Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Data Type Profile: Coded Annotation

Defining URL:http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/coded-annotation
Version:2.0.0
Name:CodedAnnotation
Title:Coded Annotation
Status:Active as of 2022-05-09 04:53:07+0000
Definition:

Annotation DataType with added CodeableConcept extension element

Publisher:HL7 Clinical Genomics Working Group
Source Resource:XML / JSON / Turtle

The official URL for this profile is:

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/coded-annotation

This profile adds a CodeableConcept extension to the Annotation data type. The Annotation data type is meant to capture text notes plus information about who made the statement and when. This new extension gives a coded meaning (e.g. test disclaimer, tumor board preparation note) to the notes. Many notes will not require this code, so this extension is optional. It can be used when implementers feel the meaning is important.

If there is a possibility of transporting the content of the note in a structured manner the usage of CodedAnnotation is forbidden and the corresponding data structures SHALL be used. For example, if the text to send resembles the interpretation or impression of the Observation, this guide adds Observation.component slice for conclusion-string which is more appropriate than a note. This would include text like interpretative information (typically canned) about a variant identified in the patient. This slice is defined in the Genomics Base profile, which every observation builds upon. Therefore, this component is a defined slice on all observations profiles defined in this Implementation Guide.

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from Annotation

Summary

Extensions

This structure refers to these extensions:

NameFlagsCard.TypeDescription & Constraintsdoco
.. Annotation 0..*AnnotationText node with attribution
... id 0..1stringUnique id for inter-element referencing
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... annotation-code 0..1CodeableConceptAnnotation Code
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code
Binding: Coded Annotation Types (example)
.... authorReferenceReference(Practitioner | Patient | RelatedPerson | Organization)
.... authorStringstring
... time Σ0..1dateTimeWhen the annotation was made
... text Σ1..1markdownThe annotation - text content (as markdown)

doco Documentation for this format

This structure is derived from Annotation

Summary

Extensions

This structure refers to these extensions:

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Annotation 0..*AnnotationText node with attribution
... id 0..1stringUnique id for inter-element referencing
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... annotation-code 0..1CodeableConceptAnnotation Code
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code
Binding: Coded Annotation Types (example)
.... authorReferenceReference(Practitioner | Patient | RelatedPerson | Organization)
.... authorStringstring
... time Σ0..1dateTimeWhen the annotation was made
... text Σ1..1markdownThe annotation - text content (as markdown)

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

Constraints

IdGradePathDetailsRequirements
ele-1errorAnnotationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorAnnotation.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorAnnotation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorAnnotation.extension:codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorAnnotation.extension:codeMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorAnnotation.author[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorAnnotation.timeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorAnnotation.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())