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

Data Type Profile: Coded Annotation

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/coded-annotation Version: 3.0.1-SNAPSHOT
Active as of 2024-07-08 Computable Name: CodedAnnotation

Annotation DataType with added CodeableConcept extension element

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 Genomic Base profile, which every observation builds upon. Therefore, this component is a defined slice on all observations profiles defined in this Implementation Guide.

Usage:

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraintsdoco
.. Annotation 0..* Annotation Text node with attribution
... Slices for extension Content/Rules for all slices
.... code 0..1 CodeableConcept Annotation Code
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code
Binding: Coded Annotation Types (example)
... text Σ 1..1 markdown The annotation - text content (as markdown)

doco Documentation for this format

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Annotation 0..* Annotation Text node with attribution
... id 0..1 string Unique id for inter-element referencing
... Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... code 0..1 CodeableConcept Annotation Code
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code
Binding: Coded Annotation Types (example)
... author[x] Σ 0..1 Individual responsible for the annotation
.... authorReference Reference(Practitioner | Patient | RelatedPerson | Organization)
.... authorString string
... text Σ 1..1 markdown The annotation - text content (as markdown)

doco Documentation for this format

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from Annotation

Summary

Extensions

This structure refers to these extensions:

Differential View

This structure is derived from Annotation

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Annotation 0..* Annotation Text node with attribution
... Slices for extension Content/Rules for all slices
.... code 0..1 CodeableConcept Annotation Code
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code
Binding: Coded Annotation Types (example)
... text Σ 1..1 markdown The annotation - text content (as markdown)

doco Documentation for this format

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Annotation 0..* Annotation Text node with attribution
... id 0..1 string Unique id for inter-element referencing
... Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... code 0..1 CodeableConcept Annotation Code
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code
Binding: Coded Annotation Types (example)
... author[x] Σ 0..1 Individual responsible for the annotation
.... authorReference Reference(Practitioner | Patient | RelatedPerson | Organization)
.... authorString string
... text Σ 1..1 markdown The annotation - text content (as markdown)

doco Documentation for this format

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

This structure is derived from Annotation

Summary

Extensions

This structure refers to these extensions:

 

Other representations of profile: CSV, Excel, Schematron