Scope and Usage

The Allele profile is a key component of this implementation guide, defining the genetic makeup at specific locations within the genomic molecules. It provides a structured representation of genetic content in two distinct states: the context state, which establishes the broader genomic setting, and the allele state, which specifies the particular genetic makeup at that location. The Allele profile builds upon the Sequence profile, using its representation of raw genetic sequences to ensure accuracy and consistency. Additionally, it serves as a foundational element that other profiles within this guide can leverage to enhance their functionality and interoperability.

In describing an allele, it is strongly recommended to employ the Allele profile. After providing the necessary identifiers and genomic location, the Allele profile features two principal slices within the representation element. These slices represent the two defined states: the allele state and the context state. While the allele state slice—representing the specific allelic genetic makeup at the designated locus—is mandatory, the context state slice, which represents the current genetic makeup within the designated sequence, remains optional yet highly encouraged to enhance clarity. Each slice captures a single state exclusively. This ensures a accurate molecular depiction.

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

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	Genomic location of the specified allele
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Slices for representation	Σ	1..*	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:alleleState	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: allele-state
display		1..1	string	Representation defined by the system Fixed Value: Allele 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	Status	Usage	ValueSet	Version	Source
MolecularDefinition.​type	Base	required	Molecule Type ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​topology	Base	required	Topology ValueSet	📦1.0.0-ballot1	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
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())

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	Genomic location of the specified allele
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		1..*	BackboneElement	A representation of a molecular entity Slice: Unordered, Open by value:focus
representation:All Slices				Content/Rules for all slices
literal
encoding		0..1	CodeableConcept	The encoding used in the value Binding: Molecular Definition Encodings ValueSet (required)
value		1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding. Additional Bindings Purpose Nucleotide DNA 1-letter Unambiguous Symbols ValueSet Extensible Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet Extensible Nucleotide DNA 1-letter Ambiguous Symbols ValueSet Extensible Nucleotide RNA 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Ambiguous Symbols ValueSet Extensible Amino Acid 3-letter Unambiguous Symbols ValueSet Extensible Amino Acid 3-letter Ambiguous Symbols ValueSet Extensible
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:alleleState	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: allele-state
display		1..1	string	Representation defined by the system Fixed Value: Allele State
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
MolecularDefinition.​type	Base	required	Molecule Type ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​topology	Base	required	Topology ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​origin	Base	required	Coordinate Origin ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​normalizationMethod	Base	required	Normalization Method ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​location.sequenceLocation.​strand	Base	required	Strand Orientation ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​representation.literal.​encoding	Base	required	Molecular Definition Encodings ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​representation.literal.​value	Base	extensible		Not Stated	Unknown

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	Genomic location of the specified allele
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	1..*	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 Binding: Molecular Definition Encodings ValueSet (required)
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding. Additional Bindings Purpose Nucleotide DNA 1-letter Unambiguous Symbols ValueSet Extensible Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet Extensible Nucleotide DNA 1-letter Ambiguous Symbols ValueSet Extensible Nucleotide RNA 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Ambiguous Symbols ValueSet Extensible Amino Acid 3-letter Unambiguous Symbols ValueSet Extensible Amino Acid 3-letter Ambiguous Symbols ValueSet Extensible
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 Binding: Molecular Definition Encodings ValueSet (required)
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding. Additional Bindings Purpose Nucleotide DNA 1-letter Unambiguous Symbols ValueSet Extensible Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet Extensible Nucleotide DNA 1-letter Ambiguous Symbols ValueSet Extensible Nucleotide RNA 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Ambiguous Symbols ValueSet Extensible Amino Acid 3-letter Unambiguous Symbols ValueSet Extensible Amino Acid 3-letter Ambiguous Symbols ValueSet Extensible
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:alleleState	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: allele-state
display		1..1	string	Representation defined by the system Fixed Value: Allele 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 Binding: Molecular Definition Encodings ValueSet (required)
value	Σ	1..1	string	A string literal representation of the molecular entity, using the encoding specified in encoding Binding Description: (extensible) ⚠: Refer to the addtional bindings for the literal encoding. Additional Bindings Purpose Nucleotide DNA 1-letter Unambiguous Symbols ValueSet Extensible Nucleotide DNA 1-letter Unambiguous Symbols Including N ValueSet Extensible Nucleotide DNA 1-letter Ambiguous Symbols ValueSet Extensible Nucleotide RNA 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Unambiguous Symbols ValueSet Extensible Amino Acid 1-letter Ambiguous Symbols ValueSet Extensible Amino Acid 3-letter Unambiguous Symbols ValueSet Extensible Amino Acid 3-letter Ambiguous Symbols ValueSet Extensible
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	Status	Usage	ValueSet	Version	Source
MolecularDefinition.​language	Base	required	All Languages	📍6.0.0-ballot3	FHIR Std.
MolecularDefinition.​type	Base	required	Molecule Type ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​topology	Base	required	Topology ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​origin	Base	required	Coordinate Origin ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​location.sequenceLocation.​coordinateInterval.coordinateSystem.​normalizationMethod	Base	required	Normalization Method ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​location.sequenceLocation.​strand	Base	required	Strand Orientation ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​representation.literal.​encoding	Base	required	Molecular Definition Encodings ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​representation.literal.​value	Base	extensible		Not Stated	Unknown
MolecularDefinition.​representation.extracted.​coordinateInterval.coordinateSystem.​system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?
MolecularDefinition.​representation.relative.​edit.coordinateInterval.​coordinateSystem.system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?
MolecularDefinition.​representation:contextState.​literal.encoding	Base	required	Molecular Definition Encodings ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​representation:contextState.​literal.value	Base	extensible		Not Stated	Unknown
MolecularDefinition.​representation:contextState.​extracted.coordinateInterval.​coordinateSystem.system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?
MolecularDefinition.​representation:contextState.​relative.edit.coordinateInterval.​coordinateSystem.system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?
MolecularDefinition.​representation:alleleState.​literal.encoding	Base	required	Molecular Definition Encodings ValueSet	📦1.0.0-ballot1	This IG
MolecularDefinition.​representation:alleleState.​literal.value	Base	extensible		Not Stated	Unknown
MolecularDefinition.​representation:alleleState.​extracted.coordinateInterval.​coordinateSystem.system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?
MolecularDefinition.​representation:alleleState.​relative.edit.coordinateInterval.​coordinateSystem.system	Base	extensible	​ LOINC Answer Codes for LL5323-2 (missing link)	📦	unknown?

Constraints

Id	Grade	Path(s)	Description	Expression
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())