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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

Definitional content for a molecular entity, such as a nucleotide or protein sequence.

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 MolecularDefinition resource represents molecular entities (e.g., nucleotide or protein sequences) for both clinical and non-clinical use cases, including translational research. The resource is definitional, in that it focuses on discrete, computable, and semantically expressive data structures that reflect the genomic domain. Because the resource focuses on the molecular entities rather than specimen source or annotated knowledge, it supports both patient/participant-specific use cases and population-based data, and both human and non-human data.

The MolecularDefinition resource itself is abstract, but it supports profiles for core molecular concepts, including Sequence (nucleotide and protein), Allele, Variation, Haplotype, and Genotype. Support for additional molecular types, such as structural variation, fusions, and biomarkers, will be considered in the future.

Use cases supported by this resource include but are not limited to:

Structured exchange of simple sequences of DNA, RNA, or amino acids (whole genome/exome sequencing)
Representation of clinically significant alleles that impact drug response (e.g., pharmacogenomic CDS)
Structured representation of simple and complex genetic variations for diagnostic purposes (clinical diagnosis or risk)
Expression of genotypes that have clinical or research significance (clinical decision making)
Representation of genomic variations that are stored within a public knowledge base
Expression of alleles that are used within risk calculators

10.8.1.1 Sequence Representation

Use cases often require expression of the same genomic concept in different ways. Since the concept is the same and only the serialization of it differs, the Molecular Definition resource supports multiple approaches to representing molecular sequences. This allows senders and receivers of messages to choose a sequence representation that is most intuitive for the particular use case.

It is important to note that all representations of a given sequence MUST resolve to the exact same primary sequence. Therefore, if a single instance of MolecularDefinition contains one literal, two resolvable files, and a code, all four of those representations must represent the same sequence. Note that this equivalence does not apply to metadata or annotations that are outside the scope of the Molecular Definition resource, since those data are not definitional to the molecule.

10.8.2 Boundaries and Relationships

The MolecularDefinition resource should be profiled and used to capture representations of molecular concepts such as sequence, allele, haplotype, and genotype.

This resource does not capture workflow (e.g., test ordering/resulting process), the method of obtaining or specifying the molecular content (e.g., the test or assay), or the interpretation of the results (e.g., clinical impact). Those concepts will be captured by profiles of Observation and by the Genomic Study resource. In particular, the Genomics Reporting Implementation Guide contains extensive support for the observation and reporting of clinical genomic results.

10.8.3 References to this Resource

Resource References: itself

Structure

Name	Flags	Card.	Type	Description & Constraints
MolecularDefinition	TU		DomainResource	Definitional content for a molecular entity Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
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	Σ	0..*	CodeableConcept	Classification of the molecule into types other than those defined by moleculeType
topology	Σ	0..*	CodeableConcept	The structural topology of the molecular entity (e.g., linear, circular)
memberState	Σ	0..*	Reference(MolecularDefinition)	Reserved for future profiles (e.g., haplotype, genotype)
location	Σ	0..*	BackboneElement	A defined location on a molecular entity
sequenceLocation	Σ	0..1	BackboneElement	A coordinate-based location on a sequence
sequenceContext	Σ	1..1	Reference(MolecularDefinition)	The sequence on which the location is defined
coordinateInterval	Σ	0..1	BackboneElement	An interval on a sequence
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LL5323-2 (Extensible)
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
strand		0..1	CodeableConcept	The strand at the coordinateInterval
cytobandLocation	Σ	0..1	BackboneElement	A cytoband-based location on a sequence
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 assembly 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..*	string	Reserved and possibly deprecated
representation	Σ	0..*	BackboneElement	A representation of a molecular entity
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
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
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
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LL5323-2 (Extensible)
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
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
sequenceElement	Σ	1..*	BackboneElement	One of the concatenated entities
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
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
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
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LL5323-2 (Extensible)
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the replacement in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The portion of the molecular entity that is replaced by the replacementMolecule
Documentation for this format

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 of an instance --></identifier>
 <description value="[markdown]"/><!-- 0..1 Description of the Molecular Definition instance -->
 <moleculeType><!-- 0..1 CodeableConcept The type of molecule (e.g., DNA, RNA, amino acid) --></moleculeType>
 <type><!-- 0..* CodeableConcept Classification of the molecule into types other than those defined by moleculeType --></type>
 <topology><!-- 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular) --></topology>
 <memberState><!-- 0..* Reference(MolecularDefinition) Reserved for future profiles (e.g., haplotype, genotype) --></memberState>
 <location>  <!-- 0..* A defined location on a molecular entity -->
  <sequenceLocation>  <!-- 0..1 A coordinate-based location on a sequence -->
   <sequenceContext><!-- 1..1 Reference(MolecularDefinition) The sequence on which the location is defined --></sequenceContext>
   <coordinateInterval>  <!-- 0..1 An interval on a sequence -->
    <coordinateSystem>  <!-- 0..1 The coordinate system used to define the location -->
     <system><!-- 0..1 CodeableConcept The type of coordinate system used  --></system>
     <origin><!-- 0..1 CodeableConcept The location of the origin of the coordinate system --></origin>
     <normalizationMethod><!-- 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system --></normalizationMethod>
    </coordinateSystem>
    <start[x]><!-- 0..1 Quantity|Range The start location of the interval --></start[x]>
    <end[x]><!-- 0..1 Quantity|Range The end location of the interval --></end[x]>
   </coordinateInterval>
   <strand><!-- 0..1 CodeableConcept The strand at the coordinateInterval --></strand>
  </sequenceLocation>
  <cytobandLocation>  <!-- 0..1 A cytoband-based location on a sequence -->
   <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 assembly 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 value="[string]"/><!-- 0..* Reserved and possibly deprecated -->
 </location>
 <representation>  <!-- 0..* A representation of a molecular entity -->
  <focus><!-- 0..1 CodeableConcept The domain concept that is the focus of a given instance of the representation --></focus>
  <code><!-- 0..* CodeableConcept A code (e.g., sequence accession number) used to represent a molecular entity --></code>
  <literal>  <!-- 0..1 A molecular entity defined as a string literal -->
   <encoding><!-- 0..1 CodeableConcept The encoding used in the value --></encoding>
   <value value="[string]"/><!-- 1..1 A string literal representation of the molecular entity, using the encoding specified in encoding -->
  </literal>
  <resolvable><!-- 0..1 Reference(DocumentReference) A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) --></resolvable>
  <extracted>  <!-- 0..1 A molecular entity that is represented as a portion of a different entity -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived --></startingMolecule>
   <coordinateInterval>  <!-- 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity -->
    <coordinateSystem>  <!-- 0..1 The coordinate system used to define the location -->
     <system><!-- 0..1 CodeableConcept The type of coordinate system used  --></system>
     <origin><!-- 0..1 CodeableConcept The location of the origin of the coordinate system --></origin>
     <normalizationMethod><!-- 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system --></normalizationMethod>
    </coordinateSystem>
    <start[x]><!-- 0..1 Quantity|Range The start location of the interval --></start[x]>
    <end[x]><!-- 0..1 Quantity|Range The end location of the interval --></end[x]>
   </coordinateInterval>
   <reverseComplement value="[boolean]"/><!-- 0..1 A flag that indicates whether the extracted sequence should be reverse complemented -->
  </extracted>
  <repeated>  <!-- 0..1 A representation as a repeated motif -->
   <sequenceMotif><!-- 1..1 Reference(MolecularDefinition) The motif that is repeated --></sequenceMotif>
   <copyCount value="[integer]"/><!-- 1..1 The number of copies of the motif -->
  </repeated>
  <concatenated>  <!-- 0..1 An ordered concatenation of molecular entities -->
   <sequenceElement>  <!-- 1..* One of the concatenated entities -->
    <sequence><!-- 1..1 Reference(MolecularDefinition) A reference to the sequence that defines this specific concatenated element --></sequence>
    <ordinalIndex value="[integer]"/><!-- 1..1 The ordinal index of the element within the concatenated representation -->
   </sequenceElement>
  </concatenated>
  <relative>  <!-- 0..1 A molecular entity represented as an ordered series of edits on a specified starting entity -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The molecular entity on which edits will be applied --></startingMolecule>
   <edit>  <!-- 0..* A defined edit (change) to be applied -->
    <editOrder value="[integer]"/><!-- 0..1 Defines the order of edits when multiple edits are to be applied to the startingMolecule -->
    <coordinateInterval>  <!-- 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity -->
     <coordinateSystem>  <!-- 0..1 The coordinate system used to define the location -->
      <system><!-- 0..1 CodeableConcept The type of coordinate system used  --></system>
      <origin><!-- 0..1 CodeableConcept The location of the origin of the coordinate system --></origin>
      <normalizationMethod><!-- 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system --></normalizationMethod>
     </coordinateSystem>
     <start[x]><!-- 0..1 Quantity|Range The start location of the interval --></start[x]>
     <end[x]><!-- 0..1 Quantity|Range The end location of the interval --></end[x]>
    </coordinateInterval>
    <replacementMolecule><!-- 1..1 Reference(MolecularDefinition) The molecular entity that serves as the replacement in the edit operation --></replacementMolecule>
    <replacedMolecule><!-- 0..1 Reference(MolecularDefinition) The portion of the molecular entity that is replaced by the replacementMolecule --></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 of an instance
  "description" : "<markdown>", // Description of the Molecular Definition instance
  "moleculeType" : { CodeableConcept }, // The type of molecule (e.g., DNA, RNA, amino acid)
  "type" : [{ CodeableConcept }], // Classification of the molecule into types other than those defined by moleculeType
  "topology" : [{ CodeableConcept }], // The structural topology of the molecular entity (e.g., linear, circular)
  "memberState" : [{ Reference(MolecularDefinition) }], // Reserved for future profiles (e.g., haplotype, genotype)
  "location" : [{ // A defined location on a molecular entity
    "sequenceLocation" : { // A coordinate-based location on a sequence
      "sequenceContext" : { Reference(MolecularDefinition) }, // R!  The sequence on which the location is defined
      "coordinateInterval" : { // An interval on a sequence
        "coordinateSystem" : { // The coordinate system used to define the location
          "system" : { CodeableConcept }, // The type of coordinate system used 
          "origin" : { CodeableConcept }, // The location of the origin of the coordinate system
          "normalizationMethod" : { CodeableConcept } // The normalization method used for determining a location within the coordinate system
        },
        // start[x]: The start location of the interval. One of these 2:
        "startQuantity" : { Quantity },
        "startRange" : { Range },
        // end[x]: The end location of the interval. One of these 2:
        "endQuantity" : { Quantity },
        "endRange" : { Range }
      },
      "strand" : { CodeableConcept } // The strand at the coordinateInterval
    },
    "cytobandLocation" : { // A cytoband-based location on a sequence
      "genomeAssembly" : { // R!  Reference Genome
        "organism" : { CodeableConcept }, // Species of the organism
        "build" : { CodeableConcept }, // Build number
        "accession" : { CodeableConcept }, // Accession
        // description[x]: Genome assembly 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" : ["<string>"] // Reserved and possibly deprecated
  }],
  "representation" : [{ // A representation of a molecular entity
    "focus" : { CodeableConcept }, // The domain concept that is the focus of a given instance of the representation
    "code" : [{ CodeableConcept }], // A code (e.g., sequence accession number) used to represent a molecular entity
    "literal" : { // A molecular entity defined as a string literal
      "encoding" : { CodeableConcept }, // The encoding used in the value
      "value" : "<string>" // R!  A string literal representation of the molecular entity, using the encoding specified in encoding
    },
    "resolvable" : { Reference(DocumentReference) }, // A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
    "extracted" : { // A molecular entity that is represented as a portion of a different entity
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
      "coordinateInterval" : { // The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
        "coordinateSystem" : { // The coordinate system used to define the location
          "system" : { CodeableConcept }, // The type of coordinate system used 
          "origin" : { CodeableConcept }, // The location of the origin of the coordinate system
          "normalizationMethod" : { CodeableConcept } // The normalization method used for determining a location within the coordinate system
        },
        // start[x]: The start location of the interval. One of these 2:
        "startQuantity" : { Quantity },
        "startRange" : { Range },
        // end[x]: The end location of the interval. One of these 2:
        "endQuantity" : { Quantity },
        "endRange" : { Range }
      },
      "reverseComplement" : <boolean> // A flag that indicates whether the extracted sequence should be reverse complemented
    },
    "repeated" : { // A representation as a repeated motif
      "sequenceMotif" : { Reference(MolecularDefinition) }, // R!  The motif that is repeated
      "copyCount" : <integer> // R!  The number of copies of the motif
    },
    "concatenated" : { // An ordered concatenation of molecular entities
      "sequenceElement" : [{ // R!  One of the concatenated entities
        "sequence" : { Reference(MolecularDefinition) }, // R!  A reference to the sequence that defines this specific concatenated element
        "ordinalIndex" : <integer> // R!  The ordinal index of the element within the concatenated representation
      }]
    },
    "relative" : { // A molecular entity represented as an ordered series of edits on a specified starting entity
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The molecular entity on which edits will be applied
      "edit" : [{ // A defined edit (change) to be applied
        "editOrder" : <integer>, // Defines the order of edits when multiple edits are to be applied to the startingMolecule
        "coordinateInterval" : { // The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
          "coordinateSystem" : { // The coordinate system used to define the location
            "system" : { CodeableConcept }, // The type of coordinate system used 
            "origin" : { CodeableConcept }, // The location of the origin of the coordinate system
            "normalizationMethod" : { CodeableConcept } // The normalization method used for determining a location within the coordinate system
          },
          // start[x]: The start location of the interval. One of these 2:
          "startQuantity" : { Quantity },
          "startRange" : { Range },
          // end[x]: The end location of the interval. One of these 2:
          "endQuantity" : { Quantity },
          "endRange" : { Range }
        },
        "replacementMolecule" : { Reference(MolecularDefinition) }, // R!  The molecular entity that serves as the replacement in the edit operation
        "replacedMolecule" : { Reference(MolecularDefinition) } // The portion of the molecular entity that is replaced by the replacementMolecule
      }]
    }
  }]
}

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 of an instance
  fhir:description [ markdown ] ; # 0..1 Description of the Molecular Definition instance
  fhir:moleculeType [ CodeableConcept ] ; # 0..1 The type of molecule (e.g., DNA, RNA, amino acid)
  fhir:type  ( [ CodeableConcept ] ... ) ; # 0..* Classification of the molecule into types other than those defined by moleculeType
  fhir:topology  ( [ CodeableConcept ] ... ) ; # 0..* The structural topology of the molecular entity (e.g., linear, circular)
  fhir:memberState  ( [ Reference(MolecularDefinition) ] ... ) ; # 0..* Reserved for future profiles (e.g., haplotype, genotype)
  fhir:location ( [ # 0..* A defined location on a molecular entity
    fhir:sequenceLocation [ # 0..1 A coordinate-based location on a sequence
      fhir:sequenceContext [ Reference(MolecularDefinition) ] ; # 1..1 The sequence on which the location is defined
      fhir:coordinateInterval [ # 0..1 An interval on a sequence
        fhir:coordinateSystem [ # 0..1 The coordinate system used to define the location
          fhir:system [ CodeableConcept ] ; # 0..1 The type of coordinate system used
          fhir:origin [ CodeableConcept ] ; # 0..1 The location of the origin of the coordinate system
          fhir:normalizationMethod [ CodeableConcept ] ; # 0..1 The normalization method used for determining a location within the coordinate system
        ] ;
        # start[x] : 0..1 The start location of the interval. One of these 2
          fhir:start [  a fhir:Quantity ; Quantity ]
          fhir:start [  a fhir:Range ; Range ]
        # end[x] : 0..1 The end location of the interval. One of these 2
          fhir:end [  a fhir:Quantity ; Quantity ]
          fhir:end [  a fhir:Range ; Range ]
      ] ;
      fhir:strand [ CodeableConcept ] ; # 0..1 The strand at the coordinateInterval
    ] ;
    fhir:cytobandLocation [ # 0..1 A cytoband-based location on a sequence
      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 assembly 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  ( [ string ] ... ) ; # 0..* Reserved and possibly deprecated
  ] ... ) ;
  fhir:representation ( [ # 0..* A representation of a molecular entity
    fhir:focus [ CodeableConcept ] ; # 0..1 The domain concept that is the focus of a given instance of the representation
    fhir:code  ( [ CodeableConcept ] ... ) ; # 0..* A code (e.g., sequence accession number) used to represent a molecular entity
    fhir:literal [ # 0..1 A molecular entity defined as a string literal
      fhir:encoding [ CodeableConcept ] ; # 0..1 The encoding used in the value
      fhir:value [ string ] ; # 1..1 A string literal representation of the molecular entity, using the encoding specified in encoding
    ] ;
    fhir:resolvable [ Reference(DocumentReference) ] ; # 0..1 A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
    fhir:extracted [ # 0..1 A molecular entity that is represented as a portion of a different entity
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
      fhir:coordinateInterval [ # 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
        fhir:coordinateSystem [ # 0..1 The coordinate system used to define the location
          fhir:system [ CodeableConcept ] ; # 0..1 The type of coordinate system used
          fhir:origin [ CodeableConcept ] ; # 0..1 The location of the origin of the coordinate system
          fhir:normalizationMethod [ CodeableConcept ] ; # 0..1 The normalization method used for determining a location within the coordinate system
        ] ;
        # start[x] : 0..1 The start location of the interval. One of these 2
          fhir:start [  a fhir:Quantity ; Quantity ]
          fhir:start [  a fhir:Range ; Range ]
        # end[x] : 0..1 The end location of the interval. One of these 2
          fhir:end [  a fhir:Quantity ; Quantity ]
          fhir:end [  a fhir:Range ; Range ]
      ] ;
      fhir:reverseComplement [ boolean ] ; # 0..1 A flag that indicates whether the extracted sequence should be reverse complemented
    ] ;
    fhir:repeated [ # 0..1 A representation as a repeated motif
      fhir:sequenceMotif [ Reference(MolecularDefinition) ] ; # 1..1 The motif that is repeated
      fhir:copyCount [ integer ] ; # 1..1 The number of copies of the motif
    ] ;
    fhir:concatenated [ # 0..1 An ordered concatenation of molecular entities
      fhir:sequenceElement ( [ # 1..* One of the concatenated entities
        fhir:sequence [ Reference(MolecularDefinition) ] ; # 1..1 A reference to the sequence that defines this specific concatenated element
        fhir:ordinalIndex [ integer ] ; # 1..1 The ordinal index of the element within the concatenated representation
      ] ... ) ;
    ] ;
    fhir:relative [ # 0..1 A molecular entity represented as an ordered series of edits on a specified starting entity
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The molecular entity on which edits will be applied
      fhir:edit ( [ # 0..* A defined edit (change) to be applied
        fhir:editOrder [ integer ] ; # 0..1 Defines the order of edits when multiple edits are to be applied to the startingMolecule
        fhir:coordinateInterval [ # 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
          fhir:coordinateSystem [ # 0..1 The coordinate system used to define the location
            fhir:system [ CodeableConcept ] ; # 0..1 The type of coordinate system used
            fhir:origin [ CodeableConcept ] ; # 0..1 The location of the origin of the coordinate system
            fhir:normalizationMethod [ CodeableConcept ] ; # 0..1 The normalization method used for determining a location within the coordinate system
          ] ;
          # start[x] : 0..1 The start location of the interval. One of these 2
            fhir:start [  a fhir:Quantity ; Quantity ]
            fhir:start [  a fhir:Range ; Range ]
          # end[x] : 0..1 The end location of the interval. One of these 2
            fhir:end [  a fhir:Quantity ; Quantity ]
            fhir:end [  a fhir:Range ; Range ]
        ] ;
        fhir:replacementMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The molecular entity that serves as the replacement in the edit operation
        fhir:replacedMolecule [ Reference(MolecularDefinition) ] ; # 0..1 The portion of the molecular entity that is replaced by the replacementMolecule
      ] ... ) ;
    ] ;
  ] ... ) ;
]

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	Definitional content for a molecular entity Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
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	Σ	0..*	CodeableConcept	Classification of the molecule into types other than those defined by moleculeType
topology	Σ	0..*	CodeableConcept	The structural topology of the molecular entity (e.g., linear, circular)
memberState	Σ	0..*	Reference(MolecularDefinition)	Reserved for future profiles (e.g., haplotype, genotype)
location	Σ	0..*	BackboneElement	A defined location on a molecular entity
sequenceLocation	Σ	0..1	BackboneElement	A coordinate-based location on a sequence
sequenceContext	Σ	1..1	Reference(MolecularDefinition)	The sequence on which the location is defined
coordinateInterval	Σ	0..1	BackboneElement	An interval on a sequence
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LL5323-2 (Extensible)
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
strand		0..1	CodeableConcept	The strand at the coordinateInterval
cytobandLocation	Σ	0..1	BackboneElement	A cytoband-based location on a sequence
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 assembly 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..*	string	Reserved and possibly deprecated
representation	Σ	0..*	BackboneElement	A representation of a molecular entity
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
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
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
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LL5323-2 (Extensible)
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
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
sequenceElement	Σ	1..*	BackboneElement	One of the concatenated entities
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
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
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
coordinateSystem	Σ	0..1	BackboneElement	The coordinate system used to define the location
system	Σ	0..1	CodeableConcept	The type of coordinate system used Binding: LL5323-2 (Extensible)
origin	Σ	0..1	CodeableConcept	The location of the origin of the coordinate system
normalizationMethod	Σ	0..1	CodeableConcept	The normalization method used for determining a location within the coordinate system
start[x]	Σ	0..1		The start location of the interval
startQuantity			Quantity
startRange			Range
end[x]	Σ	0..1		The end location of the interval
endQuantity			Quantity
endRange			Range
replacementMolecule	Σ	1..1	Reference(MolecularDefinition)	The molecular entity that serves as the replacement in the edit operation
replacedMolecule	Σ	0..1	Reference(MolecularDefinition)	The portion of the molecular entity that is replaced by the replacementMolecule
Documentation for this format

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 of an instance --></identifier>
 <description value="[markdown]"/><!-- 0..1 Description of the Molecular Definition instance -->
 <moleculeType><!-- 0..1 CodeableConcept The type of molecule (e.g., DNA, RNA, amino acid) --></moleculeType>
 <type><!-- 0..* CodeableConcept Classification of the molecule into types other than those defined by moleculeType --></type>
 <topology><!-- 0..* CodeableConcept The structural topology of the molecular entity (e.g., linear, circular) --></topology>
 <memberState><!-- 0..* Reference(MolecularDefinition) Reserved for future profiles (e.g., haplotype, genotype) --></memberState>
 <location>  <!-- 0..* A defined location on a molecular entity -->
  <sequenceLocation>  <!-- 0..1 A coordinate-based location on a sequence -->
   <sequenceContext><!-- 1..1 Reference(MolecularDefinition) The sequence on which the location is defined --></sequenceContext>
   <coordinateInterval>  <!-- 0..1 An interval on a sequence -->
    <coordinateSystem>  <!-- 0..1 The coordinate system used to define the location -->
     <system><!-- 0..1 CodeableConcept The type of coordinate system used  --></system>
     <origin><!-- 0..1 CodeableConcept The location of the origin of the coordinate system --></origin>
     <normalizationMethod><!-- 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system --></normalizationMethod>
    </coordinateSystem>
    <start[x]><!-- 0..1 Quantity|Range The start location of the interval --></start[x]>
    <end[x]><!-- 0..1 Quantity|Range The end location of the interval --></end[x]>
   </coordinateInterval>
   <strand><!-- 0..1 CodeableConcept The strand at the coordinateInterval --></strand>
  </sequenceLocation>
  <cytobandLocation>  <!-- 0..1 A cytoband-based location on a sequence -->
   <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 assembly 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 value="[string]"/><!-- 0..* Reserved and possibly deprecated -->
 </location>
 <representation>  <!-- 0..* A representation of a molecular entity -->
  <focus><!-- 0..1 CodeableConcept The domain concept that is the focus of a given instance of the representation --></focus>
  <code><!-- 0..* CodeableConcept A code (e.g., sequence accession number) used to represent a molecular entity --></code>
  <literal>  <!-- 0..1 A molecular entity defined as a string literal -->
   <encoding><!-- 0..1 CodeableConcept The encoding used in the value --></encoding>
   <value value="[string]"/><!-- 1..1 A string literal representation of the molecular entity, using the encoding specified in encoding -->
  </literal>
  <resolvable><!-- 0..1 Reference(DocumentReference) A resolvable representation of a molecular entity (e.g., URI, attached and formatted file) --></resolvable>
  <extracted>  <!-- 0..1 A molecular entity that is represented as a portion of a different entity -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived --></startingMolecule>
   <coordinateInterval>  <!-- 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity -->
    <coordinateSystem>  <!-- 0..1 The coordinate system used to define the location -->
     <system><!-- 0..1 CodeableConcept The type of coordinate system used  --></system>
     <origin><!-- 0..1 CodeableConcept The location of the origin of the coordinate system --></origin>
     <normalizationMethod><!-- 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system --></normalizationMethod>
    </coordinateSystem>
    <start[x]><!-- 0..1 Quantity|Range The start location of the interval --></start[x]>
    <end[x]><!-- 0..1 Quantity|Range The end location of the interval --></end[x]>
   </coordinateInterval>
   <reverseComplement value="[boolean]"/><!-- 0..1 A flag that indicates whether the extracted sequence should be reverse complemented -->
  </extracted>
  <repeated>  <!-- 0..1 A representation as a repeated motif -->
   <sequenceMotif><!-- 1..1 Reference(MolecularDefinition) The motif that is repeated --></sequenceMotif>
   <copyCount value="[integer]"/><!-- 1..1 The number of copies of the motif -->
  </repeated>
  <concatenated>  <!-- 0..1 An ordered concatenation of molecular entities -->
   <sequenceElement>  <!-- 1..* One of the concatenated entities -->
    <sequence><!-- 1..1 Reference(MolecularDefinition) A reference to the sequence that defines this specific concatenated element --></sequence>
    <ordinalIndex value="[integer]"/><!-- 1..1 The ordinal index of the element within the concatenated representation -->
   </sequenceElement>
  </concatenated>
  <relative>  <!-- 0..1 A molecular entity represented as an ordered series of edits on a specified starting entity -->
   <startingMolecule><!-- 1..1 Reference(MolecularDefinition) The molecular entity on which edits will be applied --></startingMolecule>
   <edit>  <!-- 0..* A defined edit (change) to be applied -->
    <editOrder value="[integer]"/><!-- 0..1 Defines the order of edits when multiple edits are to be applied to the startingMolecule -->
    <coordinateInterval>  <!-- 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity -->
     <coordinateSystem>  <!-- 0..1 The coordinate system used to define the location -->
      <system><!-- 0..1 CodeableConcept The type of coordinate system used  --></system>
      <origin><!-- 0..1 CodeableConcept The location of the origin of the coordinate system --></origin>
      <normalizationMethod><!-- 0..1 CodeableConcept The normalization method used for determining a location within the coordinate system --></normalizationMethod>
     </coordinateSystem>
     <start[x]><!-- 0..1 Quantity|Range The start location of the interval --></start[x]>
     <end[x]><!-- 0..1 Quantity|Range The end location of the interval --></end[x]>
    </coordinateInterval>
    <replacementMolecule><!-- 1..1 Reference(MolecularDefinition) The molecular entity that serves as the replacement in the edit operation --></replacementMolecule>
    <replacedMolecule><!-- 0..1 Reference(MolecularDefinition) The portion of the molecular entity that is replaced by the replacementMolecule --></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 of an instance
  "description" : "<markdown>", // Description of the Molecular Definition instance
  "moleculeType" : { CodeableConcept }, // The type of molecule (e.g., DNA, RNA, amino acid)
  "type" : [{ CodeableConcept }], // Classification of the molecule into types other than those defined by moleculeType
  "topology" : [{ CodeableConcept }], // The structural topology of the molecular entity (e.g., linear, circular)
  "memberState" : [{ Reference(MolecularDefinition) }], // Reserved for future profiles (e.g., haplotype, genotype)
  "location" : [{ // A defined location on a molecular entity
    "sequenceLocation" : { // A coordinate-based location on a sequence
      "sequenceContext" : { Reference(MolecularDefinition) }, // R!  The sequence on which the location is defined
      "coordinateInterval" : { // An interval on a sequence
        "coordinateSystem" : { // The coordinate system used to define the location
          "system" : { CodeableConcept }, // The type of coordinate system used 
          "origin" : { CodeableConcept }, // The location of the origin of the coordinate system
          "normalizationMethod" : { CodeableConcept } // The normalization method used for determining a location within the coordinate system
        },
        // start[x]: The start location of the interval. One of these 2:
        "startQuantity" : { Quantity },
        "startRange" : { Range },
        // end[x]: The end location of the interval. One of these 2:
        "endQuantity" : { Quantity },
        "endRange" : { Range }
      },
      "strand" : { CodeableConcept } // The strand at the coordinateInterval
    },
    "cytobandLocation" : { // A cytoband-based location on a sequence
      "genomeAssembly" : { // R!  Reference Genome
        "organism" : { CodeableConcept }, // Species of the organism
        "build" : { CodeableConcept }, // Build number
        "accession" : { CodeableConcept }, // Accession
        // description[x]: Genome assembly 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" : ["<string>"] // Reserved and possibly deprecated
  }],
  "representation" : [{ // A representation of a molecular entity
    "focus" : { CodeableConcept }, // The domain concept that is the focus of a given instance of the representation
    "code" : [{ CodeableConcept }], // A code (e.g., sequence accession number) used to represent a molecular entity
    "literal" : { // A molecular entity defined as a string literal
      "encoding" : { CodeableConcept }, // The encoding used in the value
      "value" : "<string>" // R!  A string literal representation of the molecular entity, using the encoding specified in encoding
    },
    "resolvable" : { Reference(DocumentReference) }, // A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
    "extracted" : { // A molecular entity that is represented as a portion of a different entity
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
      "coordinateInterval" : { // The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
        "coordinateSystem" : { // The coordinate system used to define the location
          "system" : { CodeableConcept }, // The type of coordinate system used 
          "origin" : { CodeableConcept }, // The location of the origin of the coordinate system
          "normalizationMethod" : { CodeableConcept } // The normalization method used for determining a location within the coordinate system
        },
        // start[x]: The start location of the interval. One of these 2:
        "startQuantity" : { Quantity },
        "startRange" : { Range },
        // end[x]: The end location of the interval. One of these 2:
        "endQuantity" : { Quantity },
        "endRange" : { Range }
      },
      "reverseComplement" : <boolean> // A flag that indicates whether the extracted sequence should be reverse complemented
    },
    "repeated" : { // A representation as a repeated motif
      "sequenceMotif" : { Reference(MolecularDefinition) }, // R!  The motif that is repeated
      "copyCount" : <integer> // R!  The number of copies of the motif
    },
    "concatenated" : { // An ordered concatenation of molecular entities
      "sequenceElement" : [{ // R!  One of the concatenated entities
        "sequence" : { Reference(MolecularDefinition) }, // R!  A reference to the sequence that defines this specific concatenated element
        "ordinalIndex" : <integer> // R!  The ordinal index of the element within the concatenated representation
      }]
    },
    "relative" : { // A molecular entity represented as an ordered series of edits on a specified starting entity
      "startingMolecule" : { Reference(MolecularDefinition) }, // R!  The molecular entity on which edits will be applied
      "edit" : [{ // A defined edit (change) to be applied
        "editOrder" : <integer>, // Defines the order of edits when multiple edits are to be applied to the startingMolecule
        "coordinateInterval" : { // The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
          "coordinateSystem" : { // The coordinate system used to define the location
            "system" : { CodeableConcept }, // The type of coordinate system used 
            "origin" : { CodeableConcept }, // The location of the origin of the coordinate system
            "normalizationMethod" : { CodeableConcept } // The normalization method used for determining a location within the coordinate system
          },
          // start[x]: The start location of the interval. One of these 2:
          "startQuantity" : { Quantity },
          "startRange" : { Range },
          // end[x]: The end location of the interval. One of these 2:
          "endQuantity" : { Quantity },
          "endRange" : { Range }
        },
        "replacementMolecule" : { Reference(MolecularDefinition) }, // R!  The molecular entity that serves as the replacement in the edit operation
        "replacedMolecule" : { Reference(MolecularDefinition) } // The portion of the molecular entity that is replaced by the replacementMolecule
      }]
    }
  }]
}

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 of an instance
  fhir:description [ markdown ] ; # 0..1 Description of the Molecular Definition instance
  fhir:moleculeType [ CodeableConcept ] ; # 0..1 The type of molecule (e.g., DNA, RNA, amino acid)
  fhir:type  ( [ CodeableConcept ] ... ) ; # 0..* Classification of the molecule into types other than those defined by moleculeType
  fhir:topology  ( [ CodeableConcept ] ... ) ; # 0..* The structural topology of the molecular entity (e.g., linear, circular)
  fhir:memberState  ( [ Reference(MolecularDefinition) ] ... ) ; # 0..* Reserved for future profiles (e.g., haplotype, genotype)
  fhir:location ( [ # 0..* A defined location on a molecular entity
    fhir:sequenceLocation [ # 0..1 A coordinate-based location on a sequence
      fhir:sequenceContext [ Reference(MolecularDefinition) ] ; # 1..1 The sequence on which the location is defined
      fhir:coordinateInterval [ # 0..1 An interval on a sequence
        fhir:coordinateSystem [ # 0..1 The coordinate system used to define the location
          fhir:system [ CodeableConcept ] ; # 0..1 The type of coordinate system used
          fhir:origin [ CodeableConcept ] ; # 0..1 The location of the origin of the coordinate system
          fhir:normalizationMethod [ CodeableConcept ] ; # 0..1 The normalization method used for determining a location within the coordinate system
        ] ;
        # start[x] : 0..1 The start location of the interval. One of these 2
          fhir:start [  a fhir:Quantity ; Quantity ]
          fhir:start [  a fhir:Range ; Range ]
        # end[x] : 0..1 The end location of the interval. One of these 2
          fhir:end [  a fhir:Quantity ; Quantity ]
          fhir:end [  a fhir:Range ; Range ]
      ] ;
      fhir:strand [ CodeableConcept ] ; # 0..1 The strand at the coordinateInterval
    ] ;
    fhir:cytobandLocation [ # 0..1 A cytoband-based location on a sequence
      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 assembly 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  ( [ string ] ... ) ; # 0..* Reserved and possibly deprecated
  ] ... ) ;
  fhir:representation ( [ # 0..* A representation of a molecular entity
    fhir:focus [ CodeableConcept ] ; # 0..1 The domain concept that is the focus of a given instance of the representation
    fhir:code  ( [ CodeableConcept ] ... ) ; # 0..* A code (e.g., sequence accession number) used to represent a molecular entity
    fhir:literal [ # 0..1 A molecular entity defined as a string literal
      fhir:encoding [ CodeableConcept ] ; # 0..1 The encoding used in the value
      fhir:value [ string ] ; # 1..1 A string literal representation of the molecular entity, using the encoding specified in encoding
    ] ;
    fhir:resolvable [ Reference(DocumentReference) ] ; # 0..1 A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)
    fhir:extracted [ # 0..1 A molecular entity that is represented as a portion of a different entity
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived
      fhir:coordinateInterval [ # 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
        fhir:coordinateSystem [ # 0..1 The coordinate system used to define the location
          fhir:system [ CodeableConcept ] ; # 0..1 The type of coordinate system used
          fhir:origin [ CodeableConcept ] ; # 0..1 The location of the origin of the coordinate system
          fhir:normalizationMethod [ CodeableConcept ] ; # 0..1 The normalization method used for determining a location within the coordinate system
        ] ;
        # start[x] : 0..1 The start location of the interval. One of these 2
          fhir:start [  a fhir:Quantity ; Quantity ]
          fhir:start [  a fhir:Range ; Range ]
        # end[x] : 0..1 The end location of the interval. One of these 2
          fhir:end [  a fhir:Quantity ; Quantity ]
          fhir:end [  a fhir:Range ; Range ]
      ] ;
      fhir:reverseComplement [ boolean ] ; # 0..1 A flag that indicates whether the extracted sequence should be reverse complemented
    ] ;
    fhir:repeated [ # 0..1 A representation as a repeated motif
      fhir:sequenceMotif [ Reference(MolecularDefinition) ] ; # 1..1 The motif that is repeated
      fhir:copyCount [ integer ] ; # 1..1 The number of copies of the motif
    ] ;
    fhir:concatenated [ # 0..1 An ordered concatenation of molecular entities
      fhir:sequenceElement ( [ # 1..* One of the concatenated entities
        fhir:sequence [ Reference(MolecularDefinition) ] ; # 1..1 A reference to the sequence that defines this specific concatenated element
        fhir:ordinalIndex [ integer ] ; # 1..1 The ordinal index of the element within the concatenated representation
      ] ... ) ;
    ] ;
    fhir:relative [ # 0..1 A molecular entity represented as an ordered series of edits on a specified starting entity
      fhir:startingMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The molecular entity on which edits will be applied
      fhir:edit ( [ # 0..* A defined edit (change) to be applied
        fhir:editOrder [ integer ] ; # 0..1 Defines the order of edits when multiple edits are to be applied to the startingMolecule
        fhir:coordinateInterval [ # 0..1 The interval on startingMolecule that defines the portion to be extracted to produce the intended entity
          fhir:coordinateSystem [ # 0..1 The coordinate system used to define the location
            fhir:system [ CodeableConcept ] ; # 0..1 The type of coordinate system used
            fhir:origin [ CodeableConcept ] ; # 0..1 The location of the origin of the coordinate system
            fhir:normalizationMethod [ CodeableConcept ] ; # 0..1 The normalization method used for determining a location within the coordinate system
          ] ;
          # start[x] : 0..1 The start location of the interval. One of these 2
            fhir:start [  a fhir:Quantity ; Quantity ]
            fhir:start [  a fhir:Range ; Range ]
          # end[x] : 0..1 The end location of the interval. One of these 2
            fhir:end [  a fhir:Quantity ; Quantity ]
            fhir:end [  a fhir:Range ; Range ]
        ] ;
        fhir:replacementMolecule [ Reference(MolecularDefinition) ] ; # 1..1 The molecular entity that serves as the replacement in the edit operation
        fhir:replacedMolecule [ Reference(MolecularDefinition) ] ; # 0..1 The portion of the molecular entity that is replaced by the replacementMolecule
      ] ... ) ;
    ] ;
  ] ... ) ;
]

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
MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system	http://loinc.org/vs/LL5323-2	Extensible
MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.system	http://loinc.org/vs/LL5323-2	Extensible
MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.system	http://loinc.org/vs/LL5323-2	Extensible

Path

ValueSet

Type

Documentation

MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system

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

Extensible

MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.system

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

Extensible

MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.system

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

Extensible

10.8.5 Notes

10.8.5.1 Encodings

Molecular sequences are represented using numerous encodings, which are not always explicitly specified. The representation.literal.encoding attribute captures this information directly, so that implementors can validate the content of messages and computationally determine how a particular sequence should be interpreted.

The examples below illustrate different encodings, which could be used to create terms for this attribute. They are based on the IUPAC symbols for nucleotide and amino acid sequences.

10.8.5.1.1 Nucleotide Symbols (1-letter, no ambiguity, DNA residues)

Symbol	Meaning	Origin of designation
G	Guanine	G
A	Adenine	A
T	Thymine	T
C	Cytosine	C

10.8.5.1.2 Nucleotide, 1-letter, no ambiguity, RNA residues

Symbol	Meaning	Origin of designation
G	Guanine	G
A	Adenine	A
U	Uracil	U
C	Cytosine	C

10.8.5.1.3 Nucleotide Symbols (1-letter, no ambiguity except N, DNA residues)

Symbol	Meaning	Origin of designation
G	Guanine	G
A	Adenine	A
T	Thymine	T
C	Cytosine	C
N	G or A or T or C	aNy

10.8.5.1.4 Nucleotide Symbols (1-letter, with ambiguity, DNA residues)

Symbol	Meaning	Origin of designation
G	Guanine	G
A	Adenine	A
T	Thymine	T
C	Cytosine	C
R	G or A	puRine
Y	T or C	pYrimidine
M	A or C	aMino
K	G or T	Keto
S	G or C	Strong interaction (3 H bonds)
W	A or T	Weak interaction (2 H bonds)
H	A or C or T	not-G, H follows G in the alphabet
B	G or T or C	not-A, B follows A
V	G or C or A	not-T (not-U), V follows U
D	G or A or T	not-C, D follows C
N	G or A or T or C	aNy

10.8.5.1.5 Amino Acid Symbols (1-letter, no ambiguity, 20 common)

Symbol	Amino acid
A	alanine
C	cysteine
D	aspartic acid
E	glutamic acid
F	phenylalanine
G	glycine
H	histidine
I	isoleucine
K	lysine
L	leucine
M	methionine
N	asparagine
P	proline
Q	glutamine
R	arginine
S	serine
T	threonine
V	valine
W	tryptophan
Y	tyrosine

10.8.5.1.6 Amino Acid Symbols (3-letter, no ambiguity, 20 common)

Symbol	Amino acid
Ala	alanine
Cys	cysteine
Asp	aspartic acid
Glu	glutamic acid
Phe	phenylalanine
Gly	glycine
His	histidine
Ile	isoleucine
Lys	lysine
Leu	leucine
Met	methionine
Asn	asparagine
Pro	proline
Gln	glutamine
Arg	arginine
Ser	serine
Thr	threonine
Val	valine
Trp	tryptophan
Tyr	tyrosine

10.8.5.1.7 Amino Acid Symbols (1-letter, with ambiguity)

Symbol	Amino acid
A	alanine
B	aspartic acid or asparagine
C	cysteine
D	aspartic acid
E	glutamic acid
F	phenylalanine
G	glycine
H	histidine
I	isoleucine
K	lysine
L	leucine
M	methionine
N	asparagine
P	proline
Q	glutamine
R	arginine
S	serine
T	threonine
U	selenocysteine
V	valine
W	tryptophan
X	unknown or 'other' amino acid
Y	tyrosine
Z	glutamic acid or glutamine

10.8.5.1.8 Amino Acid Symbols (3-letter, with ambiguity)

Symbol	Amino acid
Ala	alanine
Asx	aspartic acid or asparagine
Cys	cysteine
Asp	aspartic acid
Glu	glutamic acid
Phe	phenylalanine
Gly	glycine
His	histidine
Ile	isoleucine
Lys	lysine
Leu	leucine
Met	methionine
Asn	asparagine
Pro	proline
Gln	glutamine
Arg	arginine
Ser	serine
Thr	threonine
Sec	selenocysteine
Val	valine
Trp	tryptophan
Xaa	unknown or 'other' amino acid
Tyr	tyrosine
Glx	glutamic acid or glutamine

10.8.5.2 Molecular Representations

The Molecular Definition resource supports several different methods for representing a molecule. Some of the elements described below may apply only to sequences, and different elements may be added to support other types of molecular concepts.

Native representations: The literal, code, and resolvable are native representations, meaning they represent a sequence “as-is” without any additional computation.

Derived representations: The extracted, concatenated, repeated, and relative representations are derived representations, meaning they require one or more computational operations to be performed to create the sequence that is being represented.

10.8.5.2.1 Literal

The literal element can be used to represent a sequence as a string of characters. By convention, nucleotide sequences are expressed 5’ to 3’ and protein sequences are expressed N to C terminus. The encoding element can optionally be used to specify the encoding used for the sequence literal. The encoding can be important in disambiguating sequences that share alphabets (for example, ATG might represent a translation start codon in DNA, but it could also represent a peptide containing 3 amino acids).

10.8.5.2.2 Code

The code element can be used to represent a sequence by reference, using an accession number that identifies a specific sequence within a repository. The code, system, and version elements of the Coding data type can be used to fully disambiguate one code from another. Note that the code element does not guarantee that the repository is publicly accessible or that the sequence referenced by the code can be retrieved, it only specifies the sequence using a code that could be exchanged. Thus, this element could be used for both a public sequence repository (e.g., GenBank) and a private database (e.g., biobank).

10.8.5.2.3 Resolvable

The resolvable element can be used to represent a sequence by reference, but it also implies that the sequence is accessible and SHOULD be resolvable (although a security layer may be present). This element makes use of the Document Reference resource, which contains the content.attachment element. The Attachment datatype can be used to represent sequences that are captured as a formatted file (using .contentType and .data) or as a URL (using .contentType and .url).

10.8.5.2.4 Extracted

The extracted element can be used to represent a sequence that is derived from another, longer sequence. The startingMolecule element refers to the “parent” sequence, and is itself an instance of Molecular Definition (with its own representation). The coordinateInterval element specifies a precise interval on the “parent” sequence, which is to be extracted (conceptually or literally) and optionally reverse-complemented. This element provides a way to conveniently reference regions of very long molecules (e.g., chromosomes) without requiring either the “parent” or the extracted sequence to be serialized. Conceptually, this representation is the inverse operation of the concatenated representation.

10.8.5.2.5 Concatenated

The concatenated element can be used to represent a sequence that is comprised of other sequences that are concatenated together to form the intended sequence. Each sequenceElement is specified as an instance of Molecular Definition (and each has its own representation). The order of concatenation is explicitly defined using the ordinalIndex element. Conceptually, this representation is the inverse operation of the extracted representation.

10.8.5.2.6 Repeated

The repeated element can be used to represent a sequence that is comprised of a sequence motif that is repeated a specified number of times. The sequenceMotif is an instance of Molecular Definition (and has its own representation), and copyCount specifies the number of times the motif is copied in tandem. Conceptually, this representation is a special case of the concatenated representation, where each element is an identical copy of a given motif.

10.8.5.2.7 Relative

The relative element can be used to represent a sequence in relation to another sequence, where the difference between the two sequences can be expressed as an ordered series of edit operations. This representation can be used to conveniently represent minor but meaningful differences between long or complex sequences (e.g., HLA alleles). Algorithmically, the relative representation defines a sequence by beginning with a startingMolecule (an instance of Molecular Definition) and performing at least one edit operation on it. Each edit operation is performed in order and includes replacing the sequence (the replacedMolecule) at a defined coordinateInterval with the sequence specified by the replacementMolecule. The resulting sequence after all edits have been performed is the sequence referenced by this representation element.

Note that the edits specified in this representation are operations and NOT variations. Variations are defined as a specific comparison between two states (a reference and an alternative), and while they are sometimes called “changes” and therefore they might be confused for edit operations, they are semantically distinct concepts.

10.8.5.3 Combining Representations

Since the derived representations (extracted, concatenated, repeated, and relative) each reference Molecular Definition, representations can be combined to support complex use cases. For example:

An extracted representation can use as its startingMolecule a chromosome sequence that is specified using an accession number (represented as a code).
A repeated representation can define the sequenceMotif using a literal.
A concatenated representation for an assembled contig can include each sequenceElement as an attached, formatted file via resolvable.
A relative representation can specify the startingMolecule using a code, and the replacementMolecule for each edit could be defined using a literal.

It is possible to create arbitrarily deep structures using derived representations, and while there might be rationale for doing so implementations should avoid overly-complex representation structures.

10.8.5.4 Equivalence and Identity

Every representation, regardless of its complexity, can be resolved to a literal. Two instances of MolecularDefinition are considered equivalent if they define the same entity. For molecular sequences, this means that for two instances of MolecularDefinition to be equivalent they must resolve to the same literal sequence. Two instances are identical if their serializations are identical: they must contain the same elements, and each corresponding element must have the same value.

10.8.5.5 Profiling MolecularDefinition

10.8.5.5.0.1 Support for Molecular Concepts

The Molecular Definition resource supports several profiles that represent molecular concepts:

Sequence: a primary sequence
Allele: a Sequence at a Location on a larger, contextual Sequence
Variation: a defined comparison between a specified reference Allele and an alternative Allele, both at a given Location on a larger, contextual Sequence

In addition, profiles have been drafted to represent the concepts of Haplotype and Genotype, although they have not been exercised as deeply as the profiles listed above. Finally, preliminary work has demonstrated that the Molecular Definition resource could be used to represent concepts related to structural variation, including Adjacency and Fusion. It is anticipated that profiles to support these concepts will be developed over time.

10.8.5.5.0.2 Modular Semantics and Schemas

The MolecularDefinition resource is an abstract resource that provides building blocks for creating semantically robust, computable structures that define molecular entities. The two most complex backbone elements, location and representation, support the concept of molecular sequences but they might not be relevant to other types of entities. Conversely, other entities may require different backbone elements. As such, it is expected that these high-level backbone elements will serve as modular schemas that can be profiled as needed for a given molecular entity. Profiling could include constraints on cardinality (e.g., the Sequence profile has 0..0 location, while Allele has 1..1 location) and slicing.

10.8.5.5.0.3 Slicing the Representation Element

The representation backbone element provides a series of methods for specifying the value of a sequence. As a result, the entire structure can be used any time a sequence is referenced, and this is accomplished by slicing. For example, the current sequence-based profiles of MolecularDefinition slice the representation element as follows:

Profile	Cardinality	Focus (slice)	Semantic meaning
Sequence	1..1	Primary Sequence	The primary sequence of the molecule
Allele	1..1	Allele	The sequence of the Allele at the specified Location
Allele	0..1	Context	The sequence of the contextual sequence at the specified Location
Variation	1..1	Reference	The sequence defined as the reference allele (at the specified Location)
Variation	1..1	Alternate	The sequence defined as the alternate allele (at the specified Location)
Variation	0..1	Context	The sequence of the contextual sequence at the specified Location

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
member_state	reference	Reference to the state of the molecular member	MolecularDefinition.memberState (MolecularDefinition)
molecule_type	token	Amino Acid Sequence/ DNA Sequence / RNA Sequence	MolecularDefinition.moleculeType
topology	token	The structural topology of the molecular entity (e.g., linear, circular)	MolecularDefinition.topology
type	token	Classification of the molecule into types other than those defined by moleculeType	MolecularDefinition.type