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

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Extension: GenomicStudyAnalysisInput - Detailed Descriptions

Active as of 2024-12-12

Definitions for the genomic-study-analysis-input 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	Genomic Study Analysis Input
Short	Genomic Study Analysis Input
2. Extension.extension:file
Slice Name	file
Short	GenomicStudy.analysis.input.file
Control	0..1
4. Extension.extension:file.extension
Control	0..0
6. Extension.extension:file.url
Fixed Value	`file`
8. Extension.extension:file.value[x]
Type	Reference(Genomic Data File)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
10. Extension.extension:type
Slice Name	type
Short	GenomicStudy.analysis.input.type
Control	0..1
12. Extension.extension:type.extension
Control	0..0
14. Extension.extension:type.url
Fixed Value	`type`
16. Extension.extension:type.value[x]
Short	bam \| bed \| vcf \| ... (many)
Binding	The codes SHOULD be taken from Genomic Study Data Format ValueSet (preferred to `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genomic-study-data-format-vs`)
Type	CodeableConcept
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
18. Extension.extension:generatedBy
Slice Name	generatedBy
Short	GenomicStudy.analysis.input.generatedBy
Control	0..1
20. Extension.extension:generatedBy.extension
Control	0..0
22. Extension.extension:generatedBy.url
Fixed Value	`generatedBy`
24. Extension.extension:generatedBy.value[x]
Type	Choice of: Identifier, Reference(Genomic Study)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
26. Extension.url
Fixed Value	`http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input`
28. Extension.value[x]
Control	0..0

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

0. Extension
Definition	Genomic Study Analysis Input Optional Extension Element - found in all resources.
Short	Genomic Study Analysis InputOptional 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:file
Slice Name	file
Definition	An Extension
Short	GenomicStudy.analysis.input.fileAdditional 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())
4. Extension.extension:file.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:file.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	`file`
8. Extension.extension:file.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	Reference(Genomic Data File), 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, 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
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
10. Extension.extension:type
Slice Name	type
Definition	An Extension
Short	GenomicStudy.analysis.input.typeAdditional 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())
12. Extension.extension:type.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:type.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	`type`
16. Extension.extension:type.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	bam \| bed \| vcf \| ... (many)Value of extension
Control	0..1
Binding	The codes SHOULD be taken from For codes, see Genomic Study Data Format ValueSet (preferred to `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genomic-study-data-format-vs`)
Type	CodeableConcept, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ParameterDefinition, dateTime, code, string, 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
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
18. Extension.extension:generatedBy
Slice Name	generatedBy
Definition	An Extension
Short	GenomicStudy.analysis.input.generatedByAdditional 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:generatedBy.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:generatedBy.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	`generatedBy`
24. Extension.extension:generatedBy.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	Choice of: Identifier, Reference(Genomic Study), date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, 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, 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
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-input`
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	Genomic Study Analysis Input
Short	Genomic Study Analysis Input
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:file
Slice Name	file
Definition	An Extension
Short	GenomicStudy.analysis.input.file
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()`)
8. Extension.extension:file.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:file.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:file.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	`file`
14. Extension.extension:file.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	Reference(Genomic Data File)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
16. Extension.extension:type
Slice Name	type
Definition	An Extension
Short	GenomicStudy.analysis.input.type
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()`)
18. Extension.extension:type.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:type.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:type.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	`type`
24. Extension.extension:type.value[x]
Definition	Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).
Short	bam \| bed \| vcf \| ... (many)
Control	0..1
Binding	The codes SHOULD be taken from Genomic Study Data Format ValueSet (preferred to `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genomic-study-data-format-vs`)
Type	CodeableConcept
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
Summary	false
Invariants	ele-1: All FHIR elements must have a @value or children (`hasValue() or (children().count() > id.count())`)
26. Extension.extension:generatedBy
Slice Name	generatedBy
Definition	An Extension
Short	GenomicStudy.analysis.input.generatedBy
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:generatedBy.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:generatedBy.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:generatedBy.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	`generatedBy`
34. Extension.extension:generatedBy.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	Choice of: Identifier, Reference(Genomic Study)
[x] Note	SeeChoice of Data Typesfor further information about how to use [x]
Is Modifier	false
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-input`
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())`)