Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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

## Resource Profile: GenomicStudyAnalysis - Detailed Descriptions

Page standards status: Trial-use | Maturity Level: 2

Definitions for the genomic-study-analysis resource profile.

- Key Elements Table
- Differential Elements Table
- Snapshot Elements Table

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

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.
Short | An action that is being or was performed on a patient
Control | 0..*
Is Modifier | false
Summary | false
Invariants | dom-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.
Short | A 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.
Control | 0..1
Type | uri
Is Modifier | true 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 Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-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.
Short | ExtensionAdditional 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.
Control | 0..*
Type | Extension
Is Modifier | false
Summary | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
Slicing | This element introduces a set of slices on `Procedure.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
6. Procedure.extension:method-type
Slice Name | method-type
Definition | Defines a method type for a genomic analysis
Short | GenomicStudy.analysis.methodType
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Method Type) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
8. Procedure.extension:change-type
Slice Name | change-type
Definition | Defines the types of alterations detectable by a given genomic analysis
Short | GenomicStudy.analysis.changeType
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Change Type) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
10. Procedure.extension:genome-build
Slice Name | genome-build
Definition | Defines the genome build for a genomic analysis
Short | GenomicStudy.analysis.genomeBuild
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Genome Build) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
12. Procedure.extension:genomic-source-class
Slice Name | genomic-source-class
Definition | The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.
Short | GenomicStudy.analysis.genomicSourceClass
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Source Class) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
14. Procedure.extension:title
Slice Name | title
Definition | Defines a title for a genomic analysis
Short | GenomicStudy.analysis.title
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Title) (Extension Type: string)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
16. Procedure.extension:focus
Slice Name | focus
Definition | Defines a focus for a genomic analysis
Short | GenomicStudy.analysis.focus
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Focus) (Extension Type: Reference(Resource))
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
18. Procedure.extension:specimen
Slice Name | specimen
Definition | Defines a specimen for a genomic analysis
Short | GenomicStudy.analysis.specimen
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Specimen) (Extension Type: Reference(Specimen))
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
20. Procedure.extension:metrics
Slice Name | metrics
Definition | Metrics about the sequencing analysis that was performed
Short | Genomic Study Analysis Metrics
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Metrics) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
22. Procedure.extension:regions
Slice Name | regions
Definition | Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)
Short | Genomic Study Analysis Regions
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Regions) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
24. Procedure.extension:device
Slice Name | device
Definition | Genomic Study Analysis Device
Short | GenomicStudy.analysis.device
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Device) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
26. Procedure.extension:protocol-performed
Slice Name | protocol-performed
Definition | Defines a protocol that was performed for a genomic analysis
Short | GenomicStudy.protocolPerformed
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Protocol Performed) (Extension Type: Reference(Procedure, Task))
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
28. Procedure.extension:input
Slice Name | input
Definition | Genomic Study Analysis Input
Short | GenomicStudy.analysis.input
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Input) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
30. Procedure.extension:output
Slice Name | output
Definition | Genomic Study Analysis Output
Short | GenomicStudy.analysis.output
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Output) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
32. 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).
Short | Extensions 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Summary | false
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 Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
34. 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.
Short | GenomicStudy.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.
Note | This is a business identifier, not a resource identifier (see discussion)
Control | 0..*
Type | Identifier
Is Modifier | false
Summary | true
Requirements | Allows identification of the procedure as it is known by various participating systems and in a way that remains consistent across servers.
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
36. 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.
Short | GenomicStudy.analysis.instantiatesCanonicalInstantiates FHIR protocol or definition
Control | 0..*
Type | canonical(PlanDefinition, ActivityDefinition, PlanDefinition, ActivityDefinition, Measure, OperationDefinition, Questionnaire)
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
38. 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.
Short | GenomicStudy.analysis.instantiatesUriInstantiates external protocol or definition
Comments | This might be an HTML page, PDF, etc. or could just be a non-resolvable URI identifier.
Control | 0..*
Type | uri
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
40. Procedure.basedOn
Definition | A reference to a resource that contains details of the request for this procedure.
Short | A request for this procedure
Control | 0..0*
Type | Reference(CarePlan, ServiceRequest)
Is Modifier | false
Summary | true
Alternate Names | fulfills
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
42. Procedure.partOf
Definition | A larger event of which this particular procedure is a component or step.
Short | Part 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).
Control | 0..0*
Type | Reference(Procedure, Observation, MedicationAdministration)
Is Modifier | false
Summary | true
Alternate Names | container
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
44. Procedure.status
Definition | A code specifying the state of the procedure. Generally, this will be the in-progress or completed state.
Short | preparation | 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.
Control | 1..1
Binding | The codes SHALL be taken from EventStatus http://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.
Type | code
Is Modifier | true 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 Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Pattern Value | `completed`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
46. Procedure.statusReason
Definition | Captures the reason for the current state of the procedure.
Short | Reason 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.
Control | 0..01
Binding | For example codes, see ProcedureNotPerformedReason(SNOMED-CT)http://hl7.org/fhir/ValueSet/procedure-not-performed-reason|4.0.1 (example to `http://hl7.org/fhir/ValueSet/procedure-not-performed-reason|4.0.1` ) A code that identifies the reason a procedure was not performed.
Type | CodeableConcept
Is Modifier | false
Summary | true
Alternate Names | Suspended Reason, Cancelled Reason
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
48. Procedure.category
Definition | A code that classifies the procedure for searching, sorting and display purposes (e.g. "Surgical Procedure").
Short | Classification of the procedure
Control | 10..1
Binding | For example codes, see ProcedureCategoryCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-category|4.0.1 (example to `http://hl7.org/fhir/ValueSet/procedure-category|4.0.1` ) A code that classifies a procedure for searching, sorting and display purposes.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
50. Procedure.category.coding
Definition | A reference to a code defined by a terminology system.
Short | Code 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.
Control | 10..1*
Type | Coding
Is Modifier | false
Summary | true
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" }`
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
52. 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").
Short | Identification of the procedure
Control | 0..01
Binding | For example codes, see ProcedureCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-code|4.0.1 (example to `http://hl7.org/fhir/ValueSet/procedure-code|4.0.1` ) A code to identify a specific procedure .
Type | CodeableConcept
Is Modifier | false
Summary | true
Requirements | 0..1 to account for primarily narrative only resources.
Alternate Names | type
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
54. Procedure.subject
Definition | The person, animal or group on which the procedure was performed.
Short | Who the procedure was performed on
Control | 1..1
Type | Reference(Patient, Group)
Is Modifier | false
Summary | true
Alternate Names | patient
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
56. Procedure.encounter
Definition | The Encounter during which this Procedure was created or performed or to which the creation of this record is tightly associated.
Short | Encounter 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.
Control | 0..01
Type | Reference(Encounter)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
58. 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.
Short | GenomicStudy.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.
Control | 0..1
Type | dateTime, string, Period, Range, Age
[x] Note | SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
60. Procedure.recorder
Definition | Individual who recorded the record and takes responsibility for its content.
Short | Who recorded the procedure
Control | 0..01
Type | Reference(Patient, RelatedPerson, Practitioner, PractitionerRole)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
62. Procedure.asserter
Definition | Individual who is making the procedure statement.
Short | Person who asserts this procedure
Control | 0..01
Type | Reference(Patient, RelatedPerson, Practitioner, PractitionerRole)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
64. Procedure.location
Definition | The location where the procedure actually happened. E.g. a newborn at home, a tracheostomy at a restaurant.
Short | Where the procedure happened
Control | 0..01
Type | Reference(Location)
Is Modifier | false
Summary | true
Requirements | Ties a procedure to where the records are likely kept.
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
66. 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.
Short | Coded 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.
Control | 0..0*
Binding | For example codes, see ProcedureReasonCodes http://hl7.org/fhir/ValueSet/procedure-reason|4.0.1 (example to `http://hl7.org/fhir/ValueSet/procedure-reason|4.0.1` ) A code that identifies the reason a procedure is required.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
68. Procedure.reasonReference
Definition | The justification of why the procedure was performed.
Short | The 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.
Control | 0..0*
Type | Reference(Condition, Observation, Procedure, DiagnosticReport, DocumentReference)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
70. Procedure.bodySite
Definition | Detailed and structured anatomical location information. Multiple locations are allowed - e.g. multiple punch biopsies of a lesion.
Short | Target 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.
Control | 0..0*
Binding | For example codes, see SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site|4.0.1 (example to `http://hl7.org/fhir/ValueSet/body-site|4.0.1` ) Codes describing anatomical locations. May include laterality.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
72. Procedure.outcome
Definition | The outcome of the procedure - did it resolve the reasons for the procedure being performed?
Short | The result of procedure
Comments | If outcome contains narrative text only, it can be captured using the CodeableConcept.text.
Control | 0..01
Binding | For example codes, see ProcedureOutcomeCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-outcome|4.0.1 (example to `http://hl7.org/fhir/ValueSet/procedure-outcome|4.0.1` ) An outcome of a procedure - whether it was resolved or otherwise.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
74. Procedure.report
Definition | This could be a histology result, pathology report, surgical report, etc.
Short | Any 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.
Control | 0..0*
Type | Reference(DiagnosticReport, DocumentReference, Composition)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
76. 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.
Short | Complication following the procedure
Comments | If complications are only expressed by the narrative text, they can be captured using the CodeableConcept.text.
Control | 0..0*
Binding | For example codes, see Condition/Problem/DiagnosisCodes http://hl7.org/fhir/ValueSet/condition-code|4.0.1 (example to `http://hl7.org/fhir/ValueSet/condition-code|4.0.1` ) Codes describing complications that resulted from a procedure.
Type | CodeableConcept
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
78. Procedure.complicationDetail
Definition | Any complications that occurred during the procedure, or in the immediate post-performance period.
Short | A condition that is a result of the procedure
Control | 0..0*
Type | Reference(Condition)
Is Modifier | false
Summary | false
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.
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
80. 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.
Short | Instructions for follow up
Control | 0..0*
Binding | For example codes, see ProcedureFollowUpCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-followup|4.0.1 (example to `http://hl7.org/fhir/ValueSet/procedure-followup|4.0.1` ) Specific follow up required for a procedure e.g. removal of sutures.
Type | CodeableConcept
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
82. Procedure.note
Definition | Any other notes and comments about the procedure.
Short | GenomicStudy.analysis.noteAdditional information about the procedure
Control | 0..*
Type | Annotation
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
84. 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.
Short | Manipulated, implanted, or removed device
Control | 0..0*
Type | BackboneElement
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
88. Procedure.usedReference
Definition | Identifies medications, devices and any other substance used as part of the procedure.
Short | Items used during procedure
Comments | For devices actually implanted or removed, use Procedure.device.
Control | 0..0*
Type | Reference(Device, Medication, Substance)
Is Modifier | false
Summary | false
Requirements | Used for tracking contamination, etc.
Invariants | ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
90. Procedure.usedCode
Definition | Identifies coded items that were used as part of the procedure.
Short | Coded items used during the procedure
Comments | For devices actually implanted or removed, use Procedure.device.
Control | 0..0*
Binding | For example codes, see FHIRDeviceTypes http://hl7.org/fhir/ValueSet/device-kind|4.0.1 (example to `http://hl7.org/fhir/ValueSet/device-kind|4.0.1` ) Codes describing items used during a procedure.
Type | CodeableConcept
Is Modifier | false
Summary | false
Invariants | ele-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 foundhere

0. Procedure
2. Procedure.extension
Slicing | This element introduces a set of slices on `Procedure.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
4. Procedure.extension:method-type
Slice Name | method-type
Short | GenomicStudy.analysis.methodType
Control | 0..*
Type | Extension(Genomic Study Analysis Method Type) (Extension Type: CodeableConcept)
6. Procedure.extension:change-type
Slice Name | change-type
Short | GenomicStudy.analysis.changeType
Control | 0..*
Type | Extension(Genomic Study Analysis Change Type) (Extension Type: CodeableConcept)
8. Procedure.extension:genome-build
Slice Name | genome-build
Short | GenomicStudy.analysis.genomeBuild
Control | 0..1
Type | Extension(Genomic Study Analysis Genome Build) (Extension Type: CodeableConcept)
10. Procedure.extension:genomic-source-class
Slice Name | genomic-source-class
Short | GenomicStudy.analysis.genomicSourceClass
Control | 0..1
Type | Extension(Genomic Study Analysis Source Class) (Extension Type: CodeableConcept)
12. Procedure.extension:title
Slice Name | title
Short | GenomicStudy.analysis.title
Control | 0..1
Type | Extension(Genomic Study Analysis Title) (Extension Type: string)
14. Procedure.extension:focus
Slice Name | focus
Short | GenomicStudy.analysis.focus
Control | 0..*
Type | Extension(Genomic Study Analysis Focus) (Extension Type: Reference(Resource))
16. Procedure.extension:specimen
Slice Name | specimen
Short | GenomicStudy.analysis.specimen
Control | 0..*
Type | Extension(Genomic Study Analysis Specimen) (Extension Type: Reference(Specimen))
18. Procedure.extension:metrics
Slice Name | metrics
Short | Genomic Study Analysis Metrics
Control | 0..1
Type | Extension(Genomic Study Analysis Metrics) (Complex Extension)
20. Procedure.extension:regions
Slice Name | regions
Short | Genomic Study Analysis Regions
Control | 0..1
Type | Extension(Genomic Study Analysis Regions) (Complex Extension)
22. Procedure.extension:device
Slice Name | device
Short | GenomicStudy.analysis.device
Control | 0..*
Type | Extension(Genomic Study Analysis Device) (Complex Extension)
24. Procedure.extension:protocol-performed
Slice Name | protocol-performed
Short | GenomicStudy.protocolPerformed
Control | 0..1
Type | Extension(Genomic Study Analysis Protocol Performed) (Extension Type: Reference(Procedure, Task))
26. Procedure.extension:input
Slice Name | input
Short | GenomicStudy.analysis.input
Control | 0..*
Type | Extension(Genomic Study Analysis Input) (Complex Extension)
28. Procedure.extension:output
Slice Name | output
Short | GenomicStudy.analysis.output
Control | 0..*
Type | Extension(Genomic Study Analysis Output) (Complex Extension)
30. Procedure.identifier
Short | GenomicStudy.analysis.identifier
Note | This is a business identifier, not a resource identifier (see discussion)
32. Procedure.instantiatesCanonical
Short | GenomicStudy.analysis.instantiatesCanonical
Type | canonical(PlanDefinition, ActivityDefinition)
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
34. Procedure.instantiatesUri
Short | GenomicStudy.analysis.instantiatesUri
36. Procedure.basedOn
Control | 0..0
38. Procedure.partOf
Control | 0..0
40. Procedure.status
Pattern Value | `completed`
42. Procedure.statusReason
Control | 0..0
44. Procedure.category
Control | 1..?
46. Procedure.category.coding
Control | 1..1
Pattern Value | `{ "system" : "http://terminology.hl7.org/CodeSystem/observation-category", "code" : "laboratory" }`
48. Procedure.code
Control | 0..0
50. Procedure.encounter
Control | 0..0
52. Procedure.performed[x]
Short | GenomicStudy.analysis.date
Type | dateTime, string, Period, Range, Age
[x] Note | SeeChoice of Data Typesfor further information about how to use [x]
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
54. Procedure.recorder
Control | 0..0
56. Procedure.asserter
Control | 0..0
58. Procedure.performer
60. Procedure.performer.function
Short | GenomicStudy.analysis.performer.role
62. Procedure.performer.actor
Short | GenomicStudy.analysis.performer.actor
Type | Reference(Practitioner, PractitionerRole, Organization, Device)
64. Procedure.location
Control | 0..0
66. Procedure.reasonCode
Control | 0..0
68. Procedure.reasonReference
Control | 0..0
70. Procedure.bodySite
Control | 0..0
72. Procedure.outcome
Control | 0..0
74. Procedure.report
Control | 0..0
76. Procedure.complication
Control | 0..0
78. Procedure.complicationDetail
Control | 0..0
80. Procedure.followUp
Control | 0..0
82. Procedure.note
Short | GenomicStudy.analysis.note
84. Procedure.focalDevice
Control | 0..0
86. Procedure.usedReference
Control | 0..0
88. Procedure.usedCode
Control | 0..0

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

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.
Short | An action that is being or was performed on a patient
Control | 0..*
Is Modifier | false
Summary | false
Invariants | dom-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.
Short | Logical 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.
Control | 0..1
Type | id
Is Modifier | false
Summary | true
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.
Short | Metadata about the resource
Control | 0..1
Type | Meta
Is Modifier | false
Summary | true
Invariants | ele-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.
Short | A 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.
Control | 0..1
Type | uri
Is Modifier | true 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 Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-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.
Short | Language 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).
Control | 0..1
Binding | The codes SHOULD be taken from CommonLanguages (preferred to `http://hl7.org/fhir/ValueSet/languages|4.0.1` ) A human language.
Additional Bindings | Purpose
AllLanguages | Max Binding
Type | code
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | false
Invariants | ele-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.
Short | Text 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.
Control | 0..1
Type | Narrative
Is Modifier | false
Summary | false
Alternate Names | narrative, html, xhtml, display
Invariants | ele-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.
Short | Contained, 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.
Control | 0..*
Type | Resource
Is Modifier | false
Summary | false
Alternate Names | inline resources, anonymous resources, contained resources
14. Procedure.extension
Definition | An Extension
Short | Extension
Control | 0..*
Type | Extension
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
Slicing | This element introduces a set of slices on `Procedure.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
16. Procedure.extension:method-type
Slice Name | method-type
Definition | Defines a method type for a genomic analysis
Short | GenomicStudy.analysis.methodType
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Method Type) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
18. Procedure.extension:change-type
Slice Name | change-type
Definition | Defines the types of alterations detectable by a given genomic analysis
Short | GenomicStudy.analysis.changeType
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Change Type) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
20. Procedure.extension:genome-build
Slice Name | genome-build
Definition | Defines the genome build for a genomic analysis
Short | GenomicStudy.analysis.genomeBuild
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Genome Build) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
22. Procedure.extension:genomic-source-class
Slice Name | genomic-source-class
Definition | The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.
Short | GenomicStudy.analysis.genomicSourceClass
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Source Class) (Extension Type: CodeableConcept)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
24. Procedure.extension:title
Slice Name | title
Definition | Defines a title for a genomic analysis
Short | GenomicStudy.analysis.title
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Title) (Extension Type: string)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
26. Procedure.extension:focus
Slice Name | focus
Definition | Defines a focus for a genomic analysis
Short | GenomicStudy.analysis.focus
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Focus) (Extension Type: Reference(Resource))
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
28. Procedure.extension:specimen
Slice Name | specimen
Definition | Defines a specimen for a genomic analysis
Short | GenomicStudy.analysis.specimen
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Specimen) (Extension Type: Reference(Specimen))
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
30. Procedure.extension:metrics
Slice Name | metrics
Definition | Metrics about the sequencing analysis that was performed
Short | Genomic Study Analysis Metrics
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Metrics) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
32. Procedure.extension:regions
Slice Name | regions
Definition | Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)
Short | Genomic Study Analysis Regions
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Regions) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
34. Procedure.extension:device
Slice Name | device
Definition | Genomic Study Analysis Device
Short | GenomicStudy.analysis.device
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Device) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
36. Procedure.extension:protocol-performed
Slice Name | protocol-performed
Definition | Defines a protocol that was performed for a genomic analysis
Short | GenomicStudy.protocolPerformed
Control | 0..1 This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Protocol Performed) (Extension Type: Reference(Procedure, Task))
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
38. Procedure.extension:input
Slice Name | input
Definition | Genomic Study Analysis Input
Short | GenomicStudy.analysis.input
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Input) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
40. Procedure.extension:output
Slice Name | output
Definition | Genomic Study Analysis Output
Short | GenomicStudy.analysis.output
Control | 0..* This element is affected by the following invariants: ele-1
Type | Extension(Genomic Study Analysis Output) (Complex Extension)
Is Modifier | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
42. 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).
Short | Extensions 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them
Summary | false
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 Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
44. 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.
Short | GenomicStudy.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.
Note | This is a business identifier, not a resource identifier (see discussion)
Control | 0..*
Type | Identifier
Is Modifier | false
Summary | true
Requirements | Allows identification of the procedure as it is known by various participating systems and in a way that remains consistent across servers.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
46. 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.
Short | GenomicStudy.analysis.instantiatesCanonical
Control | 0..*
Type | canonical(PlanDefinition, ActivityDefinition)
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
48. 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.
Short | GenomicStudy.analysis.instantiatesUri
Comments | This might be an HTML page, PDF, etc. or could just be a non-resolvable URI identifier.
Control | 0..*
Type | uri
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
50. Procedure.basedOn
Definition | A reference to a resource that contains details of the request for this procedure.
Short | A request for this procedure
Control | 0..0
Type | Reference(CarePlan, ServiceRequest)
Is Modifier | false
Summary | true
Alternate Names | fulfills
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
52. Procedure.partOf
Definition | A larger event of which this particular procedure is a component or step.
Short | Part 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).
Control | 0..0
Type | Reference(Procedure, Observation, MedicationAdministration)
Is Modifier | false
Summary | true
Alternate Names | container
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
54. Procedure.status
Definition | A code specifying the state of the procedure. Generally, this will be the in-progress or completed state.
Short | preparation | 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.
Control | 1..1
Binding | The 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.
Type | code
Is Modifier | true 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 Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Pattern Value | `completed`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
56. Procedure.statusReason
Definition | Captures the reason for the current state of the procedure.
Short | Reason 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.
Control | 0..0
Binding | For example codes, see ProcedureNotPerformedReason(SNOMED-CT) (example to `http://hl7.org/fhir/ValueSet/procedure-not-performed-reason|4.0.1` ) A code that identifies the reason a procedure was not performed.
Type | CodeableConcept
Is Modifier | false
Summary | true
Alternate Names | Suspended Reason, Cancelled Reason
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
58. Procedure.category
Definition | A code that classifies the procedure for searching, sorting and display purposes (e.g. "Surgical Procedure").
Short | Classification of the procedure
Control | 1..1
Binding | For example codes, see ProcedureCategoryCodes(SNOMEDCT) (example to `http://hl7.org/fhir/ValueSet/procedure-category|4.0.1` ) A code that classifies a procedure for searching, sorting and display purposes.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
60. 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.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Summary | false
62. 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.
Short | Additional 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.
Control | 0..*
Type | Extension
Is Modifier | false
Summary | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
Slicing | This element introduces a set of slices on `Procedure.category.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
64. Procedure.category.coding
Definition | A reference to a code defined by a terminology system.
Short | Code 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.
Control | 1..1
Type | Coding
Is Modifier | false
Summary | true
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" }`
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
66. 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.
Short | Plain text representation of the concept
Comments | Very often the text is the same as a displayName of one of the codings.
Control | 0..1
Type | string
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
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.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
68. 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").
Short | Identification of the procedure
Control | 0..0
Binding | For example codes, see ProcedureCodes(SNOMEDCT) (example to `http://hl7.org/fhir/ValueSet/procedure-code|4.0.1` ) A code to identify a specific procedure .
Type | CodeableConcept
Is Modifier | false
Summary | true
Requirements | 0..1 to account for primarily narrative only resources.
Alternate Names | type
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
70. Procedure.subject
Definition | The person, animal or group on which the procedure was performed.
Short | Who the procedure was performed on
Control | 1..1
Type | Reference(Patient, Group)
Is Modifier | false
Summary | true
Alternate Names | patient
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
72. Procedure.encounter
Definition | The Encounter during which this Procedure was created or performed or to which the creation of this record is tightly associated.
Short | Encounter 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.
Control | 0..0
Type | Reference(Encounter)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
74. 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.
Short | GenomicStudy.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.
Control | 0..1
Type | dateTime
[x] Note | SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier | false
Primitive Value | This primitive element may be present, or absent, or replaced by an extension
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
76. Procedure.recorder
Definition | Individual who recorded the record and takes responsibility for its content.
Short | Who recorded the procedure
Control | 0..0
Type | Reference(Patient, RelatedPerson, Practitioner, PractitionerRole)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
78. Procedure.asserter
Definition | Individual who is making the procedure statement.
Short | Person who asserts this procedure
Control | 0..0
Type | Reference(Patient, RelatedPerson, Practitioner, PractitionerRole)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
80. Procedure.performer
Definition | Limited to "real" people rather than equipment.
Short | The people who performed the procedure
Control | 0..*
Type | BackboneElement
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
82. 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.
Short | Unique id for inter-element referencing
Control | 0..1
Type | string
Is Modifier | false
XML Format | In the XML format, this property is represented as an attribute.
Summary | false
84. 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.
Short | Additional 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.
Control | 0..*
Type | Extension
Is Modifier | false
Summary | false
Alternate Names | extensions, user content
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
86. 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).
Short | Extensions 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.
Control | 0..*
Type | Extension
Is Modifier | true because Modifier extensions are expected to modify the meaning or interpretation of the element that contains them
Summary | true
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 Names | extensions, user content, modifiers
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
88. Procedure.performer.function
Definition | Distinguishes the type of involvement of the performer in the procedure. For example, surgeon, anaesthetist, endoscopist.
Short | GenomicStudy.analysis.performer.role
Control | 0..1
Binding | For example codes, see ProcedurePerformerRoleCodes (example to `http://hl7.org/fhir/ValueSet/performer-role|4.0.1` ) A code that identifies the role of a performer of the procedure.
Type | CodeableConcept
Is Modifier | false
Summary | true
Requirements | Allows disambiguation of the types of involvement of different performers.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
90. Procedure.performer.actor
Definition | The practitioner who was involved in the procedure.
Short | GenomicStudy.analysis.performer.actor
Control | 1..1
Type | Reference(Practitioner, PractitionerRole, Organization, Device)
Is Modifier | false
Summary | true
Requirements | A reference to Device supports use cases, such as pacemakers.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
92. Procedure.performer.onBehalfOf
Definition | The organization the device or practitioner was acting on behalf of.
Short | Organization the device or practitioner was acting for
Control | 0..1
Type | Reference(Organization)
Is Modifier | false
Summary | false
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.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
94. Procedure.location
Definition | The location where the procedure actually happened. E.g. a newborn at home, a tracheostomy at a restaurant.
Short | Where the procedure happened
Control | 0..0
Type | Reference(Location)
Is Modifier | false
Summary | true
Requirements | Ties a procedure to where the records are likely kept.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
96. 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.
Short | Coded 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.
Control | 0..0
Binding | For example codes, see ProcedureReasonCodes (example to `http://hl7.org/fhir/ValueSet/procedure-reason|4.0.1` ) A code that identifies the reason a procedure is required.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
98. Procedure.reasonReference
Definition | The justification of why the procedure was performed.
Short | The 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.
Control | 0..0
Type | Reference(Condition, Observation, Procedure, DiagnosticReport, DocumentReference)
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
100. Procedure.bodySite
Definition | Detailed and structured anatomical location information. Multiple locations are allowed - e.g. multiple punch biopsies of a lesion.
Short | Target 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.
Control | 0..0
Binding | For example codes, see SNOMEDCTBodyStructures (example to `http://hl7.org/fhir/ValueSet/body-site|4.0.1` ) Codes describing anatomical locations. May include laterality.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
102. Procedure.outcome
Definition | The outcome of the procedure - did it resolve the reasons for the procedure being performed?
Short | The result of procedure
Comments | If outcome contains narrative text only, it can be captured using the CodeableConcept.text.
Control | 0..0
Binding | For example codes, see ProcedureOutcomeCodes(SNOMEDCT) (example to `http://hl7.org/fhir/ValueSet/procedure-outcome|4.0.1` ) An outcome of a procedure - whether it was resolved or otherwise.
Type | CodeableConcept
Is Modifier | false
Summary | true
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
104. Procedure.report
Definition | This could be a histology result, pathology report, surgical report, etc.
Short | Any 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.
Control | 0..0
Type | Reference(DiagnosticReport, DocumentReference, Composition)
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
106. 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.
Short | Complication following the procedure
Comments | If complications are only expressed by the narrative text, they can be captured using the CodeableConcept.text.
Control | 0..0
Binding | For example codes, see Condition/Problem/DiagnosisCodes (example to `http://hl7.org/fhir/ValueSet/condition-code|4.0.1` ) Codes describing complications that resulted from a procedure.
Type | CodeableConcept
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
108. Procedure.complicationDetail
Definition | Any complications that occurred during the procedure, or in the immediate post-performance period.
Short | A condition that is a result of the procedure
Control | 0..0
Type | Reference(Condition)
Is Modifier | false
Summary | false
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.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
110. 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.
Short | Instructions for follow up
Control | 0..0
Binding | For example codes, see ProcedureFollowUpCodes(SNOMEDCT) (example to `http://hl7.org/fhir/ValueSet/procedure-followup|4.0.1` ) Specific follow up required for a procedure e.g. removal of sutures.
Type | CodeableConcept
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
112. Procedure.note
Definition | Any other notes and comments about the procedure.
Short | GenomicStudy.analysis.note
Control | 0..*
Type | Annotation
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
114. 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.
Short | Manipulated, implanted, or removed device
Control | 0..0
Type | BackboneElement
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
121. Procedure.usedReference
Definition | Identifies medications, devices and any other substance used as part of the procedure.
Short | Items used during procedure
Comments | For devices actually implanted or removed, use Procedure.device.
Control | 0..0
Type | Reference(Device, Medication, Substance)
Is Modifier | false
Summary | false
Requirements | Used for tracking contamination, etc.
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
123. Procedure.usedCode
Definition | Identifies coded items that were used as part of the procedure.
Short | Coded items used during the procedure
Comments | For devices actually implanted or removed, use Procedure.device.
Control | 0..0
Binding | For example codes, see FHIRDeviceTypes (example to `http://hl7.org/fhir/ValueSet/device-kind|4.0.1` ) Codes describing items used during a procedure.
Type | CodeableConcept
Is Modifier | false
Summary | false
Invariants | ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)