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: Variation ( Experimental )

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

Variation profile of the MolecularDefinition resource.

Scope and Usage

The Variation profile defines a structured approach for representing genetic variations at specific genomic loci. It characterizes the genetic composition at a given location in three distinct states: context, reference, and alternative. This profile leverages MolecularDefinition resource to enable precise communication of genetic alterations. Where applicable, the Variation profile can integrate Sequence and Allele profiles to provide a comprehensive representation of genomic changes, supporting interoperability in health information systems.

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)
... location Σ 1..1 BackboneElement A defined location on a molecular entity
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
... Slices for representation Σ 2..* BackboneElement A representation of a molecular entity
Slice: Unordered, Open by value:focus
.... representation:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... representation:contextState SΣ 0..1 BackboneElement A representation of a molecular entity
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... focus Σ 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: context-state
....... display 1..1 string Representation defined by the system
Fixed Value: Context State
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... representation:referenceState SΣ 1..1 BackboneElement A representation of a molecular entity
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... focus Σ 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: reference-state
....... display 1..1 string Representation defined by the system
Fixed Value: Reference State
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... representation:alternativeState SΣ 1..1 BackboneElement A representation of a molecular entity
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... focus Σ 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: alternative-state
....... display 1..1 string Representation defined by the system
Fixed Value: Alternative State
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept

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
.... 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 (required)
....... normalizationMethod 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system
Binding: Normalization Method (required)
..... strand 0..1 CodeableConcept The strand at the coordinateInterval
Binding: Strand Orientation (required)
... Slices for representation 2..* BackboneElement A representation of a molecular entity
Slice: Unordered, Open by value:focus
.... representation:contextState S 0..1 BackboneElement A representation of a molecular entity
..... focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: context-state
....... display 1..1 string Representation defined by the system
Fixed Value: Context State
.... representation:referenceState S 1..1 BackboneElement A representation of a molecular entity
..... focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: reference-state
....... display 1..1 string Representation defined by the system
Fixed Value: Reference State
.... representation:alternativeState S 1..1 BackboneElement A representation of a molecular entity
..... focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: alternative-state
....... display 1..1 string Representation defined by the system
Fixed Value: Alternative State

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

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.location.sequenceLocation.coordinateInterval.coordinateSystem.originrequiredCoordinateOriginVS(a valid code from Coordinate Origin)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/coordinate-origin
From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.normalizationMethodrequiredNormalizationMethodVS(a valid code from Normalization Method)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/normalization-method
From this IG
MolecularDefinition.location.sequenceLocation.strandrequiredStrandOrientationVS(a valid code from Strand Orientation)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/strand-orientation
From this IG
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:contextState.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:contextState.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:referenceState.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:referenceState.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:alternativeState.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:alternativeState.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: 6 elements(1 nested mandatory element)
Must-Support: 4 elements
Prohibited: 1 element

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of MolecularDefinition.representation

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)
... location Σ 1..1 BackboneElement A defined location on a molecular entity
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
... Slices for representation Σ 2..* BackboneElement A representation of a molecular entity
Slice: Unordered, Open by value:focus
.... representation:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... representation:contextState SΣ 0..1 BackboneElement A representation of a molecular entity
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... focus Σ 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: context-state
....... display 1..1 string Representation defined by the system
Fixed Value: Context State
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... representation:referenceState SΣ 1..1 BackboneElement A representation of a molecular entity
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... focus Σ 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: reference-state
....... display 1..1 string Representation defined by the system
Fixed Value: Reference State
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... representation:alternativeState SΣ 1..1 BackboneElement A representation of a molecular entity
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... focus Σ 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: alternative-state
....... display 1..1 string Representation defined by the system
Fixed Value: Alternative State
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept

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
.... 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 (required)
....... normalizationMethod 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system
Binding: Normalization Method (required)
..... strand 0..1 CodeableConcept The strand at the coordinateInterval
Binding: Strand Orientation (required)
... Slices for representation 2..* BackboneElement A representation of a molecular entity
Slice: Unordered, Open by value:focus
.... representation:contextState S 0..1 BackboneElement A representation of a molecular entity
..... focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: context-state
....... display 1..1 string Representation defined by the system
Fixed Value: Context State
.... representation:referenceState S 1..1 BackboneElement A representation of a molecular entity
..... focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: reference-state
....... display 1..1 string Representation defined by the system
Fixed Value: Reference State
.... representation:alternativeState S 1..1 BackboneElement A representation of a molecular entity
..... focus 1..1 CodeableConcept The domain concept that is the focus of a given instance of the representation
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: alternative-state
....... display 1..1 string Representation defined by the system
Fixed Value: Alternative State

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.location.sequenceLocation.coordinateInterval.coordinateSystem.originrequiredCoordinateOriginVS(a valid code from Coordinate Origin)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/coordinate-origin
From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.normalizationMethodrequiredNormalizationMethodVS(a valid code from Normalization Method)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/normalization-method
From this IG
MolecularDefinition.location.sequenceLocation.strandrequiredStrandOrientationVS(a valid code from Strand Orientation)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/strand-orientation
From this IG

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

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.location.sequenceLocation.coordinateInterval.coordinateSystem.originrequiredCoordinateOriginVS(a valid code from Coordinate Origin)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/coordinate-origin
From this IG
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.normalizationMethodrequiredNormalizationMethodVS(a valid code from Normalization Method)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/normalization-method
From this IG
MolecularDefinition.location.sequenceLocation.strandrequiredStrandOrientationVS(a valid code from Strand Orientation)
http://hl7.org/fhir/uv/molecular-definition-data-types/ValueSet/strand-orientation
From this IG
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:contextState.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:contextState.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:referenceState.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:referenceState.relative.edit.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:alternativeState.extracted.coordinateInterval.coordinateSystem.systemextensibleLOINC LL5323-2
http://loinc.org/vs/LL5323-2
MolecularDefinition.representation:alternativeState.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: 6 elements(1 nested mandatory element)
Must-Support: 4 elements
Prohibited: 1 element

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of MolecularDefinition.representation

 

Other representations of profile: CSV, Excel, Schematron

Notes:

Additional Notes

This is the Variation profile notes section.