Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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
Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics | Version: 3.0.0 | |||
Active as of 2024-11-24 | Computable Name: GenomicStudyAnalysisMetrics |
Metrics about the sequencing analysis that was performed
Context of Use
This extension may be used on the following element(s):
This extension is used for overall, analysis level metrics. These metrics are not specific to a region that is studied in the analysis. The metrics here are specific to sequencing analysis, but others could be added if they make sense to the use case.
Usage info
Usage:
Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.
This structure is derived from Extension
Summary
Complex Extension: Metrics about the sequencing analysis that was performed
This structure is derived from Extension
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Extension | 0..* | Extension | Genomic Study Analysis Metrics | |
Slices for extension | Content/Rules for all slices | |||
extension:read-depth | 0..1 | Extension | Read Depth | |
extension | 0..0 | |||
url | 1..1 | uri | "read-depth" | |
value[x] | 0..1 | SimpleQuantity | 30, 100 | |
extension:sequencing-coverage | 0..1 | Extension | Sequencing Coverage | |
extension | 0..0 | |||
url | 1..1 | uri | "sequencing-coverage" | |
value[x] | 0..1 | SimpleQuantity | 95, 100 | |
extension:metrics-description | 0..1 | Extension | Metrics Description | |
extension | 0..0 | |||
url | 1..1 | uri | "metrics-description" | |
value[x] | 0..1 | string | Value of extension | |
url | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics" | |
value[x] | 0..0 | |||
Documentation for this format |
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Extension | 0..* | Extension | Genomic Study Analysis Metrics | |
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:read-depth | 0..1 | Extension | Read Depth | |
id | 0..1 | string | Unique id for inter-element referencing | |
extension | 0..0 | |||
url | 1..1 | uri | "read-depth" | |
value[x] | C | 0..1 | SimpleQuantity | 30, 100 qty-3: If a code for the unit is present, the system SHALL also be present |
extension:sequencing-coverage | 0..1 | Extension | Sequencing Coverage | |
id | 0..1 | string | Unique id for inter-element referencing | |
extension | 0..0 | |||
url | 1..1 | uri | "sequencing-coverage" | |
value[x] | C | 0..1 | SimpleQuantity | 95, 100 qty-3: If a code for the unit is present, the system SHALL also be present |
extension:metrics-description | 0..1 | Extension | Metrics Description | |
id | 0..1 | string | Unique id for inter-element referencing | |
extension | 0..0 | |||
url | 1..1 | uri | "metrics-description" | |
value[x] | 0..1 | string | Value of extension | |
url | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics" | |
Documentation for this format |
This structure is derived from Extension
Summary
Complex Extension: Metrics about the sequencing analysis that was performed
Differential View
This structure is derived from Extension
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Extension | 0..* | Extension | Genomic Study Analysis Metrics | |
Slices for extension | Content/Rules for all slices | |||
extension:read-depth | 0..1 | Extension | Read Depth | |
extension | 0..0 | |||
url | 1..1 | uri | "read-depth" | |
value[x] | 0..1 | SimpleQuantity | 30, 100 | |
extension:sequencing-coverage | 0..1 | Extension | Sequencing Coverage | |
extension | 0..0 | |||
url | 1..1 | uri | "sequencing-coverage" | |
value[x] | 0..1 | SimpleQuantity | 95, 100 | |
extension:metrics-description | 0..1 | Extension | Metrics Description | |
extension | 0..0 | |||
url | 1..1 | uri | "metrics-description" | |
value[x] | 0..1 | string | Value of extension | |
url | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics" | |
value[x] | 0..0 | |||
Documentation for this format |
Snapshot View
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Extension | 0..* | Extension | Genomic Study Analysis Metrics | |
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:read-depth | 0..1 | Extension | Read Depth | |
id | 0..1 | string | Unique id for inter-element referencing | |
extension | 0..0 | |||
url | 1..1 | uri | "read-depth" | |
value[x] | C | 0..1 | SimpleQuantity | 30, 100 qty-3: If a code for the unit is present, the system SHALL also be present |
extension:sequencing-coverage | 0..1 | Extension | Sequencing Coverage | |
id | 0..1 | string | Unique id for inter-element referencing | |
extension | 0..0 | |||
url | 1..1 | uri | "sequencing-coverage" | |
value[x] | C | 0..1 | SimpleQuantity | 95, 100 qty-3: If a code for the unit is present, the system SHALL also be present |
extension:metrics-description | 0..1 | Extension | Metrics Description | |
id | 0..1 | string | Unique id for inter-element referencing | |
extension | 0..0 | |||
url | 1..1 | uri | "metrics-description" | |
value[x] | 0..1 | string | Value of extension | |
url | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics" | |
Documentation for this format |
Other representations of profile: CSV, Excel, Schematron
Id | Grade | Path(s) | Details | Requirements |
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() | |
qty-3 | error | Extension.extension:read-depth.value[x], Extension.extension:sequencing-coverage.value[x] | If a code for the unit is present, the system SHALL also be present : code.empty() or system.exists() | |
sqty-1 | error | **ALL** extensions | The comparator is not used on a SimpleQuantity : comparator.empty() |