Molecular Definition Implementation Guide for Molecular Data Types
1.0.0-ballot1 - ci-build International flag

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

Resource Profile: Sequence ( Experimental )

Official URL: http://hl7.org/fhir/uv/molecular-definition-data-types/StructureDefinition/sequence Version: 1.0.0-ballot1
Standards status: Informative Computable Name: Sequence

Sequence profile of MolecularDefinition

Scope and Usage

The Sequence profile serves as a foundational component of this implementation guide, designed to represent raw genetic sequences such as DNA, RNA, and proteins. It supports multiple formats to accommodate diverse implementation needs. Unlike Allele and Variation profiles that emphasize genomic location, the Sequence profile focuses on the intrinsic composition of the genetic sequence. Additionally, it plays a crucial role in integrating with other profiles within this guide, enhancing their functionality.

Usages:

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.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology (required)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
MolecularDefinition.typerequiredMoleculeTypeVS(a valid code from Molecule Type)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type
From this IG
MolecularDefinition.topologyrequiredTopologyVS(a valid code from Topology)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology
From this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorMolecularDefinitionIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorMolecularDefinitionIf 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-4errorMolecularDefinitionIf 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-5errorMolecularDefinitionIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceMolecularDefinitionA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())

This structure is derived from MolecularDefinition

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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 (required)
... topology 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology (required)
... member 0..0
... representation
.... literal
..... encoding 0..1 CodeableConcept The encoding used in the value
Binding: Molecular Definition Encodings (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 BindingsPurpose
Nucleotide DNA 1-letter Unambiguous Symbols Extensible
Nucleotide DNA 1-letter Unambiguous Symbols Including N Extensible
Nucleotide DNA 1-letter Ambiguous Symbols Extensible
Nucleotide RNA 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Ambiguous Symbols Extensible
Amino Acid 3-letter Unambiguous Symbols Extensible
Amino Acid 3-letter Ambiguous Symbols Extensible

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
MolecularDefinition.typerequiredMoleculeTypeVS(a valid code from Molecule Type)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type
From this IG
MolecularDefinition.topologyrequiredTopologyVS(a valid code from Topology)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology
From this IG
MolecularDefinition.representation.literal.encodingrequiredEncodingsVS(a valid code from Encodings)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings
From this IG
MolecularDefinition.representation.literal.valueextensible
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... 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 (required)
... topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology (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 (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 BindingsPurpose
Nucleotide DNA 1-letter Unambiguous Symbols Extensible
Nucleotide DNA 1-letter Unambiguous Symbols Including N Extensible
Nucleotide DNA 1-letter Ambiguous Symbols Extensible
Nucleotide RNA 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Ambiguous Symbols Extensible
Amino Acid 3-letter Unambiguous Symbols Extensible
Amino Acid 3-letter Ambiguous Symbols 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
MolecularDefinition.languagerequiredAllLanguages
http://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3
From the FHIR Standard
MolecularDefinition.typerequiredMoleculeTypeVS(a valid code from Molecule Type)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type
From this IG
MolecularDefinition.topologyrequiredTopologyVS(a valid code from Topology)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology
From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.literal.encodingrequiredEncodingsVS(a valid code from Encodings)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings
From this IG
MolecularDefinition.representation.literal.valueextensible
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorMolecularDefinitionIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorMolecularDefinitionIf 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-4errorMolecularDefinitionIf 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-5errorMolecularDefinitionIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceMolecularDefinitionA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll 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

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology (required)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
MolecularDefinition.typerequiredMoleculeTypeVS(a valid code from Molecule Type)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type
From this IG
MolecularDefinition.topologyrequiredTopologyVS(a valid code from Topology)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology
From this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorMolecularDefinitionIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorMolecularDefinitionIf 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-4errorMolecularDefinitionIf 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-5errorMolecularDefinitionIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceMolecularDefinitionA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())

Differential View

This structure is derived from MolecularDefinition

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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 (required)
... topology 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology (required)
... member 0..0
... representation
.... literal
..... encoding 0..1 CodeableConcept The encoding used in the value
Binding: Molecular Definition Encodings (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 BindingsPurpose
Nucleotide DNA 1-letter Unambiguous Symbols Extensible
Nucleotide DNA 1-letter Unambiguous Symbols Including N Extensible
Nucleotide DNA 1-letter Ambiguous Symbols Extensible
Nucleotide RNA 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Ambiguous Symbols Extensible
Amino Acid 3-letter Unambiguous Symbols Extensible
Amino Acid 3-letter Ambiguous Symbols Extensible

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
MolecularDefinition.typerequiredMoleculeTypeVS(a valid code from Molecule Type)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type
From this IG
MolecularDefinition.topologyrequiredTopologyVS(a valid code from Topology)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology
From this IG
MolecularDefinition.representation.literal.encodingrequiredEncodingsVS(a valid code from Encodings)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings
From this IG
MolecularDefinition.representation.literal.valueextensible

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... 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 (required)
... topology Σ 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular)
Binding: Topology (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 (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 BindingsPurpose
Nucleotide DNA 1-letter Unambiguous Symbols Extensible
Nucleotide DNA 1-letter Unambiguous Symbols Including N Extensible
Nucleotide DNA 1-letter Ambiguous Symbols Extensible
Nucleotide RNA 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Unambiguous Symbols Extensible
Amino Acid 1-letter Ambiguous Symbols Extensible
Amino Acid 3-letter Unambiguous Symbols Extensible
Amino Acid 3-letter Ambiguous Symbols 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
MolecularDefinition.languagerequiredAllLanguages
http://hl7.org/fhir/ValueSet/all-languages|6.0.0-ballot3
From the FHIR Standard
MolecularDefinition.typerequiredMoleculeTypeVS(a valid code from Molecule Type)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/molecule-type
From this IG
MolecularDefinition.topologyrequiredTopologyVS(a valid code from Topology)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/topology
From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.literal.encodingrequiredEncodingsVS(a valid code from Encodings)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/encodings
From this IG
MolecularDefinition.representation.literal.valueextensible
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorMolecularDefinitionIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorMolecularDefinitionIf 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-4errorMolecularDefinitionIf 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-5errorMolecularDefinitionIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceMolecularDefinitionA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll 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:

Additional Notes

This section provides supplemental guidance for implementing the Sequence profile.