Procedure.reasonReference may be used to reference a very precise definition of the reason using Condition | Observation | Procedure | DiagnosticReport | DocumentReference. Both Procedure.reasonCode and Procedure.reasonReference can be used if they are describing different reasons for the procedure.

      Control0..0*
      TypeReference(Condition, Observation, Procedure, DiagnosticReport, DocumentReference)
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      68. Procedure.bodySite
      Definition

      Detailed and structured anatomical location information. Multiple locations are allowed - e.g. multiple punch biopsies of a lesion.

      ShortTarget body sites
      Comments

      If the use case requires attributes from the BodySite resource (e.g. to identify and track separately) then use the standard extension procedure-targetbodystructure.

      Control0..0*
      BindingFor example codes, see SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-site
      (example to http://hl7.org/fhir/ValueSet/body-site)

      Codes describing anatomical locations. May include laterality.

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      70. Procedure.outcome
      Definition

      The outcome of the procedure - did it resolve the reasons for the procedure being performed?

      ShortThe result of procedure
      Comments

      If outcome contains narrative text only, it can be captured using the CodeableConcept.text.

      Control0..01
      BindingFor example codes, see ProcedureOutcomeCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-outcome
      (example to http://hl7.org/fhir/ValueSet/procedure-outcome)

      An outcome of a procedure - whether it was resolved or otherwise.

      TypeCodeableConcept
      Is Modifierfalse
      Summarytrue
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      72. Procedure.report
      Definition

      This could be a histology result, pathology report, surgical report, etc.

      ShortAny report resulting from the procedure
      Comments

      There could potentially be multiple reports - e.g. if this was a procedure which took multiple biopsies resulting in a number of anatomical pathology reports.

      Control0..0*
      TypeReference(DiagnosticReport, DocumentReference, Composition)
      Is Modifierfalse
      Summaryfalse
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      74. Procedure.complication
      Definition

      Any complications that occurred during the procedure, or in the immediate post-performance period. These are generally tracked separately from the notes, which will typically describe the procedure itself rather than any 'post procedure' issues.

      ShortComplication following the procedure
      Comments

      If complications are only expressed by the narrative text, they can be captured using the CodeableConcept.text.

      Control0..0*
      BindingFor example codes, see Condition/Problem/DiagnosisCodeshttp://hl7.org/fhir/ValueSet/condition-code
      (example to http://hl7.org/fhir/ValueSet/condition-code)

      Codes describing complications that resulted from a procedure.

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

      Any complications that occurred during the procedure, or in the immediate post-performance period.

      ShortA condition that is a result of the procedure
      Control0..0*
      TypeReference(Condition)
      Is Modifierfalse
      Summaryfalse
      Requirements

      This is used to document a condition that is a result of the procedure, not the condition that was the reason for the procedure.

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

      If the procedure required specific follow up - e.g. removal of sutures. The follow up may be represented as a simple note or could potentially be more complex, in which case the CarePlan resource can be used.

      ShortInstructions for follow up
      Control0..0*
      BindingFor example codes, see ProcedureFollowUpCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-followup
      (example to http://hl7.org/fhir/ValueSet/procedure-followup)

      Specific follow up required for a procedure e.g. removal of sutures.

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

      Any other notes and comments about the procedure.

      ShortGenomicStudy.analysis.noteAdditional information about the procedure
      Control0..*
      TypeAnnotation
      Is Modifierfalse
      Summaryfalse
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      82. Procedure.focalDevice
      Definition

      A device that is implanted, removed or otherwise manipulated (calibration, battery replacement, fitting a prosthesis, attaching a wound-vac, etc.) as a focal portion of the Procedure.

      ShortManipulated, implanted, or removed device
      Control0..0*
      TypeBackboneElement
      Is Modifierfalse
      Summaryfalse
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      86. Procedure.usedReference
      Definition

      Identifies medications, devices and any other substance used as part of the procedure.

      ShortItems used during procedure
      Comments

      For devices actually implanted or removed, use Procedure.device.

      Control0..0*
      TypeReference(Device, Medication, Substance)
      Is Modifierfalse
      Summaryfalse
      Requirements

      Used for tracking contamination, etc.

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

      Identifies coded items that were used as part of the procedure.

      ShortCoded items used during the procedure
      Comments

      For devices actually implanted or removed, use Procedure.device.

      Control0..0*
      BindingFor example codes, see FHIRDeviceTypeshttp://hl7.org/fhir/ValueSet/device-kind
      (example to http://hl7.org/fhir/ValueSet/device-kind)

      Codes describing items used during a procedure.

      TypeCodeableConcept
      Is Modifierfalse
      Summaryfalse
      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. Procedure
      Definition

      An action that is or was performed on or for a patient. This can be a physical intervention like an operation, or less invasive like long term services, counseling, or hypnotherapy.

      ShortAn action that is being or was performed on a patient
      Control0..*
      Is Modifierfalse
      Summaryfalse
      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. Procedure.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. Procedure.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. Procedure.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. Procedure.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. Procedure.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. Procedure.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. Procedure.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 Procedure.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
      • value @ url
      • 16. Procedure.extension:method-type
        Slice Namemethod-type
        Definition

        Defines a method type for a genomic analysis

        ShortGenomicStudy.analysis.methodType
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Method Type) (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. Procedure.extension:change-type
        Slice Namechange-type
        Definition

        Defines the change type for a genomic analysis

        ShortGenomicStudy.analysis.changeType
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Change Type) (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())
        20. Procedure.extension:genome-build
        Slice Namegenome-build
        Definition

        Defines the genome build for a genomic analysis

        ShortGenomicStudy.analysis.genomeBuild
        Control0..1
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Genome Build) (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())
        22. Procedure.extension:title
        Slice Nametitle
        Definition

        Defines a title for a genomic analysis

        ShortGenomicStudy.analysis.title
        Control0..1
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Title) (Extension Type: string)
        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. Procedure.extension:focus
        Slice Namefocus
        Definition

        Defines a focus for a genomic analysis

        ShortGenomicStudy.analysis.focus
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Focus) (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())
        26. Procedure.extension:specimen
        Slice Namespecimen
        Definition

        Defines a specimen for a genomic analysis

        ShortGenomicStudy.analysis.specimen
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Specimen) (Extension Type: Reference(Specimen))
        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. Procedure.extension:metrics
        Slice Namemetrics
        Definition

        Metrics about the sequencing analysis that was performed

        ShortGenomic Study Analysis Metrics
        Control0..1
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Metrics) (Complex Extension)
        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())
        30. Procedure.extension:regions
        Slice Nameregions
        Definition

        Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

        ShortGenomic Study Analysis Regions
        Control0..1
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Regions) (Complex Extension)
        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())
        32. Procedure.extension:device
        Slice Namedevice
        Definition

        Genomic Study Analysis Device

        ShortGenomicStudy.analysis.device
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Device) (Complex Extension)
        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())
        34. Procedure.extension:protocol-performed
        Slice Nameprotocol-performed
        Definition

        Defines a protocol that was performed for a genomic analysis

        ShortGenomicStudy.protocolPerformed
        Control0..1
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Protocol Performed) (Extension Type: Reference(Procedure, Task))
        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())
        36. Procedure.extension:input
        Slice Nameinput
        Definition

        Genomic Study Analysis Input

        ShortGenomicStudy.analysis.input
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Input) (Complex Extension)
        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())
        38. Procedure.extension:output
        Slice Nameoutput
        Definition

        Genomic Study Analysis Output

        ShortGenomicStudy.analysis.output
        Control0..*
        This element is affected by the following invariants: ele-1
        TypeExtension(Genomic Study Analysis Output) (Complex Extension)
        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())
        40. Procedure.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())
        42. Procedure.identifier
        Definition

        Business identifiers assigned to this procedure by the performer or other systems which remain constant as the resource is updated and is propagated from server to server.

        ShortGenomicStudy.analysis.identifier
        Comments

        This is a business identifier, not a resource identifier (see discussion). It is best practice for the identifier to only appear on a single resource instance, however business practices may occasionally dictate that multiple resource instances with the same identifier can exist - possibly even with different resource types. For example, multiple Patient and Person resource instances might share the same social insurance number.

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

        Allows identification of the procedure as it is known by various participating systems and in a way that remains consistent across servers.

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

        The URL pointing to a FHIR-defined protocol, guideline, order set or other definition that is adhered to in whole or in part by this Procedure.

        ShortGenomicStudy.analysis.instantiatesCanonical
        Control0..*
        Typecanonical(PlanDefinition, ActivityDefinition)
        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()))
        46. Procedure.instantiatesUri
        Definition

        The URL pointing to an externally maintained protocol, guideline, order set or other definition that is adhered to in whole or in part by this Procedure.

        ShortGenomicStudy.analysis.instantiatesUri
        Comments

        This might be an HTML page, PDF, etc. or could just be a non-resolvable URI identifier.

        Control0..*
        Typeuri
        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()))
        48. Procedure.basedOn
        Definition

        A reference to a resource that contains details of the request for this procedure.

        ShortA request for this procedure
        Control0..0
        TypeReference(CarePlan, ServiceRequest)
        Is Modifierfalse
        Summarytrue
        Alternate Namesfulfills
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        50. Procedure.partOf
        Definition

        A larger event of which this particular procedure is a component or step.

        ShortPart of referenced event
        Comments

        The MedicationAdministration resource has a partOf reference to Procedure, but this is not a circular reference. For example, the anesthesia MedicationAdministration is part of the surgical Procedure (MedicationAdministration.partOf = Procedure). For example, the procedure to insert the IV port for an IV medication administration is part of the medication administration (Procedure.partOf = MedicationAdministration).

        Control0..0
        TypeReference(Procedure, Observation, MedicationAdministration)
        Is Modifierfalse
        Summarytrue
        Alternate Namescontainer
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        52. Procedure.status
        Definition

        A code specifying the state of the procedure. Generally, this will be the in-progress or completed state.

        Shortpreparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown
        Comments

        The "unknown" code is not to be used to convey other statuses. The "unknown" code should be used when one of the statuses applies, but the authoring system doesn't know the current state of the procedure.

        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 EventStatus
        (required to http://hl7.org/fhir/ValueSet/event-status|4.0.1)

        A code specifying the state of the procedure.

        Typecode
        Is Modifiertrue because This element is labelled 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
        Pattern Valuecompleted
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        54. Procedure.statusReason
        Definition

        Captures the reason for the current state of the procedure.

        ShortReason for current status
        Comments

        This is generally only used for "exception" statuses such as "not-done", "suspended" or "aborted". The reason for performing the event at all is captured in reasonCode, not here.

        Control0..0
        BindingFor example codes, see ProcedureNotPerformedReason(SNOMED-CT)
        (example to http://hl7.org/fhir/ValueSet/procedure-not-performed-reason)

        A code that identifies the reason a procedure was not performed.

        TypeCodeableConcept
        Is Modifierfalse
        Summarytrue
        Alternate NamesSuspended Reason, Cancelled Reason
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        56. Procedure.category
        Definition

        A code that classifies the procedure for searching, sorting and display purposes (e.g. "Surgical Procedure").

        ShortClassification of the procedure
        Control1..1
        BindingFor example codes, see ProcedureCategoryCodes(SNOMEDCT)
        (example to http://hl7.org/fhir/ValueSet/procedure-category)

        A code that classifies a procedure for searching, sorting and display purposes.

        TypeCodeableConcept
        Is Modifierfalse
        Summarytrue
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        58. Procedure.category.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
        60. Procedure.category.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 Procedure.category.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
        • value @ url
        • 62. Procedure.category.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()))
          64. Procedure.category.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()))
          66. Procedure.code
          Definition

          The specific procedure that is performed. Use text if the exact nature of the procedure cannot be coded (e.g. "Laparoscopic Appendectomy").

          ShortIdentification of the procedure
          Control0..0
          BindingFor example codes, see ProcedureCodes(SNOMEDCT)
          (example to http://hl7.org/fhir/ValueSet/procedure-code)

          A code to identify a specific procedure .

          TypeCodeableConcept
          Is Modifierfalse
          Summarytrue
          Requirements

          0..1 to account for primarily narrative only resources.

          Alternate Namestype
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          68. Procedure.subject
          Definition

          The person, animal or group on which the procedure was performed.

          ShortWho the procedure was performed on
          Control1..1
          TypeReference(Patient, Group)
          Is Modifierfalse
          Summarytrue
          Alternate Namespatient
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          70. Procedure.encounter
          Definition

          The Encounter during which this Procedure was created or performed or to which the creation of this record is tightly associated.

          ShortEncounter created as part of
          Comments

          This will typically be the encounter the event occurred within, but some activities may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter.

          Control0..0
          TypeReference(Encounter)
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          72. Procedure.performed[x]
          Definition

          Estimated or actual date, date-time, period, or age when the procedure was performed. Allows a period to support complex procedures that span more than one date, and also allows for the length of the procedure to be captured.

          ShortGenomicStudy.analysis.date
          Comments

          Age is generally used when the patient reports an age at which the procedure was performed. Range is generally used when the patient reports an age range when the procedure was performed, such as sometime between 20-25 years old. dateTime supports a range of precision due to some procedures being reported as past procedures that might not have millisecond precision while other procedures performed and documented during the encounter might have more precise UTC timestamps with timezone.

          Control0..1
          TypedateTime
          [x] NoteSee Choice of Data Types for further information about how to use [x]
          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()))
          74. Procedure.recorder
          Definition

          Individual who recorded the record and takes responsibility for its content.

          ShortWho recorded the procedure
          Control0..0
          TypeReference(Patient, RelatedPerson, Practitioner, PractitionerRole)
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          76. Procedure.asserter
          Definition

          Individual who is making the procedure statement.

          ShortPerson who asserts this procedure
          Control0..0
          TypeReference(Patient, RelatedPerson, Practitioner, PractitionerRole)
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          78. Procedure.performer
          Definition

          Limited to "real" people rather than equipment.

          ShortThe people who performed the procedure
          Control0..*
          TypeBackboneElement
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          80. Procedure.performer.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
          82. Procedure.performer.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())
          84. Procedure.performer.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())
          86. Procedure.performer.function
          Definition

          Distinguishes the type of involvement of the performer in the procedure. For example, surgeon, anaesthetist, endoscopist.

          ShortGenomicStudy.analysis.performer.role
          Control0..1
          BindingFor example codes, see ProcedurePerformerRoleCodes
          (example to http://hl7.org/fhir/ValueSet/performer-role)

          A code that identifies the role of a performer of the procedure.

          TypeCodeableConcept
          Is Modifierfalse
          Summarytrue
          Requirements

          Allows disambiguation of the types of involvement of different performers.

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

          The practitioner who was involved in the procedure.

          ShortGenomicStudy.analysis.performer.actor
          Control1..1
          TypeReference(Practitioner, PractitionerRole, Organization, Device)
          Is Modifierfalse
          Summarytrue
          Requirements

          A reference to Device supports use cases, such as pacemakers.

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

          The organization the device or practitioner was acting on behalf of.

          ShortOrganization the device or practitioner was acting for
          Control0..1
          TypeReference(Organization)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Practitioners and Devices can be associated with multiple organizations. This element indicates which organization they were acting on behalf of when performing the action.

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

          The location where the procedure actually happened. E.g. a newborn at home, a tracheostomy at a restaurant.

          ShortWhere the procedure happened
          Control0..0
          TypeReference(Location)
          Is Modifierfalse
          Summarytrue
          Requirements

          Ties a procedure to where the records are likely kept.

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

          The coded reason why the procedure was performed. This may be a coded entity of some type, or may simply be present as text.

          ShortCoded reason procedure performed
          Comments

          Use Procedure.reasonCode when a code sufficiently describes the reason. Use Procedure.reasonReference when referencing a resource, which allows more information to be conveyed, such as onset date. Procedure.reasonCode and Procedure.reasonReference are not meant to be duplicative. For a single reason, either Procedure.reasonCode or Procedure.reasonReference can be used. Procedure.reasonCode may be a summary code, or Procedure.reasonReference may be used to reference a very precise definition of the reason using Condition | Observation | Procedure | DiagnosticReport | DocumentReference. Both Procedure.reasonCode and Procedure.reasonReference can be used if they are describing different reasons for the procedure.

          Control0..0
          BindingFor example codes, see ProcedureReasonCodes
          (example to http://hl7.org/fhir/ValueSet/procedure-reason)

          A code that identifies the reason a procedure is required.

          TypeCodeableConcept
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          96. Procedure.reasonReference
          Definition

          The justification of why the procedure was performed.

          ShortThe justification that the procedure was performed
          Comments

          It is possible for a procedure to be a reason (such as C-Section) for another procedure (such as an epidural). Other examples include endoscopy for dilatation and biopsy (a combination of diagnostic and therapeutic use). Use Procedure.reasonCode when a code sufficiently describes the reason. Use Procedure.reasonReference when referencing a resource, which allows more information to be conveyed, such as onset date. Procedure.reasonCode and Procedure.reasonReference are not meant to be duplicative. For a single reason, either Procedure.reasonCode or Procedure.reasonReference can be used. Procedure.reasonCode may be a summary code, or Procedure.reasonReference may be used to reference a very precise definition of the reason using Condition | Observation | Procedure | DiagnosticReport | DocumentReference. Both Procedure.reasonCode and Procedure.reasonReference can be used if they are describing different reasons for the procedure.

          Control0..0
          TypeReference(Condition, Observation, Procedure, DiagnosticReport, DocumentReference)
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          98. Procedure.bodySite
          Definition

          Detailed and structured anatomical location information. Multiple locations are allowed - e.g. multiple punch biopsies of a lesion.

          ShortTarget body sites
          Comments

          If the use case requires attributes from the BodySite resource (e.g. to identify and track separately) then use the standard extension procedure-targetbodystructure.

          Control0..0
          BindingFor example codes, see SNOMEDCTBodyStructures
          (example to http://hl7.org/fhir/ValueSet/body-site)

          Codes describing anatomical locations. May include laterality.

          TypeCodeableConcept
          Is Modifierfalse
          Summarytrue
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          100. Procedure.outcome
          Definition

          The outcome of the procedure - did it resolve the reasons for the procedure being performed?

          ShortThe result of procedure
          Comments

          If outcome contains narrative text only, it can be captured using the CodeableConcept.text.

          Control0..0
          BindingFor example codes, see ProcedureOutcomeCodes(SNOMEDCT)
          (example to http://hl7.org/fhir/ValueSet/procedure-outcome)

          An outcome of a procedure - whether it was resolved or otherwise.

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

          This could be a histology result, pathology report, surgical report, etc.

          ShortAny report resulting from the procedure
          Comments

          There could potentially be multiple reports - e.g. if this was a procedure which took multiple biopsies resulting in a number of anatomical pathology reports.

          Control0..0
          TypeReference(DiagnosticReport, DocumentReference, Composition)
          Is Modifierfalse
          Summaryfalse
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          104. Procedure.complication
          Definition

          Any complications that occurred during the procedure, or in the immediate post-performance period. These are generally tracked separately from the notes, which will typically describe the procedure itself rather than any 'post procedure' issues.

          ShortComplication following the procedure
          Comments

          If complications are only expressed by the narrative text, they can be captured using the CodeableConcept.text.

          Control0..0
          BindingFor example codes, see Condition/Problem/DiagnosisCodes
          (example to http://hl7.org/fhir/ValueSet/condition-code)

          Codes describing complications that resulted from a procedure.

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

          Any complications that occurred during the procedure, or in the immediate post-performance period.

          ShortA condition that is a result of the procedure
          Control0..0
          TypeReference(Condition)
          Is Modifierfalse
          Summaryfalse
          Requirements

          This is used to document a condition that is a result of the procedure, not the condition that was the reason for the procedure.

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

          If the procedure required specific follow up - e.g. removal of sutures. The follow up may be represented as a simple note or could potentially be more complex, in which case the CarePlan resource can be used.

          ShortInstructions for follow up
          Control0..0
          BindingFor example codes, see ProcedureFollowUpCodes(SNOMEDCT)
          (example to http://hl7.org/fhir/ValueSet/procedure-followup)

          Specific follow up required for a procedure e.g. removal of sutures.

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

          Any other notes and comments about the procedure.

          ShortGenomicStudy.analysis.note
          Control0..*
          TypeAnnotation
          Is Modifierfalse
          Summaryfalse
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          112. Procedure.focalDevice
          Definition

          A device that is implanted, removed or otherwise manipulated (calibration, battery replacement, fitting a prosthesis, attaching a wound-vac, etc.) as a focal portion of the Procedure.

          ShortManipulated, implanted, or removed device
          Control0..0
          TypeBackboneElement
          Is Modifierfalse
          Summaryfalse
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          119. Procedure.usedReference
          Definition

          Identifies medications, devices and any other substance used as part of the procedure.

          ShortItems used during procedure
          Comments

          For devices actually implanted or removed, use Procedure.device.

          Control0..0
          TypeReference(Device, Medication, Substance)
          Is Modifierfalse
          Summaryfalse
          Requirements

          Used for tracking contamination, etc.

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

          Identifies coded items that were used as part of the procedure.

          ShortCoded items used during the procedure
          Comments

          For devices actually implanted or removed, use Procedure.device.

          Control0..0
          BindingFor example codes, see FHIRDeviceTypes
          (example to http://hl7.org/fhir/ValueSet/device-kind)

          Codes describing items used during a procedure.

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