Scope and Usage

The Variation profile defines a structured approach for representing genetic variations at specific genomic loci. It characterizes the genetic composition at a given location in three distinct states: context, reference, and alternative. This profile leverages MolecularDefinition resource to enable precise communication of genetic alterations. When applicable, the Variation profile integrates the Sequence and Allele profiles to comprehensively represent genomic changes and support interoperability across health systems.

Use the Variation profile to describe genetic variation. After specifying identifiers and genomic location, the representation element includes three primary slices: context, reference, and alternative. Each slice conveys only one specific state. Reference and alternative slices are required for a complete depiction, while the context slice is optional but recommended for better interpretability.

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from MolecularDefinition

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularDefinition		0..*	MolecularDefinition	Definitional content for a molecular entity
type	S	1..1	CodeableConcept	Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type ValueSet (required)
topology		0..*	CodeableConcept	The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (required)
member		0..0
location		1..1	BackboneElement	A defined location on a molecular entity
sequenceLocation
sequenceContext		1..1	Reference(Sequence)	The sequence on which the location is defined
coordinateInterval
coordinateSystem
origin		0..1	CodeableConcept	The location of the origin of the coordinate system Binding: Coordinate Origin ValueSet (required)
normalizationMethod		0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system Binding: Normalization Method ValueSet (required)
strand		0..1	CodeableConcept	The strand at the coordinateInterval Binding: Strand Orientation ValueSet (required)
Slices for representation		2..*	BackboneElement	A representation of a molecular entity Slice: Unordered, Open by value:focus
representation:contextState	S	0..1	BackboneElement	A representation of a molecular entity
focus		1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
code		1..1	code	Symbol in syntax defined by the system Fixed Value: context-state
display		1..1	string	Representation defined by the system Fixed Value: Context State
representation:referenceState	S	1..1	BackboneElement	A representation of a molecular entity
focus		1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
code		1..1	code	Symbol in syntax defined by the system Fixed Value: reference-state
display		1..1	string	Representation defined by the system Fixed Value: Reference State
representation:alternativeState	S	1..1	BackboneElement	A representation of a molecular entity
focus		1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
code		1..1	code	Symbol in syntax defined by the system Fixed Value: alternative-state
display		1..1	string	Representation defined by the system Fixed Value: Alternative State
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
MolecularDefinition.type	required	MoleculeTypeVS(a valid code from Molecule Type) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG
MolecularDefinition.topology	required	TopologyVS(a valid code from Topology) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.origin	required	CoordinateOriginVS(a valid code from Coordinate Origin) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/coordinate-origin From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.normalizationMethod	required	NormalizationMethodVS(a valid code from Normalization Method) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/normalization-method From this IG
MolecularDefinition.location.sequenceLocation.strand	required	StrandOrientationVS(a valid code from Strand Orientation) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/strand-orientation From this IG

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularDefinition		0..*	MolecularDefinition	Definitional content for a molecular entity
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
contained		0..*	Resource	Contained, inline Resources
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
type	SΣ	1..1	CodeableConcept	Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type ValueSet (required)
topology	Σ	0..*	CodeableConcept	The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (required)
location	Σ	1..1	BackboneElement	A defined location on a molecular entity
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Slices for representation	Σ	2..*	BackboneElement	A representation of a molecular entity Slice: Unordered, Open by value:focus
representation:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
representation:contextState	SΣ	0..1	BackboneElement	A representation of a molecular entity
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: context-state
display		1..1	string	Representation defined by the system Fixed Value: Context State
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
representation:referenceState	SΣ	1..1	BackboneElement	A representation of a molecular entity
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: reference-state
display		1..1	string	Representation defined by the system Fixed Value: Reference State
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
representation:alternativeState	SΣ	1..1	BackboneElement	A representation of a molecular entity
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: alternative-state
display		1..1	string	Representation defined by the system Fixed Value: Alternative State
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
MolecularDefinition.type	required	MoleculeTypeVS(a valid code from Molecule Type) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG
MolecularDefinition.topology	required	TopologyVS(a valid code from Topology) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	MolecularDefinition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	MolecularDefinition	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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	MolecularDefinition	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	MolecularDefinition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	MolecularDefinition	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())

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
MolecularDefinition		0..*	MolecularDefinition	Definitional content for a molecular entity
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: AllLanguages (required): IETF language tag for a human language Additional Bindings Purpose CommonLanguages Starter
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
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Unique ID of an instance
description		0..1	markdown	Description of the Molecular Definition instance
moleculeType	Σ	0..1	CodeableConcept	The type of molecule (e.g., DNA, RNA, amino acid)
type	SΣ	1..1	CodeableConcept	Classification of the molecule into types other than those defined by moleculeType Binding: Molecule Type ValueSet (required)
topology	Σ	0..*	CodeableConcept	The structural topology of the molecular entity (e.g., linear, circular) Binding: Topology ValueSet (required)
location	Σ	1..1	BackboneElement	A defined location on a molecular entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceLocation	Σ	0..1	BackboneElement	A coordinate-based location on a sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceContext	Σ	1..1	Reference(Sequence)	The sequence on which the location is defined
coordinateInterval	Σ	0..1	BackboneElement	An interval on a sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system Binding: Coordinate Origin ValueSet (required)
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system Binding: Normalization Method ValueSet (required)
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
strand		0..1	CodeableConcept	The strand at the coordinateInterval Binding: Strand Orientation ValueSet (required)
cytobandLocation	Σ	0..1	BackboneElement	A cytoband-based location on a sequence
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
genomeAssembly	Σ	1..1	BackboneElement	Reference Genome
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
organism		0..1	CodeableConcept	Species of the organism
build		0..1	CodeableConcept	Build number
accession		0..1	CodeableConcept	Accession
description[x]		0..1		Genome assembly description
descriptionMarkdown			markdown
descriptionString			string
cytobandInterval	Σ	1..1	BackboneElement	Cytoband Interval
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
chromosome	Σ	1..1	CodeableConcept	Chromosome
startCytoband	Σ	0..1	BackboneElement	Start
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
arm[x]		0..1		Arm
armCode			code
armString			string
region[x]		0..1		Region
regionCode			code
regionString			string
band[x]		0..1		Band
bandCode			code
bandString			string
subBand[x]		0..1		Sub-band
subBandCode			code
subBandString			string
endCytoband	Σ	0..1	BackboneElement	End
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
arm[x]		0..1		Arm
armCode			code
armString			string
region[x]		0..1		Region
regionCode			code
regionString			string
band[x]		0..1		Band
bandCode			code
bandString			string
subBand[x]		0..1		SuBand
subBandCode			code
subBandString			string
Slices for representation	Σ	2..*	BackboneElement	A representation of a molecular entity Slice: Unordered, Open by value:focus
representation:All Slices				Content/Rules for all slices
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	0..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation
code	Σ	0..*	CodeableConcept	A code (e.g., sequence accession number) used to represent a molecular entity
literal	Σ	0..1	BackboneElement	A molecular entity defined as a string literal
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
encoding	Σ	0..1	CodeableConcept	The encoding used in the value
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding
resolvable	Σ	0..1	Reference(DocumentReference)	A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
extracted	Σ	0..1	BackboneElement	A molecular entity that is represented as a portion of a different entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
reverseComplement	Σ	0..1	boolean	A flag that indicates whether the extracted sequence should be reverse complemented
repeated	Σ	0..1	BackboneElement	A representation as a repeated motif
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceMotif	Σ	1..1	Reference(MolecularDefinition)	The motif that is repeated
copyCount	Σ	1..1	integer	The number of copies of the motif
concatenated	Σ	0..1	BackboneElement	An ordered concatenation of molecular entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceElement	Σ	1..*	BackboneElement	One of the concatenated entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequence	Σ	1..1	Reference(MolecularDefinition)	A reference to the sequence that defines this specific concatenated element
ordinalIndex	Σ	1..1	integer	The ordinal index of the element within the concatenated representation
relative	Σ	0..1	BackboneElement	A molecular entity represented as an ordered series of edits on a specified starting entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity on which edits will be applied
edit	Σ	0..*	BackboneElement	A defined edit (change) to be applied
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
editOrder		0..1	integer	Defines the order of edits when multiple edits are to be applied to the startingMolecule
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the replacement in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The portion of the molecular entity that is replaced by the replacementMolecule
representation:contextState	SΣ	0..1	BackboneElement	A representation of a molecular entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: context-state
display		1..1	string	Representation defined by the system Fixed Value: Context State
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
code	Σ	0..*	CodeableConcept	A code (e.g., sequence accession number) used to represent a molecular entity
literal	Σ	0..1	BackboneElement	A molecular entity defined as a string literal
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
encoding	Σ	0..1	CodeableConcept	The encoding used in the value
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding
resolvable	Σ	0..1	Reference(DocumentReference)	A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
extracted	Σ	0..1	BackboneElement	A molecular entity that is represented as a portion of a different entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
reverseComplement	Σ	0..1	boolean	A flag that indicates whether the extracted sequence should be reverse complemented
repeated	Σ	0..1	BackboneElement	A representation as a repeated motif
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceMotif	Σ	1..1	Reference(MolecularDefinition)	The motif that is repeated
copyCount	Σ	1..1	integer	The number of copies of the motif
concatenated	Σ	0..1	BackboneElement	An ordered concatenation of molecular entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceElement	Σ	1..*	BackboneElement	One of the concatenated entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequence	Σ	1..1	Reference(MolecularDefinition)	A reference to the sequence that defines this specific concatenated element
ordinalIndex	Σ	1..1	integer	The ordinal index of the element within the concatenated representation
relative	Σ	0..1	BackboneElement	A molecular entity represented as an ordered series of edits on a specified starting entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity on which edits will be applied
edit	Σ	0..*	BackboneElement	A defined edit (change) to be applied
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
editOrder		0..1	integer	Defines the order of edits when multiple edits are to be applied to the startingMolecule
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the replacement in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The portion of the molecular entity that is replaced by the replacementMolecule
representation:referenceState	SΣ	1..1	BackboneElement	A representation of a molecular entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: reference-state
display		1..1	string	Representation defined by the system Fixed Value: Reference State
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
code	Σ	0..*	CodeableConcept	A code (e.g., sequence accession number) used to represent a molecular entity
literal	Σ	0..1	BackboneElement	A molecular entity defined as a string literal
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
encoding	Σ	0..1	CodeableConcept	The encoding used in the value
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding
resolvable	Σ	0..1	Reference(DocumentReference)	A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
extracted	Σ	0..1	BackboneElement	A molecular entity that is represented as a portion of a different entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
reverseComplement	Σ	0..1	boolean	A flag that indicates whether the extracted sequence should be reverse complemented
repeated	Σ	0..1	BackboneElement	A representation as a repeated motif
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceMotif	Σ	1..1	Reference(MolecularDefinition)	The motif that is repeated
copyCount	Σ	1..1	integer	The number of copies of the motif
concatenated	Σ	0..1	BackboneElement	An ordered concatenation of molecular entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceElement	Σ	1..*	BackboneElement	One of the concatenated entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequence	Σ	1..1	Reference(MolecularDefinition)	A reference to the sequence that defines this specific concatenated element
ordinalIndex	Σ	1..1	integer	The ordinal index of the element within the concatenated representation
relative	Σ	0..1	BackboneElement	A molecular entity represented as an ordered series of edits on a specified starting entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity on which edits will be applied
edit	Σ	0..*	BackboneElement	A defined edit (change) to be applied
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
editOrder		0..1	integer	Defines the order of edits when multiple edits are to be applied to the startingMolecule
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the replacement in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The portion of the molecular entity that is replaced by the replacementMolecule
representation:alternativeState	SΣ	1..1	BackboneElement	A representation of a molecular entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
focus	Σ	1..1	CodeableConcept	The domain concept that is the focus of a given instance of the representation Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: alternative-state
display		1..1	string	Representation defined by the system Fixed Value: Alternative State
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
code	Σ	0..*	CodeableConcept	A code (e.g., sequence accession number) used to represent a molecular entity
literal	Σ	0..1	BackboneElement	A molecular entity defined as a string literal
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
encoding	Σ	0..1	CodeableConcept	The encoding used in the value
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding
resolvable	Σ	0..1	Reference(DocumentReference)	A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
extracted	Σ	0..1	BackboneElement	A molecular entity that is represented as a portion of a different entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
reverseComplement	Σ	0..1	boolean	A flag that indicates whether the extracted sequence should be reverse complemented
repeated	Σ	0..1	BackboneElement	A representation as a repeated motif
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceMotif	Σ	1..1	Reference(MolecularDefinition)	The motif that is repeated
copyCount	Σ	1..1	integer	The number of copies of the motif
concatenated	Σ	0..1	BackboneElement	An ordered concatenation of molecular entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequenceElement	Σ	1..*	BackboneElement	One of the concatenated entities
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
sequence	Σ	1..1	Reference(MolecularDefinition)	A reference to the sequence that defines this specific concatenated element
ordinalIndex	Σ	1..1	integer	The ordinal index of the element within the concatenated representation
relative	Σ	0..1	BackboneElement	A molecular entity represented as an ordered series of edits on a specified starting entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity on which edits will be applied
edit	Σ	0..*	BackboneElement	A defined edit (change) to be applied
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
editOrder		0..1	integer	Defines the order of edits when multiple edits are to be applied to the startingMolecule
coordinateInterval	Σ	0..1	BackboneElement	The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LOINC Answer List LL5323-2 (extensible): Coordinate system.
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the replacement in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The portion of the molecular entity that is replaced by the replacementMolecule
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
MolecularDefinition.language	required	AllLanguages http://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3 From the FHIR Standard
MolecularDefinition.type	required	MoleculeTypeVS(a valid code from Molecule Type) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type From this IG
MolecularDefinition.topology	required	TopologyVS(a valid code from Topology) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.origin	required	CoordinateOriginVS(a valid code from Coordinate Origin) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/coordinate-origin From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.normalizationMethod	required	NormalizationMethodVS(a valid code from Normalization Method) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/normalization-method From this IG
MolecularDefinition.location.sequenceLocation.strand	required	StrandOrientationVS(a valid code from Strand Orientation) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/strand-orientation From this IG
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:contextState.extracted.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:contextState.relative.edit.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:referenceState.extracted.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:referenceState.relative.edit.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:alternativeState.extracted.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:alternativeState.relative.edit.coordinateInterval.coordinateSystem.system	extensible	LOINC LL5323-2 http://loinc.org/vs/LL5323-2

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	MolecularDefinition	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	MolecularDefinition	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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	MolecularDefinition	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	MolecularDefinition	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	MolecularDefinition	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())