10.7 Resource MolecularSequence - Content

Name	Flags	Card.	Type	Description & Constraints
MolecularSequence	TU		DomainResource	Representation of a molecular sequence Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence
type	Σ	0..1	code	aa | dna | rna Binding: sequence Type ( Required )
subject	Σ	0..1	Reference ( Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct )	Subject this sequence is associated too
focus	Σ	0..*	Reference ( Any )	What the molecular sequence is about, when it is not about the subject of record
specimen	Σ	0..1	Reference ( Specimen )	Specimen used for sequencing
device	Σ	0..1	Reference ( Device )	The method for sequencing
performer	Σ	0..1	Reference ( Organization )	Who should be responsible for test result
literal	Σ	0..1	string	Sequence that was observed
formatted	Σ	0..*	Attachment	Embedded file or a link (URL) which contains content to represent the sequence
relative	Σ	0..*	BackboneElement	A sequence defined relative to another sequence
coordinateSystem	Σ	1..1	CodeableConcept	Ways of identifying nucleotides or amino acids within a sequence Binding: LL5323-2 ( Extensible )
ordinalPosition		0..1	integer	Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
sequenceRange		0..1	Range	Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
startingSequence	Σ C	0..1	BackboneElement	A sequence used as starting sequence + Rule: Both genomeAssembly and chromosome must be both contained if either one of them is contained + Rule: Have and only have one of the following elements in startingSequence: 1. genomeAssembly; 2 sequence
genomeAssembly	Σ C	0..1	CodeableConcept	The genome assembly used for starting sequence, e.g. GRCh38 Binding: LL1040-6 ( Extensible )
chromosome	Σ C	0..1	CodeableConcept	Chromosome Identifier Binding: LL2938-0 ( Required )
sequence[x]	Σ C	0..1		The reference sequence that represents the starting sequence Binding: Multiple bindings acceptable (NCBI or LRG) ( Example )
sequenceCodeableConcept			CodeableConcept
sequenceString			string
sequenceReference			Reference ( MolecularSequence )
windowStart	Σ	0..1	integer	Start position of the window on the starting sequence
windowEnd	Σ	0..1	integer	End position of the window on the starting sequence
orientation	Σ	0..1	code	sense | antisense Binding: orientation Type ( Required )
strand	Σ	0..1	code	watson | crick Binding: strand Type ( Required )
edit	Σ	0..*	BackboneElement	Changes in sequence from the starting sequence
start	Σ	0..1	integer	Start position of the edit on the starting sequence
end	Σ	0..1	integer	End position of the edit on the starting sequence
replacementSequence	Σ	0..1	string	Allele that was observed
replacedSequence	Σ	0..1	string	Allele in the starting sequence
Documentation for this format

See the Extensions for this resource

<MolecularSequence xmlns="http://hl7.org/fhir"> 
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) Subject this sequence is associated too --></subject>
 <focus><!-- 0..* Reference(Any) What the molecular sequence is about, when it is not about the subject of record --></focus>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <literal value="[string]"/><!-- 0..1 Sequence that was observed -->
 <formatted><!-- 0..* Attachment Embedded file or a link (URL) which contains content to represent the sequence --></formatted>
 <relative>  <!-- 0..* A sequence defined relative to another sequence -->
  <coordinateSystem><!-- 1..1 CodeableConcept Ways of identifying nucleotides or amino acids within a sequence  --></coordinateSystem>
  <ordinalPosition value="[integer]"/><!-- 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together -->
  <sequenceRange><!-- 0..1 Range Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together --></sequenceRange>
  <startingSequence>  <!-- 0..1 A sequence used as starting sequence -->
   <genomeAssembly><!-- I 0..1 CodeableConcept The genome assembly used for starting sequence, e.g. GRCh38  --></genomeAssembly>
   <chromosome><!-- I 0..1 CodeableConcept Chromosome Identifier  --></chromosome>
   <sequence[x]><!-- I 0..1 CodeableConcept|string|Reference(MolecularSequence) The reference sequence that represents the starting sequence --></sequence[x]>
   <windowStart value="[integer]"/><!-- 0..1 Start position of the window on the starting sequence -->
   <windowEnd value="[integer]"/><!-- 0..1 End position of the window on the starting sequence -->
   <orientation value="[code]"/><!-- 0..1 sense | antisense -->
   <strand value="[code]"/><!-- 0..1 watson | crick -->
  </startingSequence>
  <edit>  <!-- 0..* Changes in sequence from the starting sequence -->
   <start value="[integer]"/><!-- 0..1 Start position of the edit on the starting sequence -->
   <end value="[integer]"/><!-- 0..1 End position of the edit on the starting sequence -->
   <replacementSequence value="[string]"/><!-- 0..1 Allele that was observed -->
   <replacedSequence value="[string]"/><!-- 0..1 Allele in the starting sequence -->
  </edit>
 </relative>
</MolecularSequence>

{
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // aa | dna | rna
  "subject" : { Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) }, // Subject this sequence is associated too
  "focus" : [{ Reference(Any) }], // What the molecular sequence is about, when it is not about the subject of record
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "literal" : "<string>", // Sequence that was observed
  "formatted" : [{ Attachment }], // Embedded file or a link (URL) which contains content to represent the sequence
  "relative" : [{ // A sequence defined relative to another sequence
    "coordinateSystem" : { CodeableConcept }, // R!  Ways of identifying nucleotides or amino acids within a sequence 
    "ordinalPosition" : <integer>, // Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    "sequenceRange" : { Range }, // Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    "startingSequence" : { // A sequence used as starting sequence
      "genomeAssembly" : { CodeableConcept }, // I The genome assembly used for starting sequence, e.g. GRCh38 
      "chromosome" : { CodeableConcept }, // I Chromosome Identifier 
      // sequence[x]: The reference sequence that represents the starting sequence. One of these 3:
      "sequenceCodeableConcept" : { CodeableConcept },
      "sequenceString" : "<string>",
      "sequenceReference" : { Reference(MolecularSequence) },
      "windowStart" : <integer>, // Start position of the window on the starting sequence
      "windowEnd" : <integer>, // End position of the window on the starting sequence
      "orientation" : "<code>", // sense | antisense
      "strand" : "<code>" // watson | crick
    },
    "edit" : [{ // Changes in sequence from the starting sequence
      "start" : <integer>, // Start position of the edit on the starting sequence
      "end" : <integer>, // End position of the edit on the starting sequence
      "replacementSequence" : "<string>", // Allele that was observed
      "replacedSequence" : "<string>" // Allele in the starting sequence
    }]
  }]
}

@prefix fhir: <http://hl7.org/fhir/> .


[ a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Unique ID for this particular sequence
  fhir:type [ code ] ; # 0..1 aa | dna | rna
  fhir:subject [ Reference(BiologicallyDerivedProduct|Group|NutritionProduct|Patient|Substance) ] ; # 0..1 Subject this sequence is associated too
  fhir:focus  ( [ Reference(Any) ] ... ) ; # 0..* What the molecular sequence is about, when it is not about the subject of record
  fhir:specimen [ Reference(Specimen) ] ; # 0..1 Specimen used for sequencing
  fhir:device [ Reference(Device) ] ; # 0..1 The method for sequencing
  fhir:performer [ Reference(Organization) ] ; # 0..1 Who should be responsible for test result
  fhir:literal [ string ] ; # 0..1 Sequence that was observed
  fhir:formatted  ( [ Attachment ] ... ) ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:relative ( [ # 0..* A sequence defined relative to another sequence
    fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:ordinalPosition [ integer ] ; # 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    fhir:sequenceRange [ Range ] ; # 0..1 Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    fhir:startingSequence [ # 0..1 A sequence used as starting sequence
      fhir:genomeAssembly [ CodeableConcept ] ; # 0..1 I The genome assembly used for starting sequence, e.g. GRCh38
      fhir:chromosome [ CodeableConcept ] ; # 0..1 I Chromosome Identifier
      # sequence[x] : 0..1 I The reference sequence that represents the starting sequence. One of these 3
        fhir:sequence [  a fhir:CodeableConcept ; CodeableConcept ]
        fhir:sequence [  a fhir:string ; string ]
        fhir:sequence [  a fhir:Reference ; Reference(MolecularSequence) ]
      fhir:windowStart [ integer ] ; # 0..1 Start position of the window on the starting sequence
      fhir:windowEnd [ integer ] ; # 0..1 End position of the window on the starting sequence
      fhir:orientation [ code ] ; # 0..1 sense | antisense
      fhir:strand [ code ] ; # 0..1 watson | crick
    ] ;
    fhir:edit ( [ # 0..* Changes in sequence from the starting sequence
      fhir:start [ integer ] ; # 0..1 Start position of the edit on the starting sequence
      fhir:end [ integer ] ; # 0..1 End position of the edit on the starting sequence
      fhir:replacementSequence [ string ] ; # 0..1 Allele that was observed
      fhir:replacedSequence [ string ] ; # 0..1 Allele in the starting sequence
    ] ... ) ;
  ] ... ) ;
]

Changes from both R4 and R4B

See the Full Difference for further information

This analysis is available for R4 as XML or JSON and for R4B as XML or JSON .

See R4 <--> R5 Conversion Maps (status = See Conversions Summary .)

Name	Flags	Card.	Type	Description & Constraints
MolecularSequence	TU		DomainResource	Representation of a molecular sequence Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence
type	Σ	0..1	code	aa | dna | rna Binding: sequence Type ( Required )
subject	Σ	0..1	Reference ( Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct )	Subject this sequence is associated too
focus	Σ	0..*	Reference ( Any )	What the molecular sequence is about, when it is not about the subject of record
specimen	Σ	0..1	Reference ( Specimen )	Specimen used for sequencing
device	Σ	0..1	Reference ( Device )	The method for sequencing
performer	Σ	0..1	Reference ( Organization )	Who should be responsible for test result
literal	Σ	0..1	string	Sequence that was observed
formatted	Σ	0..*	Attachment	Embedded file or a link (URL) which contains content to represent the sequence
relative	Σ	0..*	BackboneElement	A sequence defined relative to another sequence
coordinateSystem	Σ	1..1	CodeableConcept	Ways of identifying nucleotides or amino acids within a sequence Binding: LL5323-2 ( Extensible )
ordinalPosition		0..1	integer	Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
sequenceRange		0..1	Range	Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
startingSequence	Σ C	0..1	BackboneElement	A sequence used as starting sequence + Rule: Both genomeAssembly and chromosome must be both contained if either one of them is contained + Rule: Have and only have one of the following elements in startingSequence: 1. genomeAssembly; 2 sequence
genomeAssembly	Σ C	0..1	CodeableConcept	The genome assembly used for starting sequence, e.g. GRCh38 Binding: LL1040-6 ( Extensible )
chromosome	Σ C	0..1	CodeableConcept	Chromosome Identifier Binding: LL2938-0 ( Required )
sequence[x]	Σ C	0..1		The reference sequence that represents the starting sequence Binding: Multiple bindings acceptable (NCBI or LRG) ( Example )
sequenceCodeableConcept			CodeableConcept
sequenceString			string
sequenceReference			Reference ( MolecularSequence )
windowStart	Σ	0..1	integer	Start position of the window on the starting sequence
windowEnd	Σ	0..1	integer	End position of the window on the starting sequence
orientation	Σ	0..1	code	sense | antisense Binding: orientation Type ( Required )
strand	Σ	0..1	code	watson | crick Binding: strand Type ( Required )
edit	Σ	0..*	BackboneElement	Changes in sequence from the starting sequence
start	Σ	0..1	integer	Start position of the edit on the starting sequence
end	Σ	0..1	integer	End position of the edit on the starting sequence
replacementSequence	Σ	0..1	string	Allele that was observed
replacedSequence	Σ	0..1	string	Allele in the starting sequence
Documentation for this format

See the Extensions for this resource

<MolecularSequence xmlns="http://hl7.org/fhir"> 
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) Subject this sequence is associated too --></subject>
 <focus><!-- 0..* Reference(Any) What the molecular sequence is about, when it is not about the subject of record --></focus>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <literal value="[string]"/><!-- 0..1 Sequence that was observed -->
 <formatted><!-- 0..* Attachment Embedded file or a link (URL) which contains content to represent the sequence --></formatted>
 <relative>  <!-- 0..* A sequence defined relative to another sequence -->
  <coordinateSystem><!-- 1..1 CodeableConcept Ways of identifying nucleotides or amino acids within a sequence  --></coordinateSystem>
  <ordinalPosition value="[integer]"/><!-- 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together -->
  <sequenceRange><!-- 0..1 Range Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together --></sequenceRange>
  <startingSequence>  <!-- 0..1 A sequence used as starting sequence -->
   <genomeAssembly><!-- I 0..1 CodeableConcept The genome assembly used for starting sequence, e.g. GRCh38  --></genomeAssembly>
   <chromosome><!-- I 0..1 CodeableConcept Chromosome Identifier  --></chromosome>
   <sequence[x]><!-- I 0..1 CodeableConcept|string|Reference(MolecularSequence) The reference sequence that represents the starting sequence --></sequence[x]>
   <windowStart value="[integer]"/><!-- 0..1 Start position of the window on the starting sequence -->
   <windowEnd value="[integer]"/><!-- 0..1 End position of the window on the starting sequence -->
   <orientation value="[code]"/><!-- 0..1 sense | antisense -->
   <strand value="[code]"/><!-- 0..1 watson | crick -->
  </startingSequence>
  <edit>  <!-- 0..* Changes in sequence from the starting sequence -->
   <start value="[integer]"/><!-- 0..1 Start position of the edit on the starting sequence -->
   <end value="[integer]"/><!-- 0..1 End position of the edit on the starting sequence -->
   <replacementSequence value="[string]"/><!-- 0..1 Allele that was observed -->
   <replacedSequence value="[string]"/><!-- 0..1 Allele in the starting sequence -->
  </edit>
 </relative>
</MolecularSequence>

{
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // aa | dna | rna
  "subject" : { Reference(BiologicallyDerivedProduct|Group|NutritionProduct|
   Patient|Substance) }, // Subject this sequence is associated too
  "focus" : [{ Reference(Any) }], // What the molecular sequence is about, when it is not about the subject of record
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "literal" : "<string>", // Sequence that was observed
  "formatted" : [{ Attachment }], // Embedded file or a link (URL) which contains content to represent the sequence
  "relative" : [{ // A sequence defined relative to another sequence
    "coordinateSystem" : { CodeableConcept }, // R!  Ways of identifying nucleotides or amino acids within a sequence 
    "ordinalPosition" : <integer>, // Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    "sequenceRange" : { Range }, // Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    "startingSequence" : { // A sequence used as starting sequence
      "genomeAssembly" : { CodeableConcept }, // I The genome assembly used for starting sequence, e.g. GRCh38 
      "chromosome" : { CodeableConcept }, // I Chromosome Identifier 
      // sequence[x]: The reference sequence that represents the starting sequence. One of these 3:
      "sequenceCodeableConcept" : { CodeableConcept },
      "sequenceString" : "<string>",
      "sequenceReference" : { Reference(MolecularSequence) },
      "windowStart" : <integer>, // Start position of the window on the starting sequence
      "windowEnd" : <integer>, // End position of the window on the starting sequence
      "orientation" : "<code>", // sense | antisense
      "strand" : "<code>" // watson | crick
    },
    "edit" : [{ // Changes in sequence from the starting sequence
      "start" : <integer>, // Start position of the edit on the starting sequence
      "end" : <integer>, // End position of the edit on the starting sequence
      "replacementSequence" : "<string>", // Allele that was observed
      "replacedSequence" : "<string>" // Allele in the starting sequence
    }]
  }]
}

@prefix fhir: <http://hl7.org/fhir/> .


[ a fhir:MolecularSequence;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Unique ID for this particular sequence
  fhir:type [ code ] ; # 0..1 aa | dna | rna
  fhir:subject [ Reference(BiologicallyDerivedProduct|Group|NutritionProduct|Patient|Substance) ] ; # 0..1 Subject this sequence is associated too
  fhir:focus  ( [ Reference(Any) ] ... ) ; # 0..* What the molecular sequence is about, when it is not about the subject of record
  fhir:specimen [ Reference(Specimen) ] ; # 0..1 Specimen used for sequencing
  fhir:device [ Reference(Device) ] ; # 0..1 The method for sequencing
  fhir:performer [ Reference(Organization) ] ; # 0..1 Who should be responsible for test result
  fhir:literal [ string ] ; # 0..1 Sequence that was observed
  fhir:formatted  ( [ Attachment ] ... ) ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:relative ( [ # 0..* A sequence defined relative to another sequence
    fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:ordinalPosition [ integer ] ; # 0..1 Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together
    fhir:sequenceRange [ Range ] ; # 0..1 Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
    fhir:startingSequence [ # 0..1 A sequence used as starting sequence
      fhir:genomeAssembly [ CodeableConcept ] ; # 0..1 I The genome assembly used for starting sequence, e.g. GRCh38
      fhir:chromosome [ CodeableConcept ] ; # 0..1 I Chromosome Identifier
      # sequence[x] : 0..1 I The reference sequence that represents the starting sequence. One of these 3
        fhir:sequence [  a fhir:CodeableConcept ; CodeableConcept ]
        fhir:sequence [  a fhir:string ; string ]
        fhir:sequence [  a fhir:Reference ; Reference(MolecularSequence) ]
      fhir:windowStart [ integer ] ; # 0..1 Start position of the window on the starting sequence
      fhir:windowEnd [ integer ] ; # 0..1 End position of the window on the starting sequence
      fhir:orientation [ code ] ; # 0..1 sense | antisense
      fhir:strand [ code ] ; # 0..1 watson | crick
    ] ;
    fhir:edit ( [ # 0..* Changes in sequence from the starting sequence
      fhir:start [ integer ] ; # 0..1 Start position of the edit on the starting sequence
      fhir:end [ integer ] ; # 0..1 End position of the edit on the starting sequence
      fhir:replacementSequence [ string ] ; # 0..1 Allele that was observed
      fhir:replacedSequence [ string ] ; # 0..1 Allele in the starting sequence
    ] ... ) ;
  ] ... ) ;
]

Changes from both R4 and R4B

See the Full Difference for further information

This analysis is available for R4 as XML or JSON and for R4B as XML or JSON .

See R4 <--> R5 Conversion Maps (status = See Conversions Summary .)