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10.8 Resource MolecularDefinition - Content

Clinical Genomics icon

Work Group

Maturity Level: 0

Trial Use

Security Category: N/A

Compartments: No defined compartments

Representation of a molecular definition.

Note to Implementers: Molecular Definition resource will replace Molecular Sequence resource. Current page of the Molecular Sequence is temporarily available for referencing and review purposes.

10.8.1 Scope and Usage

The MoleculerDefinition resource is designed for representing genetic molecules (e.g., sequence). It can represent the genetic molecules in different ways, allowing implementations to adopt the most effective ones for their use cases.

The MoleculerDefinition resource is designed to represent a single sequence or a composite of genetic sequences (e.g., haplotype). Each genetic molecule might have multiple representations, but implementers SHALL ensure all representations are for the same molecule. This means that if a single MoleculerDefinition instance contains a literal, two formatted files, and a relative, all four of those representations must represent the same genetic molecule (e.g.,sequence). This can be a challenge across systems, as semantic equivalency of sequences cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.

10.8.2 Boundaries and Relationships

The MoleculerDefinition resource should only be used to capture molecular representations of genetic concepts such as sequence, allele, and haplotype. It will not be used for observational data related to specific patient. Those concepts will be captured in Observation profiles found in the Genomics Reporting Implementation Guide icon . The molecule that was observed and that led to the identification of those concepts can be delivered with this resource, and will be referenced by those observations.

MoleculerDefinition will not be used to capture data such as precise read of DNA sequences and sequence alignment are not included; such data may be accessible through references to GA4GH icon (Global Alliance for Genomics and Health) API, and may be referenced to by the literal element.

10.8.3 References to this Resource

Resource References: itself

10.8.4 Resource Content

Structure

Name	Flags	Card.	Type	Description & Constraints
MolecularDefinition	TU		DomainResource	Representation of a molecular definition Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
identifier	Σ	0..*	Identifier	Unique ID for this particular resource
type	Σ	0..1	code	aa \| dna \| rna Binding: sequence Type (Required)
location	Σ	0..*	BackboneElement	Location of this molecule
sequenceLocation	Σ	0..1	BackboneElement	Location of this molecule in context of a sequence
sequenceContext	Σ	1..1	Reference(MolecularDefinition)	Reference sequence
coordinateInterval	Σ	0..1	BackboneElement	Coordinate Interval for this location
numberingSystem	Σ	0..1	CodeableConcept	Coordinate System
start[x]	Σ	0..1		Start
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		End
endQuantity			Quantity
endRange			Range
strand		0..1	CodeableConcept	Forward or Reverse
cytobandLocation	Σ	0..1	BackboneElement	Location of this molecule in context of a cytoband
genomeAssembly	Σ	1..1	BackboneElement	Reference Genome
organism		0..1	CodeableConcept	Species of the organism
build		0..1	CodeableConcept	Build number
accession		0..1	CodeableConcept	Accession
description[x]		0..1		Genome assemble description
descriptionMarkdown			markdown
descriptionString			string
cytobandInterval	Σ	1..1	BackboneElement	Cytoband Interval
chromosome	Σ	1..1	CodeableConcept	Chromosome
startCytoband	Σ	0..1	BackboneElement	Start
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
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
featureLocation	Σ	0..*	BackboneElement	Location in context of a feature
geneId	Σ	0..*	CodeableConcept	Gene Id
memberState	Σ	0..*	Reference(MolecularDefinition)	Member
representation	Σ	0..*	BackboneElement	Representation
focus	Σ	0..1	CodeableConcept	The focus of the representation
code	Σ	0..*	CodeableConcept	A code of the representation
literal	Σ	0..1	BackboneElement	A literal representation
encoding	Σ	0..1	CodeableConcept	The encoding used for the expression of the primary sequence
value	Σ	1..1	string	The primary (linear) sequence, expressed as a literal string
resolvable	Σ	0..1	Attachment	A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself
extracted	Σ	0..1	BackboneElement	A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
start	Σ	1..1	integer	The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
end	Σ	1..1	integer	The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
coordinateSystem	Σ	1..1	CodeableConcept	The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
reverseComplement	Σ	0..1	boolean	A flag that indicates whether the extracted sequence should be reverse complemented
repeated	Σ	0..1	BackboneElement	A Molecular Sequence that is represented as a repeated sequence motif
sequenceMotif	Σ	1..1	Reference(MolecularDefinition)	The sequence that defines the repeated motif
copyCount	Σ	1..1	integer	The number of repeats (copies) of the sequence motif
concatenated	Σ	0..1	BackboneElement	A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
sequenceElement	Σ	1..*	BackboneElement	One element of a concatenated Molecular Sequence
sequence	Σ	1..1	Reference(MolecularDefinition)	The Molecular Sequence corresponding to this element
ordinalIndex	Σ	1..1	integer	The ordinal position of this sequence element within the concatenated Molecular Sequence
relative	Σ	0..1	BackboneElement	A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The Molecular Sequence that serves as the starting sequence, on which edits will be applied
edit	Σ	0..*	BackboneElement	An edit (change) made to a sequence
editOrder		0..1	integer	The order of this edit, relative to other edits on the starting sequence
coordinateSystem	Σ	1..1	CodeableConcept	The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based Binding: LL5323-2 (Extensible)
start	Σ	1..1	integer	The start coordinate of the interval that will be edited
end	Σ	1..1	integer	The end coordinate of the interval that will be edited
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The sequence that defines the replacement sequence used in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
Documentation for this format

See the Extensions for this resource

UML Diagram (Legend)

XML Template

<MolecularDefinition 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 resource --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <location>  <!-- 0..* Location of this molecule -->
  <sequenceLocation>  <!-- 0..1 Location of this molecule in context of a sequence -->
   <sequenceContext><!-- 1..1 Reference(MolecularDefinition) Reference sequence --></sequenceContext>
   <coordinateInterval>  <!-- 0..1 Coordinate Interval for this location -->
    <numberingSystem><!-- 0..1 CodeableConcept Coordinate System --></numberingSystem>
    <start[x]><!-- 0..1 Quantity|Range Start --></start[x]>
    <end[x]><!-- 0..1 Quantity|Range End --></end[x]>
   </coordinateInterval>
   <strand><!-- 0..1 CodeableConcept Forward or Reverse --></strand>
  </sequenceLocation>
  <cytobandLocation>  <!-- 0..1 Location of this molecule in context of a cytoband -->
   <genomeAssembly>  <!-- 1..1 Reference Genome -->
    <organism><!-- 0..1 CodeableConcept Species of the organism --></organism>
    <build><!-- 0..1 CodeableConcept Build number --></build>
    <accession><!-- 0..1 CodeableConcept Accession --></accession>
    <description[x]><!-- 0..1 markdown|string Genome assemble description --></description[x]>
   </genomeAssembly>
   <cytobandInterval>  <!-- 1..1 Cytoband Interval -->
    <chromosome><!-- 1..1 CodeableConcept Chromosome --></chromosome>
    <startCytoband>  <!-- 0..1 Start -->
     <arm[x]><!-- 0..1 code|string Arm --></arm[x]>
     <region[x]><!-- 0..1 code|string Region --></region[x]>
     <band[x]><!-- 0..1 code|string Band --></band[x]>
     <subBand[x]><!-- 0..1 code|string Sub-band --></subBand[x]>
    </startCytoband>
    <endCytoband>  <!-- 0..1 End -->
     <arm[x]><!-- 0..1 code|string Arm --></arm[x]>
     <region[x]><!-- 0..1 code|string Region --></region[x]>
     <band[x]><!-- 0..1 code|string Band --></band[x]>
     <subBand[x]><!-- 0..1 code|string SuBand --></subBand[x]>
    </endCytoband>
   </cytobandInterval>
  </cytobandLocation>
  <featureLocation>  <!-- 0..* Location in context of a feature -->
   <geneId><!-- 0..* CodeableConcept Gene Id --></geneId>
  </featureLocation>
 </location>
 <memberState><!-- 0..* Reference(MolecularDefinition) Member --></memberState>
 <representation>  <!-- 0..* Representation -->
  <focus><!-- 0..1 CodeableConcept The focus of the representation --></focus>
  <code><!-- 0..* CodeableConcept A code of the representation --></code>
  <literal>  <!-- 0..1 A literal representation -->
   <encoding><!-- 0..1 CodeableConcept The encoding used for the expression of the primary sequence --></encoding>
   <value value="[string]"/><!-- 1..1 The primary (linear) sequence, expressed as a literal string -->
  </literal>
  <resolvable><!-- 0..1 Attachment A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself --></resolvable>
  <extracted>  <!-- 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted --></startingMolecule>
   <start value="[integer]"/><!-- 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted -->
   <end value="[integer]"/><!-- 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted -->
   <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based --></coordinateSystem>
   <reverseComplement value="[boolean]"/><!-- 0..1 A flag that indicates whether the extracted sequence should be reverse complemented -->
  </extracted>
  <repeated>  <!-- 0..1 A Molecular Sequence that is represented as a repeated sequence motif -->
   <sequenceMotif><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the repeated motif --></sequenceMotif>
   <copyCount value="[integer]"/><!-- 1..1 The number of repeats (copies) of the sequence motif -->
  </repeated>
  <concatenated>  <!-- 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences -->
   <sequenceElement>  <!-- 1..* One element of a concatenated Molecular Sequence -->
    <sequence><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence corresponding to this element --></sequence>
    <ordinalIndex value="[integer]"/><!-- 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence -->
   </sequenceElement>
  </concatenated>
  <relative>  <!-- 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the starting sequence, on which edits will be applied --></startingMolecule>
   <edit>  <!-- 0..* An edit (change) made to a sequence -->
    <editOrder value="[integer]"/><!-- 0..1 The order of this edit, relative to other edits on the starting sequence -->
    <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based  --></coordinateSystem>
    <start value="[integer]"/><!-- 1..1 The start coordinate of the interval that will be edited -->
    <end value="[integer]"/><!-- 1..1 The end coordinate of the interval that will be edited -->
    <replacementMolecule><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the replacement sequence used in the edit operation --></replacementMolecule>
    <replacedMolecule><!-- 0..1 Reference(MolecularDefinition) The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit --></replacedMolecule>
   </edit>
  </relative>
 </representation>
</MolecularDefinition>

JSON Template

{
  "resourceType" : "MolecularDefinition",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular resource
  "type" : "<code>", // aa | dna | rna
  "location" : [{ // Location of this molecule
    "sequenceLocation" : { // Location of this molecule in context of a sequence
      "sequenceContext" : { Reference(MolecularDefinition) }, // R!  Reference sequence
      "coordinateInterval" : { // Coordinate Interval for this location
        "numberingSystem" : { CodeableConcept }, // Coordinate System
        // start[x]: Start. One of these 2:
        "startQuantity" : { Quantity },
        "startRange" : { Range },
        // end[x]: End. One of these 2:
        "endQuantity" : { Quantity },
        "endRange" : { Range }
      },
      "strand" : { CodeableConcept } // Forward or Reverse
    },
    "cytobandLocation" : { // Location of this molecule in context of a cytoband
      "genomeAssembly" : { // R!  Reference Genome
        "organism" : { CodeableConcept }, // Species of the organism
        "build" : { CodeableConcept }, // Build number
        "accession" : { CodeableConcept }, // Accession
        // description[x]: Genome assemble description. One of these 2:
        "descriptionMarkdown" : "<markdown>",
        "descriptionString" : "<string>"
      },
      "cytobandInterval" : { // R!  Cytoband Interval
        "chromosome" : { CodeableConcept }, // R!  Chromosome
        "startCytoband" : { // Start
          // arm[x]: Arm. One of these 2:
          "armCode" : "<code>",
          "armString" : "<string>",
          // region[x]: Region. One of these 2:
          "regionCode" : "<code>",
          "regionString" : "<string>",
          // band[x]: Band. One of these 2:
          "bandCode" : "<code>",
          "bandString" : "<string>",
          // subBand[x]: Sub-band. One of these 2:
          "subBandCode" : "<code>",
          "subBandString" : "<string>"
        },
        "endCytoband" : { // End
          // arm[x]: Arm. One of these 2:
          "armCode" : "<code>",
          "armString" : "<string>",
          // region[x]: Region. One of these 2:
          "regionCode" : "<code>",
          "regionString" : "<string>",
          // band[x]: Band. One of these 2:
          "bandCode" : "<code>",
          "bandString" : "<string>",
          // subBand[x]: SuBand. One of these 2:
          "subBandCode" : "<code>",
          "subBandString" : "<string>"
        }
      }
    },
    "featureLocation" : [{ // Location in context of a feature
      "geneId" : [{ CodeableConcept }] // Gene Id
    }]
  }],
  "memberState" : [{ Reference(MolecularDefinition) }], // Member
  "representation" : [{ // Representation
    "focus" : { CodeableConcept }, // The focus of the representation
    "code" : [{ CodeableConcept }], // A code of the representation
    "literal" : { // A literal representation
      "encoding" : { CodeableConcept }, // The encoding used for the expression of the primary sequence
      "value" : "<string>" // R!  The primary (linear) sequence, expressed as a literal string
    },
    "resolvable" : { Attachment }, // A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself
    "extracted" : { // A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
      "start" : <integer>, // R!  The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      "end" : <integer>, // R!  The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      "coordinateSystem" : { CodeableConcept }, // R!  The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
      "reverseComplement" : <boolean> // A flag that indicates whether the extracted sequence should be reverse complemented
    },
    "repeated" : { // A Molecular Sequence that is represented as a repeated sequence motif
      "sequenceMotif" : { Reference(MolecularDefinition) }, // R!  The sequence that defines the repeated motif
      "copyCount" : <integer> // R!  The number of repeats (copies) of the sequence motif
    },
    "concatenated" : { // A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
      "sequenceElement" : [{ // R!  One element of a concatenated Molecular Sequence
        "sequence" : { Reference(MolecularDefinition) }, // R!  The Molecular Sequence corresponding to this element
        "ordinalIndex" : <integer> // R!  The ordinal position of this sequence element within the concatenated Molecular Sequence
      }]
    },
    "relative" : { // A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The Molecular Sequence that serves as the starting sequence, on which edits will be applied
      "edit" : [{ // An edit (change) made to a sequence
        "editOrder" : <integer>, // The order of this edit, relative to other edits on the starting sequence
        "coordinateSystem" : { CodeableConcept }, // R!  The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based 
        "start" : <integer>, // R!  The start coordinate of the interval that will be edited
        "end" : <integer>, // R!  The end coordinate of the interval that will be edited
        "replacementMolecule" : { Reference(MolecularDefinition) }, // R!  The sequence that defines the replacement sequence used in the edit operation
        "replacedMolecule" : { Reference(MolecularDefinition) } // The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
      }]
    }
  }]
}

Turtle Template

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


[ a fhir:MolecularDefinition;
  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 resource
  fhir:type [ code ] ; # 0..1 aa | dna | rna
  fhir:location ( [ # 0..* Location of this molecule
    fhir:sequenceLocation [ # 0..1 Location of this molecule in context of a sequence
      fhir:sequenceContext [ Reference(MolecularDefinition) ] ; # 1..1 Reference sequence
      fhir:coordinateInterval [ # 0..1 Coordinate Interval for this location
        fhir:numberingSystem [ CodeableConcept ] ; # 0..1 Coordinate System
        # start[x] : 0..1 Start. One of these 2
          fhir:start [  a fhir:Quantity ; Quantity ]
          fhir:start [  a fhir:Range ; Range ]
        # end[x] : 0..1 End. One of these 2
          fhir:end [  a fhir:Quantity ; Quantity ]
          fhir:end [  a fhir:Range ; Range ]
      ] ;
      fhir:strand [ CodeableConcept ] ; # 0..1 Forward or Reverse
    ] ;
    fhir:cytobandLocation [ # 0..1 Location of this molecule in context of a cytoband
      fhir:genomeAssembly [ # 1..1 Reference Genome
        fhir:organism [ CodeableConcept ] ; # 0..1 Species of the organism
        fhir:build [ CodeableConcept ] ; # 0..1 Build number
        fhir:accession [ CodeableConcept ] ; # 0..1 Accession
        # description[x] : 0..1 Genome assemble description. One of these 2
          fhir:description [  a fhir:markdown ; markdown ]
          fhir:description [  a fhir:string ; string ]
      ] ;
      fhir:cytobandInterval [ # 1..1 Cytoband Interval
        fhir:chromosome [ CodeableConcept ] ; # 1..1 Chromosome
        fhir:startCytoband [ # 0..1 Start
          # arm[x] : 0..1 Arm. One of these 2
            fhir:arm [  a fhir:code ; code ]
            fhir:arm [  a fhir:string ; string ]
          # region[x] : 0..1 Region. One of these 2
            fhir:region [  a fhir:code ; code ]
            fhir:region [  a fhir:string ; string ]
          # band[x] : 0..1 Band. One of these 2
            fhir:band [  a fhir:code ; code ]
            fhir:band [  a fhir:string ; string ]
          # subBand[x] : 0..1 Sub-band. One of these 2
            fhir:subBand [  a fhir:code ; code ]
            fhir:subBand [  a fhir:string ; string ]
        ] ;
        fhir:endCytoband [ # 0..1 End
          # arm[x] : 0..1 Arm. One of these 2
            fhir:arm [  a fhir:code ; code ]
            fhir:arm [  a fhir:string ; string ]
          # region[x] : 0..1 Region. One of these 2
            fhir:region [  a fhir:code ; code ]
            fhir:region [  a fhir:string ; string ]
          # band[x] : 0..1 Band. One of these 2
            fhir:band [  a fhir:code ; code ]
            fhir:band [  a fhir:string ; string ]
          # subBand[x] : 0..1 SuBand. One of these 2
            fhir:subBand [  a fhir:code ; code ]
            fhir:subBand [  a fhir:string ; string ]
        ] ;
      ] ;
    ] ;
    fhir:featureLocation ( [ # 0..* Location in context of a feature
      fhir:geneId  ( [ CodeableConcept ] ... ) ; # 0..* Gene Id
    ] ... ) ;
  ] ... ) ;
  fhir:memberState  ( [ Reference(MolecularDefinition) ] ... ) ; # 0..* Member
  fhir:representation ( [ # 0..* Representation
    fhir:focus [ CodeableConcept ] ; # 0..1 The focus of the representation
    fhir:code  ( [ CodeableConcept ] ... ) ; # 0..* A code of the representation
    fhir:literal [ # 0..1 A literal representation
      fhir:encoding [ CodeableConcept ] ; # 0..1 The encoding used for the expression of the primary sequence
      fhir:value [ string ] ; # 1..1 The primary (linear) sequence, expressed as a literal string
    ] ;
    fhir:resolvable [ Attachment ] ; # 0..1 A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself
    fhir:extracted [ # 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
      fhir:start [ integer ] ; # 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      fhir:end [ integer ] ; # 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
      fhir:reverseComplement [ boolean ] ; # 0..1 A flag that indicates whether the extracted sequence should be reverse complemented
    ] ;
    fhir:repeated [ # 0..1 A Molecular Sequence that is represented as a repeated sequence motif
      fhir:sequenceMotif [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the repeated motif
      fhir:copyCount [ integer ] ; # 1..1 The number of repeats (copies) of the sequence motif
    ] ;
    fhir:concatenated [ # 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
      fhir:sequenceElement ( [ # 1..* One element of a concatenated Molecular Sequence
        fhir:sequence [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence corresponding to this element
        fhir:ordinalIndex [ integer ] ; # 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence
      ] ... ) ;
    ] ;
    fhir:relative [ # 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the starting sequence, on which edits will be applied
      fhir:edit ( [ # 0..* An edit (change) made to a sequence
        fhir:editOrder [ integer ] ; # 0..1 The order of this edit, relative to other edits on the starting sequence
        fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based
        fhir:start [ integer ] ; # 1..1 The start coordinate of the interval that will be edited
        fhir:end [ integer ] ; # 1..1 The end coordinate of the interval that will be edited
        fhir:replacementMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the replacement sequence used in the edit operation
        fhir:replacedMolecule [ Reference(MolecularDefinition) ] ; # 0..1 The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
      ] ... ) ;
    ] ;
  ] ... ) ;
]

Changes from both R4 and R4B

This resource did not exist in Release R4

See the Full Difference for further information

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

Structure

Name	Flags	Card.	Type	Description & Constraints
MolecularDefinition	TU		DomainResource	Representation of a molecular definition Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
identifier	Σ	0..*	Identifier	Unique ID for this particular resource
type	Σ	0..1	code	aa \| dna \| rna Binding: sequence Type (Required)
location	Σ	0..*	BackboneElement	Location of this molecule
sequenceLocation	Σ	0..1	BackboneElement	Location of this molecule in context of a sequence
sequenceContext	Σ	1..1	Reference(MolecularDefinition)	Reference sequence
coordinateInterval	Σ	0..1	BackboneElement	Coordinate Interval for this location
numberingSystem	Σ	0..1	CodeableConcept	Coordinate System
start[x]	Σ	0..1		Start
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		End
endQuantity			Quantity
endRange			Range
strand		0..1	CodeableConcept	Forward or Reverse
cytobandLocation	Σ	0..1	BackboneElement	Location of this molecule in context of a cytoband
genomeAssembly	Σ	1..1	BackboneElement	Reference Genome
organism		0..1	CodeableConcept	Species of the organism
build		0..1	CodeableConcept	Build number
accession		0..1	CodeableConcept	Accession
description[x]		0..1		Genome assemble description
descriptionMarkdown			markdown
descriptionString			string
cytobandInterval	Σ	1..1	BackboneElement	Cytoband Interval
chromosome	Σ	1..1	CodeableConcept	Chromosome
startCytoband	Σ	0..1	BackboneElement	Start
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
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
featureLocation	Σ	0..*	BackboneElement	Location in context of a feature
geneId	Σ	0..*	CodeableConcept	Gene Id
memberState	Σ	0..*	Reference(MolecularDefinition)	Member
representation	Σ	0..*	BackboneElement	Representation
focus	Σ	0..1	CodeableConcept	The focus of the representation
code	Σ	0..*	CodeableConcept	A code of the representation
literal	Σ	0..1	BackboneElement	A literal representation
encoding	Σ	0..1	CodeableConcept	The encoding used for the expression of the primary sequence
value	Σ	1..1	string	The primary (linear) sequence, expressed as a literal string
resolvable	Σ	0..1	Attachment	A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself
extracted	Σ	0..1	BackboneElement	A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
start	Σ	1..1	integer	The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
end	Σ	1..1	integer	The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
coordinateSystem	Σ	1..1	CodeableConcept	The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
reverseComplement	Σ	0..1	boolean	A flag that indicates whether the extracted sequence should be reverse complemented
repeated	Σ	0..1	BackboneElement	A Molecular Sequence that is represented as a repeated sequence motif
sequenceMotif	Σ	1..1	Reference(MolecularDefinition)	The sequence that defines the repeated motif
copyCount	Σ	1..1	integer	The number of repeats (copies) of the sequence motif
concatenated	Σ	0..1	BackboneElement	A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
sequenceElement	Σ	1..*	BackboneElement	One element of a concatenated Molecular Sequence
sequence	Σ	1..1	Reference(MolecularDefinition)	The Molecular Sequence corresponding to this element
ordinalIndex	Σ	1..1	integer	The ordinal position of this sequence element within the concatenated Molecular Sequence
relative	Σ	0..1	BackboneElement	A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence
startingMolecule	Σ	1..1	Reference(MolecularDefinition)	The Molecular Sequence that serves as the starting sequence, on which edits will be applied
edit	Σ	0..*	BackboneElement	An edit (change) made to a sequence
editOrder		0..1	integer	The order of this edit, relative to other edits on the starting sequence
coordinateSystem	Σ	1..1	CodeableConcept	The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based Binding: LL5323-2 (Extensible)
start	Σ	1..1	integer	The start coordinate of the interval that will be edited
end	Σ	1..1	integer	The end coordinate of the interval that will be edited
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The sequence that defines the replacement sequence used in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
Documentation for this format

See the Extensions for this resource

UML Diagram (Legend)

XML Template

<MolecularDefinition 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 resource --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <location>  <!-- 0..* Location of this molecule -->
  <sequenceLocation>  <!-- 0..1 Location of this molecule in context of a sequence -->
   <sequenceContext><!-- 1..1 Reference(MolecularDefinition) Reference sequence --></sequenceContext>
   <coordinateInterval>  <!-- 0..1 Coordinate Interval for this location -->
    <numberingSystem><!-- 0..1 CodeableConcept Coordinate System --></numberingSystem>
    <start[x]><!-- 0..1 Quantity|Range Start --></start[x]>
    <end[x]><!-- 0..1 Quantity|Range End --></end[x]>
   </coordinateInterval>
   <strand><!-- 0..1 CodeableConcept Forward or Reverse --></strand>
  </sequenceLocation>
  <cytobandLocation>  <!-- 0..1 Location of this molecule in context of a cytoband -->
   <genomeAssembly>  <!-- 1..1 Reference Genome -->
    <organism><!-- 0..1 CodeableConcept Species of the organism --></organism>
    <build><!-- 0..1 CodeableConcept Build number --></build>
    <accession><!-- 0..1 CodeableConcept Accession --></accession>
    <description[x]><!-- 0..1 markdown|string Genome assemble description --></description[x]>
   </genomeAssembly>
   <cytobandInterval>  <!-- 1..1 Cytoband Interval -->
    <chromosome><!-- 1..1 CodeableConcept Chromosome --></chromosome>
    <startCytoband>  <!-- 0..1 Start -->
     <arm[x]><!-- 0..1 code|string Arm --></arm[x]>
     <region[x]><!-- 0..1 code|string Region --></region[x]>
     <band[x]><!-- 0..1 code|string Band --></band[x]>
     <subBand[x]><!-- 0..1 code|string Sub-band --></subBand[x]>
    </startCytoband>
    <endCytoband>  <!-- 0..1 End -->
     <arm[x]><!-- 0..1 code|string Arm --></arm[x]>
     <region[x]><!-- 0..1 code|string Region --></region[x]>
     <band[x]><!-- 0..1 code|string Band --></band[x]>
     <subBand[x]><!-- 0..1 code|string SuBand --></subBand[x]>
    </endCytoband>
   </cytobandInterval>
  </cytobandLocation>
  <featureLocation>  <!-- 0..* Location in context of a feature -->
   <geneId><!-- 0..* CodeableConcept Gene Id --></geneId>
  </featureLocation>
 </location>
 <memberState><!-- 0..* Reference(MolecularDefinition) Member --></memberState>
 <representation>  <!-- 0..* Representation -->
  <focus><!-- 0..1 CodeableConcept The focus of the representation --></focus>
  <code><!-- 0..* CodeableConcept A code of the representation --></code>
  <literal>  <!-- 0..1 A literal representation -->
   <encoding><!-- 0..1 CodeableConcept The encoding used for the expression of the primary sequence --></encoding>
   <value value="[string]"/><!-- 1..1 The primary (linear) sequence, expressed as a literal string -->
  </literal>
  <resolvable><!-- 0..1 Attachment A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself --></resolvable>
  <extracted>  <!-- 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted --></startingMolecule>
   <start value="[integer]"/><!-- 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted -->
   <end value="[integer]"/><!-- 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted -->
   <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based --></coordinateSystem>
   <reverseComplement value="[boolean]"/><!-- 0..1 A flag that indicates whether the extracted sequence should be reverse complemented -->
  </extracted>
  <repeated>  <!-- 0..1 A Molecular Sequence that is represented as a repeated sequence motif -->
   <sequenceMotif><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the repeated motif --></sequenceMotif>
   <copyCount value="[integer]"/><!-- 1..1 The number of repeats (copies) of the sequence motif -->
  </repeated>
  <concatenated>  <!-- 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences -->
   <sequenceElement>  <!-- 1..* One element of a concatenated Molecular Sequence -->
    <sequence><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence corresponding to this element --></sequence>
    <ordinalIndex value="[integer]"/><!-- 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence -->
   </sequenceElement>
  </concatenated>
  <relative>  <!-- 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The Molecular Sequence that serves as the starting sequence, on which edits will be applied --></startingMolecule>
   <edit>  <!-- 0..* An edit (change) made to a sequence -->
    <editOrder value="[integer]"/><!-- 0..1 The order of this edit, relative to other edits on the starting sequence -->
    <coordinateSystem><!-- 1..1 CodeableConcept The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based  --></coordinateSystem>
    <start value="[integer]"/><!-- 1..1 The start coordinate of the interval that will be edited -->
    <end value="[integer]"/><!-- 1..1 The end coordinate of the interval that will be edited -->
    <replacementMolecule><!-- 1..1 Reference(MolecularDefinition) The sequence that defines the replacement sequence used in the edit operation --></replacementMolecule>
    <replacedMolecule><!-- 0..1 Reference(MolecularDefinition) The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit --></replacedMolecule>
   </edit>
  </relative>
 </representation>
</MolecularDefinition>

JSON Template

{
  "resourceType" : "MolecularDefinition",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular resource
  "type" : "<code>", // aa | dna | rna
  "location" : [{ // Location of this molecule
    "sequenceLocation" : { // Location of this molecule in context of a sequence
      "sequenceContext" : { Reference(MolecularDefinition) }, // R!  Reference sequence
      "coordinateInterval" : { // Coordinate Interval for this location
        "numberingSystem" : { CodeableConcept }, // Coordinate System
        // start[x]: Start. One of these 2:
        "startQuantity" : { Quantity },
        "startRange" : { Range },
        // end[x]: End. One of these 2:
        "endQuantity" : { Quantity },
        "endRange" : { Range }
      },
      "strand" : { CodeableConcept } // Forward or Reverse
    },
    "cytobandLocation" : { // Location of this molecule in context of a cytoband
      "genomeAssembly" : { // R!  Reference Genome
        "organism" : { CodeableConcept }, // Species of the organism
        "build" : { CodeableConcept }, // Build number
        "accession" : { CodeableConcept }, // Accession
        // description[x]: Genome assemble description. One of these 2:
        "descriptionMarkdown" : "<markdown>",
        "descriptionString" : "<string>"
      },
      "cytobandInterval" : { // R!  Cytoband Interval
        "chromosome" : { CodeableConcept }, // R!  Chromosome
        "startCytoband" : { // Start
          // arm[x]: Arm. One of these 2:
          "armCode" : "<code>",
          "armString" : "<string>",
          // region[x]: Region. One of these 2:
          "regionCode" : "<code>",
          "regionString" : "<string>",
          // band[x]: Band. One of these 2:
          "bandCode" : "<code>",
          "bandString" : "<string>",
          // subBand[x]: Sub-band. One of these 2:
          "subBandCode" : "<code>",
          "subBandString" : "<string>"
        },
        "endCytoband" : { // End
          // arm[x]: Arm. One of these 2:
          "armCode" : "<code>",
          "armString" : "<string>",
          // region[x]: Region. One of these 2:
          "regionCode" : "<code>",
          "regionString" : "<string>",
          // band[x]: Band. One of these 2:
          "bandCode" : "<code>",
          "bandString" : "<string>",
          // subBand[x]: SuBand. One of these 2:
          "subBandCode" : "<code>",
          "subBandString" : "<string>"
        }
      }
    },
    "featureLocation" : [{ // Location in context of a feature
      "geneId" : [{ CodeableConcept }] // Gene Id
    }]
  }],
  "memberState" : [{ Reference(MolecularDefinition) }], // Member
  "representation" : [{ // Representation
    "focus" : { CodeableConcept }, // The focus of the representation
    "code" : [{ CodeableConcept }], // A code of the representation
    "literal" : { // A literal representation
      "encoding" : { CodeableConcept }, // The encoding used for the expression of the primary sequence
      "value" : "<string>" // R!  The primary (linear) sequence, expressed as a literal string
    },
    "resolvable" : { Attachment }, // A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself
    "extracted" : { // A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
      "start" : <integer>, // R!  The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      "end" : <integer>, // R!  The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      "coordinateSystem" : { CodeableConcept }, // R!  The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
      "reverseComplement" : <boolean> // A flag that indicates whether the extracted sequence should be reverse complemented
    },
    "repeated" : { // A Molecular Sequence that is represented as a repeated sequence motif
      "sequenceMotif" : { Reference(MolecularDefinition) }, // R!  The sequence that defines the repeated motif
      "copyCount" : <integer> // R!  The number of repeats (copies) of the sequence motif
    },
    "concatenated" : { // A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
      "sequenceElement" : [{ // R!  One element of a concatenated Molecular Sequence
        "sequence" : { Reference(MolecularDefinition) }, // R!  The Molecular Sequence corresponding to this element
        "ordinalIndex" : <integer> // R!  The ordinal position of this sequence element within the concatenated Molecular Sequence
      }]
    },
    "relative" : { // A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The Molecular Sequence that serves as the starting sequence, on which edits will be applied
      "edit" : [{ // An edit (change) made to a sequence
        "editOrder" : <integer>, // The order of this edit, relative to other edits on the starting sequence
        "coordinateSystem" : { CodeableConcept }, // R!  The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based 
        "start" : <integer>, // R!  The start coordinate of the interval that will be edited
        "end" : <integer>, // R!  The end coordinate of the interval that will be edited
        "replacementMolecule" : { Reference(MolecularDefinition) }, // R!  The sequence that defines the replacement sequence used in the edit operation
        "replacedMolecule" : { Reference(MolecularDefinition) } // The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
      }]
    }
  }]
}

Turtle Template

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


[ a fhir:MolecularDefinition;
  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 resource
  fhir:type [ code ] ; # 0..1 aa | dna | rna
  fhir:location ( [ # 0..* Location of this molecule
    fhir:sequenceLocation [ # 0..1 Location of this molecule in context of a sequence
      fhir:sequenceContext [ Reference(MolecularDefinition) ] ; # 1..1 Reference sequence
      fhir:coordinateInterval [ # 0..1 Coordinate Interval for this location
        fhir:numberingSystem [ CodeableConcept ] ; # 0..1 Coordinate System
        # start[x] : 0..1 Start. One of these 2
          fhir:start [  a fhir:Quantity ; Quantity ]
          fhir:start [  a fhir:Range ; Range ]
        # end[x] : 0..1 End. One of these 2
          fhir:end [  a fhir:Quantity ; Quantity ]
          fhir:end [  a fhir:Range ; Range ]
      ] ;
      fhir:strand [ CodeableConcept ] ; # 0..1 Forward or Reverse
    ] ;
    fhir:cytobandLocation [ # 0..1 Location of this molecule in context of a cytoband
      fhir:genomeAssembly [ # 1..1 Reference Genome
        fhir:organism [ CodeableConcept ] ; # 0..1 Species of the organism
        fhir:build [ CodeableConcept ] ; # 0..1 Build number
        fhir:accession [ CodeableConcept ] ; # 0..1 Accession
        # description[x] : 0..1 Genome assemble description. One of these 2
          fhir:description [  a fhir:markdown ; markdown ]
          fhir:description [  a fhir:string ; string ]
      ] ;
      fhir:cytobandInterval [ # 1..1 Cytoband Interval
        fhir:chromosome [ CodeableConcept ] ; # 1..1 Chromosome
        fhir:startCytoband [ # 0..1 Start
          # arm[x] : 0..1 Arm. One of these 2
            fhir:arm [  a fhir:code ; code ]
            fhir:arm [  a fhir:string ; string ]
          # region[x] : 0..1 Region. One of these 2
            fhir:region [  a fhir:code ; code ]
            fhir:region [  a fhir:string ; string ]
          # band[x] : 0..1 Band. One of these 2
            fhir:band [  a fhir:code ; code ]
            fhir:band [  a fhir:string ; string ]
          # subBand[x] : 0..1 Sub-band. One of these 2
            fhir:subBand [  a fhir:code ; code ]
            fhir:subBand [  a fhir:string ; string ]
        ] ;
        fhir:endCytoband [ # 0..1 End
          # arm[x] : 0..1 Arm. One of these 2
            fhir:arm [  a fhir:code ; code ]
            fhir:arm [  a fhir:string ; string ]
          # region[x] : 0..1 Region. One of these 2
            fhir:region [  a fhir:code ; code ]
            fhir:region [  a fhir:string ; string ]
          # band[x] : 0..1 Band. One of these 2
            fhir:band [  a fhir:code ; code ]
            fhir:band [  a fhir:string ; string ]
          # subBand[x] : 0..1 SuBand. One of these 2
            fhir:subBand [  a fhir:code ; code ]
            fhir:subBand [  a fhir:string ; string ]
        ] ;
      ] ;
    ] ;
    fhir:featureLocation ( [ # 0..* Location in context of a feature
      fhir:geneId  ( [ CodeableConcept ] ... ) ; # 0..* Gene Id
    ] ... ) ;
  ] ... ) ;
  fhir:memberState  ( [ Reference(MolecularDefinition) ] ... ) ; # 0..* Member
  fhir:representation ( [ # 0..* Representation
    fhir:focus [ CodeableConcept ] ; # 0..1 The focus of the representation
    fhir:code  ( [ CodeableConcept ] ... ) ; # 0..* A code of the representation
    fhir:literal [ # 0..1 A literal representation
      fhir:encoding [ CodeableConcept ] ; # 0..1 The encoding used for the expression of the primary sequence
      fhir:value [ string ] ; # 1..1 The primary (linear) sequence, expressed as a literal string
    ] ;
    fhir:resolvable [ Attachment ] ; # 0..1 A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself
    fhir:extracted [ # 0..1 A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
      fhir:start [ integer ] ; # 1..1 The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      fhir:end [ integer ] ; # 1..1 The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
      fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
      fhir:reverseComplement [ boolean ] ; # 0..1 A flag that indicates whether the extracted sequence should be reverse complemented
    ] ;
    fhir:repeated [ # 0..1 A Molecular Sequence that is represented as a repeated sequence motif
      fhir:sequenceMotif [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the repeated motif
      fhir:copyCount [ integer ] ; # 1..1 The number of repeats (copies) of the sequence motif
    ] ;
    fhir:concatenated [ # 0..1 A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
      fhir:sequenceElement ( [ # 1..* One element of a concatenated Molecular Sequence
        fhir:sequence [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence corresponding to this element
        fhir:ordinalIndex [ integer ] ; # 1..1 The ordinal position of this sequence element within the concatenated Molecular Sequence
      ] ... ) ;
    ] ;
    fhir:relative [ # 0..1 A Molecular Definition that is represented as an ordered series of edits on a specified starting sequence
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The Molecular Sequence that serves as the starting sequence, on which edits will be applied
      fhir:edit ( [ # 0..* An edit (change) made to a sequence
        fhir:editOrder [ integer ] ; # 0..1 The order of this edit, relative to other edits on the starting sequence
        fhir:coordinateSystem [ CodeableConcept ] ; # 1..1 The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based
        fhir:start [ integer ] ; # 1..1 The start coordinate of the interval that will be edited
        fhir:end [ integer ] ; # 1..1 The end coordinate of the interval that will be edited
        fhir:replacementMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The sequence that defines the replacement sequence used in the edit operation
        fhir:replacedMolecule [ Reference(MolecularDefinition) ] ; # 0..1 The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
      ] ... ) ;
    ] ;
  ] ... ) ;
]

Changes from both R4 and R4B

This resource did not exist in Release R4

See the Full Difference for further information

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

Additional definitions: Master Definition XML JSON, XML Schema/Schematron JSON Schema, ShEx (for Turtle) see the extensions, the spreadsheet version & the dependency analysis

10.8.4.1 Terminology Bindings

Path	ValueSet	Type	Documentation
MolecularDefinition.type	SequenceType	Required	Type if a sequence -- DNA, RNA, or amino acid sequence.
MolecularDefinition.representation.relative.edit.coordinateSystem	http://loinc.org/LL5323-2/	Extensible

Path

ValueSet

Type

Documentation

MolecularDefinition.type

SequenceType

Required

Type if a sequence -- DNA, RNA, or amino acid sequence.

MolecularDefinition.representation.relative.edit.coordinateSystem

http://loinc.org/LL5323-2/ icon

Extensible

10.8.5 Notes

10.8.5.1 Representing the Sequence

This resource supports three patterns for representing a sequence of interest:

By providing a literal string of IUPAC codes representing nucleotides or amino acids.
By linking to a formatted file or link containing the sequence information (e.g. FASTA file or GA4GH sequence repository).
By providing a list of edits from a starting sequence.

The MolecularSequence resource is designed to represent a single sequence in an instance. Each sequence might have multiple representations, but implementers SHALL ensure all representations are for the same sequence.

10.8.5.1.1 Sequence as a literal string

literal: This string element can be used to hold the sequence as a string of characters.

10.8.5.1.2 Sequence as a file or URL

formatted: This Attachment is used to refer to the sequence as embedded file content or via a URL reference.

This method can be used to refer to sequence data from in an external source. If the sequence is referring to a GA4GH repository, the formatted.url should refer to a GA4GH compliant endpoint that conforms to GA4GH data models.

10.8.5.1.3 Sequence as a series of edits from a known sequence

relative: This complex element is used for encoding sequence. When the information of starting sequence and edits are provided, the observed sequence will be derived. Here is a picture below:

10.8.5.1.3.1 Composing multiple relative sequences into one new sequence

relative.ordinalPosition: Indicates the order in which the sequence should be considered when putting multiple relative instances together.

relative.sequenceRange: Indicates the nucleotide range in the composed sequence when multiple relative instances are used together.

These attributes help to clarify what sequence is being represented with less computation/inference on the recipient side. Implementers SHOULD use sequenceRange first to determine order as the most reliable. If sequenceRange is not present then ordinalPosition SHOULD be used. Finally, if both sequenceRange and ordinalPosition are absent, then the order of the relative data elements SHOULD be used to calculate a composition. It is the responsibility of the data sender to ensure the message can be consistently understood. Additionally, gaps in sequenceRange are considered intentional (i.e. the composed sequence contains a sequence of N's, the placeholder nucleotide, for the gap range).

10.8.5.1.3.2 Representing the Starting Sequence

relative.startingSequence: There are four optional ways to represent a starting sequence in MolecularSequence resource:

relative.startingSequence.sequenceCodeableConcept: Starting sequence id in public database;
relative.startingSequence.sequenceString: Starting sequence string;
relative.startingSequence.sequenceReference: Reference to starting sequence stored in another sequence entity;
relative.startingSequence.genomeAssembly, relative.startingSequence.chromosome: The combination of genome assembly and chromosome.

The relative.startingSequence.windowStart and relative.startingSequence.windowEnddefines a range from the starting sequence that is used to define a subsequence used as the starting sequence.

10.8.5.1.3.3 Coordinate System

When saving the sequence information, the nucleic acid will be numbered with order. Some representations use a 0-based system (e.g. GA4GH API, BAM files) while some use a 1-based system (e.g. VCF file format). The element coordinateSystem contains this information.

relative.coordinateSystem binds to a LOINC answer list, please review those answers here icon as well as the detailed description found here icon .

10.8.5.1.3.4 Choice of Strand

There are many considerations concerning the directionality of DNA or RNA. Here we are using relative.startingSequence.orientation and relative.startingSequence.strand. Orientation represents the sense of the sequence, which has different meanings depending on the type. Strand represents the sequence writing order. Watson strand refers to 5' to 3' top strand (5' -> 3'), whereas Crick strand refers to 5' to 3' bottom strand (3' <- 5').

Only two possible values can be made by strand, watson and crick. Since the directionality of the sequence string might be represented in different ways in different omics scenario, below are examples of how to map other expressions into its correlated value:

Watson	Crick
5′-to-3′ direction	3′-to-5′ direction
1	-1
Sense	Antisense
Positive	Negative

10.8.5.2 Character usage for sequence as strings

There are attributes where the sequence is represented as a string of characters.

relative.startingSequence.sequenceString
relative.edit.replacementSequence
relative.edit.replacedSequence
literal

The characters used in these string representations of a sequence should be constrained to the IUPAC codes found here https://www.bioinformatics.org/sms2/iupac.html icon .

10.8.6 Search Parameters

Search parameters for this resource. See also the full list of search parameters for this resource, and check the Extensions registry for search parameters on extensions related to this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

Name	Type	Description	Expression	In Common
identifier	token	The unique identity for a particular sequence	MolecularDefinition.identifier
type	token	Amino Acid Sequence/ DNA Sequence / RNA Sequence	MolecularDefinition.type