Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build 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 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

Extension: Genomic Study Analysis Metrics

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics Version: 4.0.0-cibuild
Standards status: Trial-use Maturity Level: 2 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

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Extension Content

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

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Extension 0..* Extension Genomic Study Analysis Metrics
Extension.Slices for extension Content/Rules for all slices
Extension.Slices for extension.extension:read-depth 0..1 Extension Read Depth
Extension.Slices for extension.extension:read-depth.extension 0..0 Extension
Extension.Slices for extension.extension:read-depth.url 1..1 uri "read-depth"
Extension.Slices for extension.extension:read-depth.value[x] 0..1 SimpleQuantity 30, 100
Extension.Slices for extension.extension:sequencing-coverage 0..1 Extension Sequencing Coverage
Extension.Slices for extension.extension:sequencing-coverage.extension 0..0 Extension
Extension.Slices for extension.extension:sequencing-coverage.url 1..1 uri "sequencing-coverage"
Extension.Slices for extension.extension:sequencing-coverage.value[x] 0..1 SimpleQuantity 95, 100
Extension.Slices for extension.extension:metrics-description 0..1 Extension Metrics Description
Extension.Slices for extension.extension:metrics-description.extension 0..0 Extension
Extension.Slices for extension.extension:metrics-description.url 1..1 uri "metrics-description"
Extension.Slices for extension.extension:metrics-description.value[x] 0..1 string Value of extension
Extension.url 1..1 uri "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
Extension.value[x] 0..0 Value of extension

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: doco
Extension 0..* Extension Genomic Study Analysis Metrics
Extension.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:read-depth 0..1 Extension Read Depth
Extension.Slices for extension.extension:read-depth.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension.extension:read-depth.extension 0..0 Extension
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:read-depth.url 1..1 uri "read-depth"
Extension.Slices for extension.extension:read-depth.value[x] C 0..1 SimpleQuantity 30, 100
Constraints: sqty-1
Extension.Slices for extension.extension:sequencing-coverage 0..1 Extension Sequencing Coverage
Extension.Slices for extension.extension:sequencing-coverage.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension.extension:sequencing-coverage.extension 0..0 Extension
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:sequencing-coverage.url 1..1 uri "sequencing-coverage"
Extension.Slices for extension.extension:sequencing-coverage.value[x] C 0..1 SimpleQuantity 95, 100
Constraints: sqty-1
Extension.Slices for extension.extension:metrics-description 0..1 Extension Metrics Description
Extension.Slices for extension.extension:metrics-description.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension.extension:metrics-description.extension 0..0 Extension
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:metrics-description.url 1..1 uri "metrics-description"
Extension.Slices for extension.extension:metrics-description.value[x] 0..1 string Value of extension
Extension.url 1..1 uri "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"

doco Documentation for this format

This structure is derived from Extension

Summary

Complex Extension: Metrics about the sequencing analysis that was performed

  • read-depth: Quantity: The average read depth (number of reads for a position) for the sequencing test
  • sequencing-coverage: Quantity: The percentage of the studied regions that were sequenced
  • metrics-description: string: Freetext description of the coverage metrics for the sequencing test

Maturity: 2

Differential View

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Extension 0..* Extension Genomic Study Analysis Metrics
Extension.Slices for extension Content/Rules for all slices
Extension.Slices for extension.extension:read-depth 0..1 Extension Read Depth
Extension.Slices for extension.extension:read-depth.extension 0..0 Extension
Extension.Slices for extension.extension:read-depth.url 1..1 uri "read-depth"
Extension.Slices for extension.extension:read-depth.value[x] 0..1 SimpleQuantity 30, 100
Extension.Slices for extension.extension:sequencing-coverage 0..1 Extension Sequencing Coverage
Extension.Slices for extension.extension:sequencing-coverage.extension 0..0 Extension
Extension.Slices for extension.extension:sequencing-coverage.url 1..1 uri "sequencing-coverage"
Extension.Slices for extension.extension:sequencing-coverage.value[x] 0..1 SimpleQuantity 95, 100
Extension.Slices for extension.extension:metrics-description 0..1 Extension Metrics Description
Extension.Slices for extension.extension:metrics-description.extension 0..0 Extension
Extension.Slices for extension.extension:metrics-description.url 1..1 uri "metrics-description"
Extension.Slices for extension.extension:metrics-description.value[x] 0..1 string Value of extension
Extension.url 1..1 uri "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
Extension.value[x] 0..0 Value of extension

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: doco
Extension 0..* Extension Genomic Study Analysis Metrics
Extension.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:read-depth 0..1 Extension Read Depth
Extension.Slices for extension.extension:read-depth.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension.extension:read-depth.extension 0..0 Extension
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:read-depth.url 1..1 uri "read-depth"
Extension.Slices for extension.extension:read-depth.value[x] C 0..1 SimpleQuantity 30, 100
Constraints: sqty-1
Extension.Slices for extension.extension:sequencing-coverage 0..1 Extension Sequencing Coverage
Extension.Slices for extension.extension:sequencing-coverage.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension.extension:sequencing-coverage.extension 0..0 Extension
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:sequencing-coverage.url 1..1 uri "sequencing-coverage"
Extension.Slices for extension.extension:sequencing-coverage.value[x] C 0..1 SimpleQuantity 95, 100
Constraints: sqty-1
Extension.Slices for extension.extension:metrics-description 0..1 Extension Metrics Description
Extension.Slices for extension.extension:metrics-description.id 0..1 string Unique id for inter-element referencing
Extension.Slices for extension.extension:metrics-description.extension 0..0 Extension
Slice: Unordered, Open by value:url
Extension.Slices for extension.extension:metrics-description.url 1..1 uri "metrics-description"
Extension.Slices for extension.extension:metrics-description.value[x] 0..1 string Value of extension
Extension.url 1..1 uri "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"

doco Documentation for this format

This structure is derived from Extension

Summary

Complex Extension: Metrics about the sequencing analysis that was performed

  • read-depth: Quantity: The average read depth (number of reads for a position) for the sequencing test
  • sequencing-coverage: Quantity: The percentage of the studied regions that were sequenced
  • metrics-description: string: Freetext description of the coverage metrics for the sequencing test

Maturity: 2

 

Other representations of profile: CSV, Excel, Schematron

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()
sqty-1 error Extension.extension:read-depth.value[x], Extension.extension:sequencing-coverage.value[x] The comparator is not used on a SimpleQuantity comparator.empty()