Genomic Study Analysis Metrics - Definitions - Genomics Reporting Implementation Guide v3.0.0

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

Extension: GenomicStudyAnalysisMetrics - Detailed Descriptions

Active as of 2024-11-19

Definitions for the genomic-study-analysis-metrics extension.

Differential Elements Table
Key Elements Table
Snapshot Elements Table

Guidance on how to interpret the contents of this table can be found here

0. Extension
Definition	Metrics about the sequencing analysis that was performed
Short	Genomic Study Analysis Metrics
2. Extension.extension:read-depth
Slice Name	read-depth
Definition	The average read depth (number of reads for a position) for the sequencing test
Short	Read Depth
Control	0..1
Requirements	This value is typically represented with an 'x' after the number (30x). Simply share the quantity here.
4. Extension.extension:read-depth.extension
Control	0..0
6. Extension.extension:read-depth.url
Fixed Value	`read-depth`
8. Extension.extension:read-depth.value[x]
Short	30, 100
Type	Quantity(SimpleQuantity)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
10. Extension.extension:sequencing-coverage
Slice Name	sequencing-coverage
Definition	The percentage of the studied regions that were sequenced
Short	Sequencing Coverage
Control	0..1
Requirements	This value is typically represented with an '%' after the number (95%). Simply share the quantity here.
12. Extension.extension:sequencing-coverage.extension
Control	0..0
14. Extension.extension:sequencing-coverage.url
Fixed Value	`sequencing-coverage`
16. Extension.extension:sequencing-coverage.value[x]
Short	95, 100
Type	Quantity(SimpleQuantity)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
18. Extension.extension:metrics-description
Slice Name	metrics-description
Definition	Freetext description of the coverage metrics for the sequencing test
Short	Metrics Description
Control	0..1
20. Extension.extension:metrics-description.extension
Control	0..0
22. Extension.extension:metrics-description.url
Fixed Value	`metrics-description`
24. Extension.extension:metrics-description.value[x]
Type	string
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Primitive Value	This primitive element may be present, or absent, or replaced by an extension
26. Extension.url
Fixed Value	`http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics`
28. Extension.value[x]
Control	0..0

Guidance on how to interpret the contents of this table can be found here

0. Extension
Definition	Metrics about the sequencing analysis that was performed Optional Extension Element - found in all resources.
Short	Genomic Study Analysis MetricsOptional Extensions Element
Control	0..* This element is affected by the following invariants: ele-1
Is Modifier	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
2. Extension.extension:read-depth
Slice Name	read-depth
Definition	The average read depth (number of reads for a position) for the sequencing test
Short	Read DepthAdditional content defined by implementations
Control	0..1*
Type	Extension
Is Modifier	false
Summary	false
Requirements	This value is typically represented with an 'x' after the number (30x). Simply share the quantity here.
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
4. Extension.extension:read-depth.extension
Definition	An Extension May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Short	ExtensionAdditional content defined by implementations
Comments	There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Control	0..0*
Type	Extension
Is Modifier	false
Summary	false
Alternate Names	extensions, user content
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
Slicing	This element introduces a set of slices on `Extension.extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
6. Extension.extension:read-depth.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`read-depth`
8. Extension.extension:read-depth.value[x]
Definition	The comparator is not used on a SimpleQuantity Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	30, 100Value of extension
Comments	The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.
Control	0..1 This element is affected by the following invariants: ele-1
Type	Quantity(SimpleQuantity), date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, CodeableConcept, ParameterDefinition, dateTime, code, string, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) qty-3: If a code for the unit is present, the system SHALL also be present (`code.empty() or system.exists()`) sqty-1: The comparator is not used on a SimpleQuantity (`comparator.empty()`)
10. Extension.extension:sequencing-coverage
Slice Name	sequencing-coverage
Definition	The percentage of the studied regions that were sequenced
Short	Sequencing CoverageAdditional content defined by implementations
Control	0..1*
Type	Extension
Is Modifier	false
Summary	false
Requirements	This value is typically represented with an '%' after the number (95%). Simply share the quantity here.
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
12. Extension.extension:sequencing-coverage.extension
Definition	An Extension May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Short	ExtensionAdditional content defined by implementations
Comments	There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Control	0..0*
Type	Extension
Is Modifier	false
Summary	false
Alternate Names	extensions, user content
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
Slicing	This element introduces a set of slices on `Extension.extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
14. Extension.extension:sequencing-coverage.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`sequencing-coverage`
16. Extension.extension:sequencing-coverage.value[x]
Definition	The comparator is not used on a SimpleQuantity Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	95, 100Value of extension
Comments	The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.
Control	0..1 This element is affected by the following invariants: ele-1
Type	Quantity(SimpleQuantity), date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, CodeableConcept, ParameterDefinition, dateTime, code, string, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) qty-3: If a code for the unit is present, the system SHALL also be present (`code.empty() or system.exists()`) sqty-1: The comparator is not used on a SimpleQuantity (`comparator.empty()`)
18. Extension.extension:metrics-description
Slice Name	metrics-description
Definition	Freetext description of the coverage metrics for the sequencing test
Short	Metrics DescriptionAdditional content defined by implementations
Control	0..1*
Type	Extension
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
20. Extension.extension:metrics-description.extension
Definition	An Extension May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Short	ExtensionAdditional content defined by implementations
Comments	There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Control	0..0*
Type	Extension
Is Modifier	false
Summary	false
Alternate Names	extensions, user content
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count())) ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
Slicing	This element introduces a set of slices on `Extension.extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
22. Extension.extension:metrics-description.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`metrics-description`
24. Extension.extension:metrics-description.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	Value of extension
Control	0..1
Type	string, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, CodeableConcept, ParameterDefinition, dateTime, code, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Primitive Value	This primitive element may be present, or absent, or replaced by an extension
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
26. Extension.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics`
28. Extension.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	Value of extension
Control	0..01
Type	Choice of: base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, Reference, SampledData, Signature, Timing, ContactDetail, Contributor, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Dosage, Meta
Is Modifier	false
Primitive Value	This primitive element may be present, or absent, or replaced by an extension
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))

Guidance on how to interpret the contents of this table can be found here

0. Extension
Definition	Metrics about the sequencing analysis that was performed
Short	Genomic Study Analysis Metrics
Control	0..* This element is affected by the following invariants: ele-1
Is Modifier	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
2. Extension.id
Definition	Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short	Unique id for inter-element referencing
Control	0..1
Type	string
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
4. Extension.extension
Definition	May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Short	Additional content defined by implementations
Comments	There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Control	0..*
Type	Extension
Is Modifier	false
Summary	false
Alternate Names	extensions, user content
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
Slicing	This element introduces a set of slices on `Extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
6. Extension.extension:read-depth
Slice Name	read-depth
Definition	The average read depth (number of reads for a position) for the sequencing test
Short	Read Depth
Control	0..1
Type	Extension
Is Modifier	false
Summary	false
Requirements	This value is typically represented with an 'x' after the number (30x). Simply share the quantity here.
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
8. Extension.extension:read-depth.id
Definition	Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short	Unique id for inter-element referencing
Control	0..1
Type	string
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
10. Extension.extension:read-depth.extension
Definition	An Extension
Short	Extension
Control	0..0
Type	Extension
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
Slicing	This element introduces a set of slices on `Extension.extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
12. Extension.extension:read-depth.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`read-depth`
14. Extension.extension:read-depth.value[x]
Definition	The comparator is not used on a SimpleQuantity
Short	30, 100
Comments	The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.
Control	0..1 This element is affected by the following invariants: ele-1
Type	Quantity(SimpleQuantity)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) qty-3: If a code for the unit is present, the system SHALL also be present (`code.empty() or system.exists()`) sqty-1: The comparator is not used on a SimpleQuantity (`comparator.empty()`)
16. Extension.extension:sequencing-coverage
Slice Name	sequencing-coverage
Definition	The percentage of the studied regions that were sequenced
Short	Sequencing Coverage
Control	0..1
Type	Extension
Is Modifier	false
Summary	false
Requirements	This value is typically represented with an '%' after the number (95%). Simply share the quantity here.
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
18. Extension.extension:sequencing-coverage.id
Definition	Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short	Unique id for inter-element referencing
Control	0..1
Type	string
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
20. Extension.extension:sequencing-coverage.extension
Definition	An Extension
Short	Extension
Control	0..0
Type	Extension
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
Slicing	This element introduces a set of slices on `Extension.extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
22. Extension.extension:sequencing-coverage.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`sequencing-coverage`
24. Extension.extension:sequencing-coverage.value[x]
Definition	The comparator is not used on a SimpleQuantity
Short	95, 100
Comments	The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.
Control	0..1 This element is affected by the following invariants: ele-1
Type	Quantity(SimpleQuantity)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) qty-3: If a code for the unit is present, the system SHALL also be present (`code.empty() or system.exists()`) sqty-1: The comparator is not used on a SimpleQuantity (`comparator.empty()`)
26. Extension.extension:metrics-description
Slice Name	metrics-description
Definition	Freetext description of the coverage metrics for the sequencing test
Short	Metrics Description
Control	0..1
Type	Extension
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
28. Extension.extension:metrics-description.id
Definition	Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Short	Unique id for inter-element referencing
Control	0..1
Type	string
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
30. Extension.extension:metrics-description.extension
Definition	An Extension
Short	Extension
Control	0..0
Type	Extension
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`) ext-1: Must have either extensions or value[x], not both (`extension.exists() != value.exists()`)
Slicing	This element introduces a set of slices on `Extension.extension.extension`. The slices areUnordered and Open, and can be differentiated using the following discriminators: value @ url
32. Extension.extension:metrics-description.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`metrics-description`
34. Extension.extension:metrics-description.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	Value of extension
Control	0..1
Type	string
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Primitive Value	This primitive element may be present, or absent, or replaced by an extension
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
36. Extension.url
Definition	Source of the definition for the extension code - a logical name or a URL.
Short	identifies the meaning of the extension
Comments	The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
Control	1..1
Type	uri
Is Modifier	false
XML Format	In the XML format, this property is represented as an attribute.
Summary	false
Fixed Value	`http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics`
38. Extension.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	Value of extension
Control	0..0
Type	Choice of: base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, Reference, SampledData, Signature, Timing, ContactDetail, Contributor, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Dosage, Meta
Is Modifier	false
Primitive Value	This primitive element may be present, or absent, or replaced by an extension
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)