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

## Data Type Profile: Coded Annotation

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/coded-annotation | Version: 4.0.0-cibuild
Standards status: Trial-use | Maturity Level: 2 | 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.

Usages:

- Use this DataType Profile: Genomic Base and Genomic Report Note

You can also check for usages in the FHIR IG Statistics

### Formal Views of Profile Content

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

- Key Elements Table
- Differential Table
- Snapshot Table
- Statistics/References
- All

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Annotation |  | 0..* | Annotation | Text node with attribution
Slices for extension |  |  |  | Content/Rules for all slices
extension: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)
Documentation for this format

#### Constraints

Id | Grade | Path(s) | Description | Expression
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`

This structure is derived from Annotation

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Annotation |  | 0..* | Annotation | Text node with attribution
Slices for extension |  |  |  | Content/Rules for all slices
extension:code |  | 0..1 | CodeableConcept | Annotation Code URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code Binding: Coded Annotation Types (example)
Documentation for this format

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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
extension: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 |
time | Σ | 0..1 | dateTime | When the annotation was made
text | Σ | 1..1 | markdown | The annotation - text content (as markdown)
Documentation for this format

#### Constraints

Id | Grade | Path(s) | Description | Expression
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must 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:

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

Maturity: 2

Key Elements View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Annotation |  | 0..* | Annotation | Text node with attribution
Slices for extension |  |  |  | Content/Rules for all slices
extension: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)
Documentation for this format

#### Constraints

Id | Grade | Path(s) | Description | Expression
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`

Differential View

This structure is derived from Annotation

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Annotation |  | 0..* | Annotation | Text node with attribution
Slices for extension |  |  |  | Content/Rules for all slices
extension:code |  | 0..1 | CodeableConcept | Annotation Code URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code Binding: Coded Annotation Types (example)
Documentation for this format

Snapshot View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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
extension: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 |
time | Σ | 0..1 | dateTime | When the annotation was made
text | Σ | 1..1 | markdown | The annotation - text content (as markdown)
Documentation for this format

#### Constraints

Id | Grade | Path(s) | Description | Expression
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must 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:

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

Maturity: 2

Other representations of profile: CSV, Excel, Schematron