PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions

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Resource Profile: Reference Genome

Reference genome definition used by genomic tests, including build_name and FASTA path.

Usages:

• Refer to this Profile: Reference Genome ID relationship and Reference genome ID relationship
• Examples for this Profile: Basic/reference-genome-grch38

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
Basic		0..*	Basic	Resource for non-supported content
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:fasta_path	S	0..1	string	fasta_path – filesystem or URI of the reference genome FASTA URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	reference_genome_id – identifier for the reference genome
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
system	Σ	1..1	uri	The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/reference-genome-id
value	Σ	1..1	string	The value that is unique Example General: 123456
code	?!SΣ	1..1	CodeableConcept	build_name – reference genome build name Binding: Reference Genome Build ValueSet (required): Codes for identifying types of resources not yet defined by FHIR.
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Basic.identifier.use	Base	required	IdentifierUse	📍4.0.1	FHIR Std.
Basic.code	Base	required	Reference Genome Build ValueSet	📦0.1.0-ci-build	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	Basic	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Basic	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Basic	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Basic	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Basic	A resource should have narrative for robust management	text.`div`.exists()
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 Basic

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Basic		0..*	Basic	Resource for non-supported content
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:fasta_path	S	0..1	string	fasta_path – filesystem or URI of the reference genome FASTA URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path
identifier	S	1..1	Identifier	reference_genome_id – identifier for the reference genome
system		1..1	uri	The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/reference-genome-id
value		1..1	string	The value that is unique
code	S	1..1	CodeableConcept	build_name – reference genome build name Binding: Reference Genome Build ValueSet (required): Codes for identifying types of resources not yet defined by FHIR.
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Basic.code	Base	required	Reference Genome Build ValueSet	📦0.1.0-ci-build	This IG

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Basic		0..*	Basic	Resource for non-supported content
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:fasta_path	S	0..1	string	fasta_path – filesystem or URI of the reference genome FASTA URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	reference_genome_id – identifier for the reference genome
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
type	Σ	0..1	CodeableConcept	Description of identifier Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.
system	Σ	1..1	uri	The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/reference-genome-id
value	Σ	1..1	string	The value that is unique Example General: 123456
period	Σ	0..1	Period	Time period when id is/was valid for use
assigner	Σ	0..1	Reference(Organization)	Organization that issued id (may be just text)
code	?!SΣ	1..1	CodeableConcept	build_name – reference genome build name Binding: Reference Genome Build ValueSet (required): Codes for identifying types of resources not yet defined by FHIR.
subject	Σ	0..1	Reference(Resource)	Identifies the focus of this resource
created	Σ	0..1	date	When created
author	Σ	0..1	Reference(Practitioner | PractitionerRole | Patient | RelatedPerson | Organization)	Who created
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Basic.language	Base	preferred	Common Languages	📍4.0.1	FHIR Std.
Basic.identifier.use	Base	required	IdentifierUse	📍4.0.1	FHIR Std.
Basic.identifier.type	Base	extensible	IdentifierType	📍4.0.1	FHIR Std.
Basic.code	Base	required	Reference Genome Build ValueSet	📦0.1.0-ci-build	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	Basic	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Basic	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Basic	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Basic	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Basic	A resource should have narrative for robust management	text.`div`.exists()
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 Basic

Summary

Mandatory: 3 elements
Must-Support: 3 elements
Fixed: 1 element

Extensions

This structure refers to these extensions:

• https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path

Key Elements View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Basic		0..*	Basic	Resource for non-supported content
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:fasta_path	S	0..1	string	fasta_path – filesystem or URI of the reference genome FASTA URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	reference_genome_id – identifier for the reference genome
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
system	Σ	1..1	uri	The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/reference-genome-id
value	Σ	1..1	string	The value that is unique Example General: 123456
code	?!SΣ	1..1	CodeableConcept	build_name – reference genome build name Binding: Reference Genome Build ValueSet (required): Codes for identifying types of resources not yet defined by FHIR.
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Basic.identifier.use	Base	required	IdentifierUse	📍4.0.1	FHIR Std.
Basic.code	Base	required	Reference Genome Build ValueSet	📦0.1.0-ci-build	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	Basic	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Basic	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Basic	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Basic	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Basic	A resource should have narrative for robust management	text.`div`.exists()
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 Basic

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Basic		0..*	Basic	Resource for non-supported content
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:fasta_path	S	0..1	string	fasta_path – filesystem or URI of the reference genome FASTA URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path
identifier	S	1..1	Identifier	reference_genome_id – identifier for the reference genome
system		1..1	uri	The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/reference-genome-id
value		1..1	string	The value that is unique
code	S	1..1	CodeableConcept	build_name – reference genome build name Binding: Reference Genome Build ValueSet (required): Codes for identifying types of resources not yet defined by FHIR.
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Basic.code	Base	required	Reference Genome Build ValueSet	📦0.1.0-ci-build	This IG

Snapshot View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Basic		0..*	Basic	Resource for non-supported content
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:fasta_path	S	0..1	string	fasta_path – filesystem or URI of the reference genome FASTA URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	reference_genome_id – identifier for the reference genome
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
type	Σ	0..1	CodeableConcept	Description of identifier Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.
system	Σ	1..1	uri	The namespace for the identifier value Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/reference-genome-id
value	Σ	1..1	string	The value that is unique Example General: 123456
period	Σ	0..1	Period	Time period when id is/was valid for use
assigner	Σ	0..1	Reference(Organization)	Organization that issued id (may be just text)
code	?!SΣ	1..1	CodeableConcept	build_name – reference genome build name Binding: Reference Genome Build ValueSet (required): Codes for identifying types of resources not yet defined by FHIR.
subject	Σ	0..1	Reference(Resource)	Identifies the focus of this resource
created	Σ	0..1	date	When created
author	Σ	0..1	Reference(Practitioner | PractitionerRole | Patient | RelatedPerson | Organization)	Who created
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Basic.language	Base	preferred	Common Languages	📍4.0.1	FHIR Std.
Basic.identifier.use	Base	required	IdentifierUse	📍4.0.1	FHIR Std.
Basic.identifier.type	Base	extensible	IdentifierType	📍4.0.1	FHIR Std.
Basic.code	Base	required	Reference Genome Build ValueSet	📦0.1.0-ci-build	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
dom-2	error	Basic	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Basic	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Basic	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Basic	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Basic	A resource should have narrative for robust management	text.`div`.exists()
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 Basic

Summary

Mandatory: 3 elements
Must-Support: 3 elements
Fixed: 1 element

Extensions

This structure refers to these extensions:

• https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/reference-genome-fasta-path

Other representations of profile: CSV, Excel, Schematron