Molecular Definition Implementation Guide for Molecular Data Types, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 1.0.0-ballot1 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/molecular-definition-data-types/ and changes regularly. See the Directory of published versions

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Resource Profile: Sequence ( Experimental )

Sequence profile of MolecularDefinition

Usages:

• Refer to this Profile: Allele and Variation
• Examples for this Profile: MolecularDefinition/example-genomic-cyp2c19-accession, MolecularDefinition/example-sequence-a-aa-iupac, MolecularDefinition/example-sequence-a-dna-iupac, MolecularDefinition/example-sequence-c-dna-iupac... Show 14 more, MolecularDefinition/example-sequence-cgg, MolecularDefinition/example-sequence-cyp2c19-accession, MolecularDefinition/example-sequence-cyp2c19-attached, MolecularDefinition/example-sequence-cyp2c19-concatenated-regions, MolecularDefinition/example-sequence-cyp2c19-downstream-region, MolecularDefinition/example-sequence-cyp2c19-gene-region, MolecularDefinition/example-sequence-cyp2c19-upstream-region, MolecularDefinition/example-sequence-cyp2c19-url, MolecularDefinition/example-sequence-fmr1-cgg-20x-edited-contained, MolecularDefinition/example-sequence-fmr1-cgg-20x-edited-referenced, MolecularDefinition/example-sequence-fmr1-cgg-20x-repeat, MolecularDefinition/example-sequence-hla000011, MolecularDefinition/example-sequence-nc00000714-url and MolecularDefinition/example-sequence-nm0007694-url

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
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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		0..0
representation
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
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.representation.literal.encoding	required	EncodingsVS(a valid code from Encodings) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG
MolecularDefinition.representation.literal.value	extensible

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)
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)
representation	Σ	0..*	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	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
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.representation.literal.encoding	required	EncodingsVS(a valid code from Encodings) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG
MolecularDefinition.representation.literal.value	extensible
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

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())

This structure is derived from MolecularDefinition

Summary

Mandatory: 1 element
Must-Support: 1 element
Prohibited: 2 elements

Differential View

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		0..0
representation
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
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.representation.literal.encoding	required	EncodingsVS(a valid code from Encodings) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG
MolecularDefinition.representation.literal.value	extensible

Key Elements View

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)
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())

Snapshot View

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)
representation	Σ	0..*	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	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
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.representation.literal.encoding	required	EncodingsVS(a valid code from Encodings) http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings From this IG
MolecularDefinition.representation.literal.value	extensible
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

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())

This structure is derived from MolecularDefinition

Summary

Mandatory: 1 element
Must-Support: 1 element
Prohibited: 2 elements

Other representations of profile: CSV, Excel, Schematron

Notes: