Release 5 Draft Ballot

This is the Continuous Integration Build of FHIR (will be incorrect/inconsistent at times).
See the Directory of published versions

10.6 Resource MolecularSequence - Content

Clinical Genomics Work GroupMaturity Level: 1 Trial UseSecurity Category: Patient Compartments: Patient

Representation of a molecular sequence.

The MolecularSequence resource is designed for representing molecular sequences. It can represent the sequence in different ways, allowing implementations to adopt the most effective one for their use case.

It is strongly encouraged to provide as much information in this resource for any reported sequences, because receiving systems (e.g. discovery research, outcomes analysis, and public health reporting) may use this information to normalize sequences over time or across sources. However, these data should not be used to dynamically correct/change sequence representations for clinical use outside of the laboratory, due to insufficient information.

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. This means that if a single MolecularSequence instance contains a literal, two formatted files, and a relative, all four of those representions must represent the same 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.

The MolecularSequence resource should only be used to capture a molecular sequence. It will not be used for other entities such as variant, variant annotations, genotypes, haplotypes, etc. Those concepts will be captured in Observation profiles found in the Genomics Reporting Implementation Guide . The sequence that was observed that led to the identification of those concepts can be delivered with this resource, and will be referenced by those observations.

MolecularSequence 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 (Global Alliance for Genomics and Health) API, and may be referenced to by the formatted element.

This resource is referenced by itself and Observation.

This resource does not implement any patterns.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. MolecularSequence TUDomainResourceRepresentation of a molecular sequence
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... identifier Σ0..*IdentifierUnique ID for this particular sequence
... type Σ0..1codeaa | dna | rna
sequenceType (Required)
... patient Σ0..1Reference(Patient)Patient this sequence is associated too
... device Σ0..1Reference(Device)The method for sequencing
... performer Σ0..1Reference(Organization)Who should be responsible for test result
... literal Σ0..1stringSequence that was observed
... formatted Σ0..*AttachmentEmbedded file or a link (URL) which contains content to represent the sequence
... relative Σ0..*BackboneElementA sequence defined relative to another sequence
.... coordinateSystem Σ1..1CodeableConceptWays of identifying nucleotides or amino acids within a sequence
LL5323-2 (Extensible)
.... reference ΣI0..1BackboneElementA sequence used as reference
+ Rule: Both referenceSequenceAssembly and chromosome must be both contained if either one of them is contained
+ Rule: Have and only have one of the following elements in referenceSeq : 1. referenceSequenceAssembly ; 2 referenceSequence
..... referenceSequenceAssembly Σ0..1CodeableConceptThe reference assembly used for reference, e.g. GRCh38
LL1040-6 (Extensible)
..... chromosome Σ0..1CodeableConceptChromosome Identifier
LL2938-0 (Required)
..... referenceSequence[x] Σ0..1The reference sequence that represents the starting sequence
Multiple bindings acceptable (NCBI or LRG) (Example)
...... referenceSequenceCodeableConceptCodeableConcept
...... referenceSequenceStringstring
...... referenceSequenceReferenceReference(MolecularSequence)
..... windowStart Σ0..1integerStart position of the window on the reference sequence
..... windowEnd Σ0..1integerEnd position of the window on the reference sequence
..... orientation Σ0..1codesense | antisense
orientationType (Required)
..... strand Σ0..1codewatson | crick
strandType (Required)
.... edit Σ0..*BackboneElementChanges in sequence from the reference
..... start Σ0..1integerStart position of the edit on the reference sequence
..... end Σ0..1integerEnd position of the edit on the reference sequence
..... observedAllele Σ0..1stringAllele that was observed
..... referenceAllele Σ0..1stringAllele in the reference sequence

doco Documentation for this format

UML Diagram (Legend)

MolecularSequence (DomainResource)A unique identifier for this particular sequence instanceidentifier : Identifier [0..*]Amino Acid Sequence/ DNA Sequence / RNA Sequencetype : code [0..1] « null (Strength=Required)sequenceType! »Indicates the patient this sequence is associated toopatient : Reference [0..1] « Patient »Specimen used for sequencingspecimen : Reference [0..1] « Specimen »The method for sequencing, for example, chip informationdevice : Reference [0..1] « Device »The organization or lab that should be responsible for this resultperformer : Reference [0..1] « Organization »Sequence that was observedliteral : string [0..1]Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external systemformatted : Attachment [0..*]RelativeThese are different ways of identifying nucleotides or amino acids within a sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detailcoordinateSystem : CodeableConcept [1..1] « null (Strength=Extensible)LL5323-2+ »ReferenceThe reference assembly used for reference, e.g. GRCh38referenceSequenceAssembly : CodeableConcept [0..1] « null (Strength=Extensible)LL1040-6+ »Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340))chromosome : CodeableConcept [0..1] « null (Strength=Required)LL2938-0! »The reference sequence that represents the starting sequencereferenceSequence[x] : DataType [0..1] « CodeableConcept|string| Reference(MolecularSequence); null (Strength=Example)Multiple bindings acceptable ...?? »Start position of the window on the reference sequence. This value should honor the rules of the coordinateSystemwindowStart : integer [0..1]End position of the window on the reference sequence. This value should honor the rules of the coordinateSystemwindowEnd : integer [0..1]A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strandorientation : code [0..1] « null (Strength=Required)orientationType! »An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long armstrand : code [0..1] « null (Strength=Required)strandType! »EditStart position of the edit on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusivestart : integer [0..1]End position of the edit on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last positionend : integer [0..1]Allele that was observed. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.endobservedAllele : string [0..1]Allele in the reference sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.endreferenceAllele : string [0..1]A sequence that is used as a reference to describe variants that are present in a sequence analyzedreference[0..1]Changes in sequence from the referenceedit[0..*]A sequence defined relative to another sequencerelative[0..*]

XML Template

<MolecularSequence xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <patient><!-- 0..1 Reference(Patient) Patient this sequence is associated too --></patient>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <literal value="[string]"/><!-- 0..1 Sequence that was observed -->
 <formatted><!-- 0..* Attachment Embedded file or a link (URL) which contains content to represent the sequence --></formatted>
 <relative>  <!-- 0..* A sequence defined relative to another sequence -->
  <coordinateSystem><!-- 1..1 CodeableConcept Ways of identifying nucleotides or amino acids within a sequence  --></coordinateSystem>
  <reference>  <!-- 0..1 A sequence used as reference -->
   <referenceSequenceAssembly><!-- 0..1 CodeableConcept The reference assembly used for reference, e.g. GRCh38  --></referenceSequenceAssembly>
   <chromosome><!-- 0..1 CodeableConcept Chromosome Identifier  --></chromosome>
   <referenceSequence[x]><!-- 0..1 CodeableConcept|string|Reference(
     MolecularSequence) The reference sequence that represents the starting sequence --></referenceSequence[x]>
   <windowStart value="[integer]"/><!-- 0..1 Start position of the window on the  reference sequence -->
   <windowEnd value="[integer]"/><!-- 0..1 End position of the window on the reference sequence -->
   <orientation value="[code]"/><!-- 0..1 sense | antisense -->
   <strand value="[code]"/><!-- 0..1 watson | crick -->
  </reference>
  <edit>  <!-- 0..* Changes in sequence from the reference -->
   <start value="[integer]"/><!-- 0..1 Start position of the edit on the reference sequence -->
   <end value="[integer]"/><!-- 0..1 End position of the edit on the reference sequence -->
   <observedAllele value="[string]"/><!-- 0..1 Allele that was observed -->
   <referenceAllele value="[string]"/><!-- 0..1 Allele in the reference sequence -->
  </edit>
 </relative>
</MolecularSequence>

JSON Template

{doco
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // aa | dna | rna
  "patient" : { Reference(Patient) }, // Patient this sequence is associated too
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "literal" : "<string>", // Sequence that was observed
  "formatted" : [{ Attachment }], // Embedded file or a link (URL) which contains content to represent the sequence
  "relative" : [{ // A sequence defined relative to another sequence
    "coordinateSystem" : { CodeableConcept }, // R!  Ways of identifying nucleotides or amino acids within a sequence 
    "reference" : { // A sequence used as reference
      "referenceSequenceAssembly" : { CodeableConcept }, // The reference assembly used for reference, e.g. GRCh38 
      "chromosome" : { CodeableConcept }, // Chromosome Identifier 
      // referenceSequence[x]: The reference sequence that represents the starting sequence. One of these 3:
      "referenceSequenceCodeableConcept" : { CodeableConcept },
      "referenceSequenceString" : "<string>",
      "referenceSequenceReference" : { Reference(MolecularSequence) },
      "windowStart" : <integer>, // Start position of the window on the  reference sequence
      "windowEnd" : <integer>, // End position of the window on the reference sequence
      "orientation" : "<code>", // sense | antisense
      "strand" : "<code>" // watson | crick
    },
    "edit" : [{ // Changes in sequence from the reference
      "start" : <integer>, // Start position of the edit on the reference sequence
      "end" : <integer>, // End position of the edit on the reference sequence
      "observedAllele" : "<string>", // Allele that was observed
      "referenceAllele" : "<string>" // Allele in the reference sequence
    }]
  }]
}

Turtle Template

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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:MolecularSequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence
  fhir:MolecularSequence.type [ code ]; # 0..1 aa | dna | rna
  fhir:MolecularSequence.patient [ Reference(Patient) ]; # 0..1 Patient this sequence is associated too
  fhir:MolecularSequence.specimen [ Reference(Specimen) ]; # 0..1 Specimen used for sequencing
  fhir:MolecularSequence.device [ Reference(Device) ]; # 0..1 The method for sequencing
  fhir:MolecularSequence.performer [ Reference(Organization) ]; # 0..1 Who should be responsible for test result
  fhir:MolecularSequence.literal [ string ]; # 0..1 Sequence that was observed
  fhir:MolecularSequence.formatted [ Attachment ], ... ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:MolecularSequence.relative [ # 0..* A sequence defined relative to another sequence
    fhir:MolecularSequence.relative.coordinateSystem [ CodeableConcept ]; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:MolecularSequence.relative.reference [ # 0..1 A sequence used as reference
      fhir:MolecularSequence.relative.reference.referenceSequenceAssembly [ CodeableConcept ]; # 0..1 The reference assembly used for reference, e.g. GRCh38
      fhir:MolecularSequence.relative.reference.chromosome [ CodeableConcept ]; # 0..1 Chromosome Identifier
      # MolecularSequence.relative.reference.referenceSequence[x] : 0..1 The reference sequence that represents the starting sequence. One of these 3
        fhir:MolecularSequence.relative.reference.referenceSequenceCodeableConcept [ CodeableConcept ]
        fhir:MolecularSequence.relative.reference.referenceSequenceString [ string ]
        fhir:MolecularSequence.relative.reference.referenceSequenceReference [ Reference(MolecularSequence) ]
      fhir:MolecularSequence.relative.reference.windowStart [ integer ]; # 0..1 Start position of the window on the  reference sequence
      fhir:MolecularSequence.relative.reference.windowEnd [ integer ]; # 0..1 End position of the window on the reference sequence
      fhir:MolecularSequence.relative.reference.orientation [ code ]; # 0..1 sense | antisense
      fhir:MolecularSequence.relative.reference.strand [ code ]; # 0..1 watson | crick
    ];
    fhir:MolecularSequence.relative.edit [ # 0..* Changes in sequence from the reference
      fhir:MolecularSequence.relative.edit.start [ integer ]; # 0..1 Start position of the edit on the reference sequence
      fhir:MolecularSequence.relative.edit.end [ integer ]; # 0..1 End position of the edit on the reference sequence
      fhir:MolecularSequence.relative.edit.observedAllele [ string ]; # 0..1 Allele that was observed
      fhir:MolecularSequence.relative.edit.referenceAllele [ string ]; # 0..1 Allele in the reference sequence
    ], ...;
  ], ...;
]

Changes since R3

MolecularSequence
MolecularSequence.type
  • Change value set from http://hl7.org/fhir/ValueSet/sequence-type|4.0.0 to http://hl7.org/fhir/ValueSet/sequence-type|4.6.0
MolecularSequence.literal
  • Added Element
MolecularSequence.formatted
  • Added Element
MolecularSequence.relative
  • Added Element
MolecularSequence.relative.coordinateSystem
  • Added Mandatory Element
MolecularSequence.relative.reference
  • Added Element
MolecularSequence.relative.reference.referenceSequenceAssembly
  • Added Element
MolecularSequence.relative.reference.chromosome
  • Added Element
MolecularSequence.relative.reference.referenceSequence[x]
  • Added Element
MolecularSequence.relative.reference.windowStart
  • Added Element
MolecularSequence.relative.reference.windowEnd
  • Added Element
MolecularSequence.relative.reference.orientation
  • Added Element
MolecularSequence.relative.reference.strand
  • Added Element
MolecularSequence.relative.edit
  • Added Element
MolecularSequence.relative.edit.start
  • Added Element
MolecularSequence.relative.edit.end
  • Added Element
MolecularSequence.relative.edit.observedAllele
  • Added Element
MolecularSequence.relative.edit.referenceAllele
  • Added Element
MolecularSequence.coordinateSystem
  • deleted
MolecularSequence.quantity
  • deleted
MolecularSequence.referenceSeq
  • deleted
MolecularSequence.variant
  • deleted
MolecularSequence.observedSeq
  • deleted
MolecularSequence.quality
  • deleted
MolecularSequence.readCoverage
  • deleted
MolecularSequence.repository
  • deleted
MolecularSequence.pointer
  • deleted
MolecularSequence.structureVariant
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. MolecularSequence TUDomainResourceRepresentation of a molecular sequence
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... identifier Σ0..*IdentifierUnique ID for this particular sequence
... type Σ0..1codeaa | dna | rna
sequenceType (Required)
... patient Σ0..1Reference(Patient)Patient this sequence is associated too
... device Σ0..1Reference(Device)The method for sequencing
... performer Σ0..1Reference(Organization)Who should be responsible for test result
... literal Σ0..1stringSequence that was observed
... formatted Σ0..*AttachmentEmbedded file or a link (URL) which contains content to represent the sequence
... relative Σ0..*BackboneElementA sequence defined relative to another sequence
.... coordinateSystem Σ1..1CodeableConceptWays of identifying nucleotides or amino acids within a sequence
LL5323-2 (Extensible)
.... reference ΣI0..1BackboneElementA sequence used as reference
+ Rule: Both referenceSequenceAssembly and chromosome must be both contained if either one of them is contained
+ Rule: Have and only have one of the following elements in referenceSeq : 1. referenceSequenceAssembly ; 2 referenceSequence
..... referenceSequenceAssembly Σ0..1CodeableConceptThe reference assembly used for reference, e.g. GRCh38
LL1040-6 (Extensible)
..... chromosome Σ0..1CodeableConceptChromosome Identifier
LL2938-0 (Required)
..... referenceSequence[x] Σ0..1The reference sequence that represents the starting sequence
Multiple bindings acceptable (NCBI or LRG) (Example)
...... referenceSequenceCodeableConceptCodeableConcept
...... referenceSequenceStringstring
...... referenceSequenceReferenceReference(MolecularSequence)
..... windowStart Σ0..1integerStart position of the window on the reference sequence
..... windowEnd Σ0..1integerEnd position of the window on the reference sequence
..... orientation Σ0..1codesense | antisense
orientationType (Required)
..... strand Σ0..1codewatson | crick
strandType (Required)
.... edit Σ0..*BackboneElementChanges in sequence from the reference
..... start Σ0..1integerStart position of the edit on the reference sequence
..... end Σ0..1integerEnd position of the edit on the reference sequence
..... observedAllele Σ0..1stringAllele that was observed
..... referenceAllele Σ0..1stringAllele in the reference sequence

doco Documentation for this format

UML Diagram (Legend)

MolecularSequence (DomainResource)A unique identifier for this particular sequence instanceidentifier : Identifier [0..*]Amino Acid Sequence/ DNA Sequence / RNA Sequencetype : code [0..1] « null (Strength=Required)sequenceType! »Indicates the patient this sequence is associated toopatient : Reference [0..1] « Patient »Specimen used for sequencingspecimen : Reference [0..1] « Specimen »The method for sequencing, for example, chip informationdevice : Reference [0..1] « Device »The organization or lab that should be responsible for this resultperformer : Reference [0..1] « Organization »Sequence that was observedliteral : string [0..1]Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external systemformatted : Attachment [0..*]RelativeThese are different ways of identifying nucleotides or amino acids within a sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detailcoordinateSystem : CodeableConcept [1..1] « null (Strength=Extensible)LL5323-2+ »ReferenceThe reference assembly used for reference, e.g. GRCh38referenceSequenceAssembly : CodeableConcept [0..1] « null (Strength=Extensible)LL1040-6+ »Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340))chromosome : CodeableConcept [0..1] « null (Strength=Required)LL2938-0! »The reference sequence that represents the starting sequencereferenceSequence[x] : DataType [0..1] « CodeableConcept|string| Reference(MolecularSequence); null (Strength=Example)Multiple bindings acceptable ...?? »Start position of the window on the reference sequence. This value should honor the rules of the coordinateSystemwindowStart : integer [0..1]End position of the window on the reference sequence. This value should honor the rules of the coordinateSystemwindowEnd : integer [0..1]A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strandorientation : code [0..1] « null (Strength=Required)orientationType! »An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long armstrand : code [0..1] « null (Strength=Required)strandType! »EditStart position of the edit on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusivestart : integer [0..1]End position of the edit on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last positionend : integer [0..1]Allele that was observed. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.endobservedAllele : string [0..1]Allele in the reference sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.endreferenceAllele : string [0..1]A sequence that is used as a reference to describe variants that are present in a sequence analyzedreference[0..1]Changes in sequence from the referenceedit[0..*]A sequence defined relative to another sequencerelative[0..*]

XML Template

<MolecularSequence xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <patient><!-- 0..1 Reference(Patient) Patient this sequence is associated too --></patient>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <literal value="[string]"/><!-- 0..1 Sequence that was observed -->
 <formatted><!-- 0..* Attachment Embedded file or a link (URL) which contains content to represent the sequence --></formatted>
 <relative>  <!-- 0..* A sequence defined relative to another sequence -->
  <coordinateSystem><!-- 1..1 CodeableConcept Ways of identifying nucleotides or amino acids within a sequence  --></coordinateSystem>
  <reference>  <!-- 0..1 A sequence used as reference -->
   <referenceSequenceAssembly><!-- 0..1 CodeableConcept The reference assembly used for reference, e.g. GRCh38  --></referenceSequenceAssembly>
   <chromosome><!-- 0..1 CodeableConcept Chromosome Identifier  --></chromosome>
   <referenceSequence[x]><!-- 0..1 CodeableConcept|string|Reference(
     MolecularSequence) The reference sequence that represents the starting sequence --></referenceSequence[x]>
   <windowStart value="[integer]"/><!-- 0..1 Start position of the window on the  reference sequence -->
   <windowEnd value="[integer]"/><!-- 0..1 End position of the window on the reference sequence -->
   <orientation value="[code]"/><!-- 0..1 sense | antisense -->
   <strand value="[code]"/><!-- 0..1 watson | crick -->
  </reference>
  <edit>  <!-- 0..* Changes in sequence from the reference -->
   <start value="[integer]"/><!-- 0..1 Start position of the edit on the reference sequence -->
   <end value="[integer]"/><!-- 0..1 End position of the edit on the reference sequence -->
   <observedAllele value="[string]"/><!-- 0..1 Allele that was observed -->
   <referenceAllele value="[string]"/><!-- 0..1 Allele in the reference sequence -->
  </edit>
 </relative>
</MolecularSequence>

JSON Template

{doco
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // aa | dna | rna
  "patient" : { Reference(Patient) }, // Patient this sequence is associated too
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "literal" : "<string>", // Sequence that was observed
  "formatted" : [{ Attachment }], // Embedded file or a link (URL) which contains content to represent the sequence
  "relative" : [{ // A sequence defined relative to another sequence
    "coordinateSystem" : { CodeableConcept }, // R!  Ways of identifying nucleotides or amino acids within a sequence 
    "reference" : { // A sequence used as reference
      "referenceSequenceAssembly" : { CodeableConcept }, // The reference assembly used for reference, e.g. GRCh38 
      "chromosome" : { CodeableConcept }, // Chromosome Identifier 
      // referenceSequence[x]: The reference sequence that represents the starting sequence. One of these 3:
      "referenceSequenceCodeableConcept" : { CodeableConcept },
      "referenceSequenceString" : "<string>",
      "referenceSequenceReference" : { Reference(MolecularSequence) },
      "windowStart" : <integer>, // Start position of the window on the  reference sequence
      "windowEnd" : <integer>, // End position of the window on the reference sequence
      "orientation" : "<code>", // sense | antisense
      "strand" : "<code>" // watson | crick
    },
    "edit" : [{ // Changes in sequence from the reference
      "start" : <integer>, // Start position of the edit on the reference sequence
      "end" : <integer>, // End position of the edit on the reference sequence
      "observedAllele" : "<string>", // Allele that was observed
      "referenceAllele" : "<string>" // Allele in the reference sequence
    }]
  }]
}

Turtle Template

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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:MolecularSequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence
  fhir:MolecularSequence.type [ code ]; # 0..1 aa | dna | rna
  fhir:MolecularSequence.patient [ Reference(Patient) ]; # 0..1 Patient this sequence is associated too
  fhir:MolecularSequence.specimen [ Reference(Specimen) ]; # 0..1 Specimen used for sequencing
  fhir:MolecularSequence.device [ Reference(Device) ]; # 0..1 The method for sequencing
  fhir:MolecularSequence.performer [ Reference(Organization) ]; # 0..1 Who should be responsible for test result
  fhir:MolecularSequence.literal [ string ]; # 0..1 Sequence that was observed
  fhir:MolecularSequence.formatted [ Attachment ], ... ; # 0..* Embedded file or a link (URL) which contains content to represent the sequence
  fhir:MolecularSequence.relative [ # 0..* A sequence defined relative to another sequence
    fhir:MolecularSequence.relative.coordinateSystem [ CodeableConcept ]; # 1..1 Ways of identifying nucleotides or amino acids within a sequence
    fhir:MolecularSequence.relative.reference [ # 0..1 A sequence used as reference
      fhir:MolecularSequence.relative.reference.referenceSequenceAssembly [ CodeableConcept ]; # 0..1 The reference assembly used for reference, e.g. GRCh38
      fhir:MolecularSequence.relative.reference.chromosome [ CodeableConcept ]; # 0..1 Chromosome Identifier
      # MolecularSequence.relative.reference.referenceSequence[x] : 0..1 The reference sequence that represents the starting sequence. One of these 3
        fhir:MolecularSequence.relative.reference.referenceSequenceCodeableConcept [ CodeableConcept ]
        fhir:MolecularSequence.relative.reference.referenceSequenceString [ string ]
        fhir:MolecularSequence.relative.reference.referenceSequenceReference [ Reference(MolecularSequence) ]
      fhir:MolecularSequence.relative.reference.windowStart [ integer ]; # 0..1 Start position of the window on the  reference sequence
      fhir:MolecularSequence.relative.reference.windowEnd [ integer ]; # 0..1 End position of the window on the reference sequence
      fhir:MolecularSequence.relative.reference.orientation [ code ]; # 0..1 sense | antisense
      fhir:MolecularSequence.relative.reference.strand [ code ]; # 0..1 watson | crick
    ];
    fhir:MolecularSequence.relative.edit [ # 0..* Changes in sequence from the reference
      fhir:MolecularSequence.relative.edit.start [ integer ]; # 0..1 Start position of the edit on the reference sequence
      fhir:MolecularSequence.relative.edit.end [ integer ]; # 0..1 End position of the edit on the reference sequence
      fhir:MolecularSequence.relative.edit.observedAllele [ string ]; # 0..1 Allele that was observed
      fhir:MolecularSequence.relative.edit.referenceAllele [ string ]; # 0..1 Allele in the reference sequence
    ], ...;
  ], ...;
]

Changes since Release 3

MolecularSequence
MolecularSequence.type
  • Change value set from http://hl7.org/fhir/ValueSet/sequence-type|4.0.0 to http://hl7.org/fhir/ValueSet/sequence-type|4.6.0
MolecularSequence.literal
  • Added Element
MolecularSequence.formatted
  • Added Element
MolecularSequence.relative
  • Added Element
MolecularSequence.relative.coordinateSystem
  • Added Mandatory Element
MolecularSequence.relative.reference
  • Added Element
MolecularSequence.relative.reference.referenceSequenceAssembly
  • Added Element
MolecularSequence.relative.reference.chromosome
  • Added Element
MolecularSequence.relative.reference.referenceSequence[x]
  • Added Element
MolecularSequence.relative.reference.windowStart
  • Added Element
MolecularSequence.relative.reference.windowEnd
  • Added Element
MolecularSequence.relative.reference.orientation
  • Added Element
MolecularSequence.relative.reference.strand
  • Added Element
MolecularSequence.relative.edit
  • Added Element
MolecularSequence.relative.edit.start
  • Added Element
MolecularSequence.relative.edit.end
  • Added Element
MolecularSequence.relative.edit.observedAllele
  • Added Element
MolecularSequence.relative.edit.referenceAllele
  • Added Element
MolecularSequence.coordinateSystem
  • deleted
MolecularSequence.quantity
  • deleted
MolecularSequence.referenceSeq
  • deleted
MolecularSequence.variant
  • deleted
MolecularSequence.observedSeq
  • deleted
MolecularSequence.quality
  • deleted
MolecularSequence.readCoverage
  • deleted
MolecularSequence.repository
  • deleted
MolecularSequence.pointer
  • deleted
MolecularSequence.structureVariant
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON.

 

See the Profiles & Extensions and the alternate definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions, the spreadsheet version & the dependency analysis a

PathDefinitionTypeReference
MolecularSequence.type RequiredsequenceType
MolecularSequence.relative.coordinateSystem Extensiblehttp://loinc.org/LL5323-2/
MolecularSequence.relative.reference.referenceSequenceAssembly Extensiblehttp://loinc.org/LL1040-6/
MolecularSequence.relative.reference.chromosome Requiredhttp://loinc.org/LL2938-0/
MolecularSequence.relative.reference.referenceSequence[x] Example??
MolecularSequence.relative.reference.orientation RequiredorientationType
MolecularSequence.relative.reference.strand RequiredstrandType

idLevelLocationDescriptionExpression
msq-5Rule MolecularSequence.relative.referenceBoth referenceSequenceAssembly and chromosome must be both contained if either one of them is contained(chromosome.empty() and referenceSequenceAssembly.empty()) or (chromosome.exists() and referenceSequenceAssembly.exists())
msq-6Rule MolecularSequence.relative.referenceHave and only have one of the following elements in referenceSeq : 1. referenceSequenceAssembly ; 2 referenceSequence(referenceSequenceAssembly.count()+referenceSequenceCodeableConcept.count()+ referenceSequenceReference.count()+ referenceSequenceString.count()) = 1

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 reference 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.

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

MolecularSequence.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 an an external source. If the sequence is referring to a GA4GH repository, the MolecularSequence.formatted.url should refer to a GA4GH compliant endpoint that conforms to GA4GH data models.

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

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

  1. MolecularSequence.relative.reference.referenceSequenceCodeableConcept: Reference sequence id in public database;
  2. MolecularSequence.relative.reference.referenceSequenceString: Reference sequence string;
  3. MolecularSequence.relative.reference.referenceSequenceReference: Reference to observed sequence stored in another sequence entity;
  4. MolecularSequence.relative.reference.referenceSequenceAssembly, MolecularSequence.relative.reference.chromosome: The combination of reference assembly and chromosome.

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

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.

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

Here are two examples:

  • 0-based example: here
  • 1-based example: here

There are lots of definition concerning with the directionality of DNA or RNA. Here we are using MolecularSequence.relative.reference.orientation and MolecularSequence.relative.reference.strand. Orientation represents the sense of the sequence, which has different meanings depending on the MolecularSequence.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 word in different omics scenario, below are simple example 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

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

  • relative.reference.referenceSequenceString
  • relative.edit.observedAllele
  • relative.edit.referenceAllele
  • 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 .

Search parameters for this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

NameTypeDescriptionExpressionIn Common
identifiertokenThe unique identity for a particular sequenceMolecularSequence.identifier
patientreferenceThe subject that the sequence is aboutMolecularSequence.patient
(Patient)
typetokenAmino Acid Sequence/ DNA Sequence / RNA SequenceMolecularSequence.type