STU 3 Ballot

This page is part of the FHIR Specification (v1.6.0: STU 3 Ballot 4). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

10.4 Resource Sequence - Content

Clinical Genomics Work GroupMaturity Level: 0Compartments: Not linked to any defined compartments

Raw data describing a biological sequence.

10.4.1 Scope and Usage

The Sequence resource is designed to describe an atomic sequence which contains more than one bases but has at most one variation. Atomic sequences can be connected by link element and they will lead to sequence graph. By this method, a sequence can be reported. Complete genetic sequence information, of which specific genetic variations are a part, is reported by reference to the GA4GH repository. Thus, the FHIR Sequence resource avoids large genomic payloads in a manner analogous to how the FHIR ImagingStudy resource references large images maintained in other systems. This resource contextualizes well established standards from the field of clinical genetics into the standards of healthcare (e.g. HGNC - HUGO Gene Nomenclature Committee's international standard for gene names, symbols, and identifiers).

10.4.1.1 Genetic Standards and Resources include:

This resource is designed to describe a sequence variation with clinical significance with information such as:

  • Name of the variation represented
  • Type of the variation
  • Gene region occupied by the variation
  • Name of the gene
  • Tissue source used to determine genotype of the variation

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

Implementers should be aware that semantic equivalency of results of genetic variants cannot be guaranteed unless there is an agreed upon standard between sending and receiving systems.

10.4.2 Boundaries and Relationships

Focus of the resource is to provide data immediately relevant to clinical decision-making. Hence data such as precise read of DNA sequences and sequence alignment are not included; such data are nonetheless accessible through references to GA4GH (Global Alliance for Genomics and Health) API. The Sequence resource will be referenced by Observation to provide variant information. As clinical assessments/diagnosis of a patient are typically captured in the Condition resource or the ClinicalImpression resource, the Sequence resource can be referenced by the Condition resource to provide specific genetic data to support an assertions. This is analogous to how Condition references other resources, such as AllergyIntolerance, Procedure, and Questionnaire resources.

This resource is referenced by observation

10.4.3 Resource Content

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceInformation about a biological sequence
... identifier Σ0..*IdentifierUnique ID for this particular sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... coordinateSystem Σ1..1integerNumbering used for sequence (0-based or 1-based)
... patient Σ0..1Reference(Patient)Who and/or what this is about
... specimen Σ0..1Reference(Specimen)Specimen used for sequencing
... device Σ0..1Reference(Device)The method for sequencing
... quantity Σ0..1QuantityQuantity of the sequence
... referenceSeq Σ0..1BackboneElementReference sequence
.... chromosome Σ0..1CodeableConceptChromosome containing genetic finding
chromosome-human (Example)
.... genomeBuild Σ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ1..1CodeableConceptReference identifier
ENSEMBL (Example)
.... referenceSeqPointer Σ0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString Σ0..1stringA Reference Sequence string
.... strand Σ1..1integerStrand of DNA
.... windowStart Σ1..1integerStart position (inclusive) of the window on the reference sequence
.... windowEnd Σ1..1integerEnd position (exclusive) of the window on the reference sequence
... variant Σ0..*BackboneElementSequence variant
.... start Σ0..1integerStart position (inclusive) of the variant on the reference sequence
.... end Σ0..1integerEnd position (exclusive) of the variant on the reference sequence
.... observedAllele Σ0..1stringAllele that was observed
.... referenceAllele Σ0..1stringAllele of reference sequence
.... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
.... variantPointer Σ0..1Reference(Observation)Pointer to observed variant information
... observedSeq Σ0..1stringObserved sequence
... quality Σ0..*BackboneElementSequence quality
.... standardSequence Σ0..1CodeableConceptStandard sequence for comparison
.... start Σ0..1integerStart position (inclusive) of the sequence
.... end Σ0..1integerEnd position (exclusive) of the sequence
.... score Σ0..1QuantityQuality score
.... method Σ0..1CodeableConceptMethod for quality
.... truthTP Σ0..1decimalTrue positives from the perspective of the truth data
.... queryTP Σ0..1decimalTrue positives from the perspective of the query data
.... truthFN Σ0..1decimalFalse negatives
.... queryFP Σ0..1decimalFalse positives
.... gtFP Σ0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
.... precision Σ0..1decimalPrecision
.... recall Σ0..1decimalRecall
.... fScore Σ0..1decimalF-score
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... variantId Σ0..1stringId of the variant
.... readId Σ0..1stringId of the read
... pointer Σ0..*Reference(Sequence)Pointer to next atomic sequence
... structureVariant Σ0..*BackboneElement
.... precisionOfBoundaries Σ0..1stringPrecision of boundaries
.... reportedaCGHRatio Σ0..1decimalStructural Variant reported aCGH ratio
.... length Σ0..1integerStructural Variant Length
.... outer Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Outer Start-End
..... end Σ0..1integerStructural Variant Outer Start-End
.... inner Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Inner Start-End
..... end Σ0..1integerStructural Variant Inner Start-End

doco Documentation for this format

UML Diagram (Legend)

Sequence (DomainResource)A unique identifier for this particular sequence instanceidentifier : Identifier [0..*]Amino acid / cDNA transcript / RNA varianttype : code [1..1] « Type if a sequence -- DNA, RNA, or amino acid sequence (Strength=Example)sequenceType?? »Whether the sequence is numbered starting at 0 (0-based numbering or coordinates) or starting at 1 (1-based numbering). Values are "0" for 0-based numbering and "1" for one-basedcoordinateSystem : integer [1..1]The patient whose sequencing results are described by this resourcepatient : Reference [0..1] « Patient »Specimen used for sequencingspecimen : Reference [0..1] « Specimen »The method for sequencing, for example, chip informationdevice : Reference [0..1] « Device »Quantity of the sequencequantity : Quantity [0..1]Sequence that was observedobservedSeq : string [0..1]Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequencereadCoverage : integer [0..1]Pointer to next atomic sequence which at most contains one variantpointer : Reference [0..*] « Sequence »ReferenceSeqStructural 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] « Chromosome number for human (Strength=Example)chromosome-human?? »The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was usedgenomeBuild : string [0..1]Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequencesreferenceSeqId : CodeableConcept [1..1] « Reference identifier (Strength=Example)ENSEMBL?? »A Pointer to another Sequence entity as refence sequencereferenceSeqPointer : Reference [0..1] « Sequence »A Reference Sequence stringreferenceSeqString : string [0..1]Strand of DNA. Available values are "1" for the plus strand and "-1" for the minus strandstrand : integer [1..1]Start position (inclusive) of the window on the reference sequencewindowStart : integer [1..1]End position (exclusive) of the window on the reference sequencewindowEnd : integer [1..1]VariantStart position (inclusive) of the variant on the reference sequencestart : integer [0..1]End position (exclusive) of the variant on the reference sequenceend : integer [0..1]An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 (+) strandobservedAllele : string [0..1]An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 (+) strandreferenceAllele : string [0..1]Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm)cigar : string [0..1]A pointer to an Observation containing variant informationvariantPointer : Reference [0..1] « Observation »QualityGold standard sequence used for comparing againststandardSequence : CodeableConcept [0..1]Start position (inclusive) of the sequencestart : integer [0..1]End position (exclusive) of the sequenceend : integer [0..1]The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685))score : Quantity [0..1]Method for qualitymethod : CodeableConcept [0..1]True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the eventtruthTP : decimal [0..1]True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the eventqueryTP : decimal [0..1]False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted heretruthFN : decimal [0..1]False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted herequeryFP : decimal [0..1]The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar)gtFP : decimal [0..1]QUERY.TP / (QUERY.TP + QUERY.FP)precision : decimal [0..1]TRUTH.TP / (TRUTH.TP + TRUTH.FN)recall : decimal [0..1]Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall)fScore : decimal [0..1]RepositoryURI of an external repository which contains further details about the genetics dataurl : uri [0..1]URI of an external repository which contains further details about the genetics dataname : string [0..1]Id of the variant in this external repositoryvariantId : string [0..1]Id of the read in this external repositoryreadId : string [0..1]StructureVariantPrecision of boundariesprecisionOfBoundaries : string [0..1]Structural Variant reported aCGH ratioreportedaCGHRatio : decimal [0..1]Structural Variant Lengthlength : integer [0..1]OuterStructural Variant Outer Start-Endstart : integer [0..1]Structural Variant Outer Start-Endend : integer [0..1]InnerStructural Variant Inner Start-Endstart : integer [0..1]Structural Variant Inner Start-Endend : integer [0..1]A reference sequence is a sequence that is used to represent an allele or variantreferenceSeq[0..1]A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of))variant[0..*]An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686))quality[0..*]Configurations of the external repositoryrepository[0..*]Structural variant outerouter[0..1]Structural variant innerinner[0..1]Structural variantstructureVariant[0..*]

XML Template

<Sequence 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]"/><!-- 1..1 AA | DNA | RNA -->
 <coordinateSystem value="[integer]"/><!-- 1..1 Numbering used for sequence (0-based or 1-based) -->
 <patient><!-- 0..1 Reference(Patient) Who and/or what this is about --></patient>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <quantity><!-- 0..1 Quantity Quantity of the sequence --></quantity>
 <referenceSeq>  <!-- 0..1 Reference sequence -->
  <chromosome><!-- 0..1 CodeableConcept Chromosome containing genetic finding --></chromosome>
  <genomeBuild value="[string]"/><!-- 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' -->
  <referenceSeqId><!-- 1..1 CodeableConcept Reference identifier --></referenceSeqId>
  <referenceSeqPointer><!-- 0..1 Reference(Sequence) A Pointer to another Sequence entity as refence sequence --></referenceSeqPointer>
  <referenceSeqString value="[string]"/><!-- 0..1 A Reference Sequence string -->
  <strand value="[integer]"/><!-- 1..1 Strand of DNA -->
  <windowStart value="[integer]"/><!-- 1..1 Start position (inclusive) of the window on the  reference sequence -->
  <windowEnd value="[integer]"/><!-- 1..1 End position (exclusive) of the window on the reference sequence -->
 </referenceSeq>
 <variant>  <!-- 0..* Sequence variant -->
  <start value="[integer]"/><!-- 0..1 Start position (inclusive) of the variant on the  reference sequence -->
  <end value="[integer]"/><!-- 0..1 End position (exclusive) of the variant on the reference sequence -->
  <observedAllele value="[string]"/><!-- 0..1 Allele that was observed -->
  <referenceAllele value="[string]"/><!-- 0..1 Allele of reference sequence -->
  <cigar value="[string]"/><!-- 0..1 Extended CIGAR string for aligning the sequence with reference bases -->
  <variantPointer><!-- 0..1 Reference(Observation) Pointer to observed variant information --></variantPointer>
 </variant>
 <observedSeq value="[string]"/><!-- 0..1 Observed sequence -->
 <quality>  <!-- 0..* Sequence quality -->
  <standardSequence><!-- 0..1 CodeableConcept Standard sequence for comparison --></standardSequence>
  <start value="[integer]"/><!-- 0..1 Start position (inclusive) of the sequence -->
  <end value="[integer]"/><!-- 0..1 End position (exclusive) of the sequence -->
  <score><!-- 0..1 Quantity Quality score --></score>
  <method><!-- 0..1 CodeableConcept Method for quality --></method>
  <truthTP value="[decimal]"/><!-- 0..1 True positives from the perspective of the truth data -->
  <queryTP value="[decimal]"/><!-- 0..1 True positives from the perspective of the query data -->
  <truthFN value="[decimal]"/><!-- 0..1 False negatives -->
  <queryFP value="[decimal]"/><!-- 0..1 False positives -->
  <gtFP value="[decimal]"/><!-- 0..1 False positives where the non-REF alleles in the Truth and Query Call Sets match -->
  <precision value="[decimal]"/><!-- 0..1 Precision -->
  <recall value="[decimal]"/><!-- 0..1 Recall -->
  <fScore value="[decimal]"/><!-- 0..1 F-score -->
 </quality>
 <readCoverage value="[integer]"/><!-- 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence -->
 <repository>  <!-- 0..* External repository -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Name of the repository -->
  <variantId value="[string]"/><!-- 0..1 Id of the variant -->
  <readId value="[string]"/><!-- 0..1 Id of the read -->
 </repository>
 <pointer><!-- 0..* Reference(Sequence) Pointer to next atomic sequence --></pointer>
 <structureVariant>  <!-- 0..* -->
  <precisionOfBoundaries value="[string]"/><!-- 0..1 Precision of boundaries -->
  <reportedaCGHRatio value="[decimal]"/><!-- 0..1 Structural Variant reported aCGH ratio -->
  <length value="[integer]"/><!-- 0..1 Structural Variant Length -->
  <outer> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
  </outer>
  <inner> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
  </inner>
 </structureVariant>
</Sequence>

JSON Template

{doco
  "resourceType" : "Sequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // R!  AA | DNA | RNA
  "coordinateSystem" : <integer>, // R!  Numbering used for sequence (0-based or 1-based)
  "patient" : { Reference(Patient) }, // Who and/or what this is about
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "quantity" : { Quantity }, // Quantity of the sequence
  "referenceSeq" : { // Reference sequence
    "chromosome" : { CodeableConcept }, // Chromosome containing genetic finding
    "genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    "referenceSeqId" : { CodeableConcept }, // R!  Reference identifier
    "referenceSeqPointer" : { Reference(Sequence) }, // A Pointer to another Sequence entity as refence sequence
    "referenceSeqString" : "<string>", // A Reference Sequence string
    "strand" : <integer>, // R!  Strand of DNA
    "windowStart" : <integer>, // R!  Start position (inclusive) of the window on the  reference sequence
    "windowEnd" : <integer> // R!  End position (exclusive) of the window on the reference sequence
  },
  "variant" : [{ // Sequence variant
    "start" : <integer>, // Start position (inclusive) of the variant on the  reference sequence
    "end" : <integer>, // End position (exclusive) of the variant on the reference sequence
    "observedAllele" : "<string>", // Allele that was observed
    "referenceAllele" : "<string>", // Allele of reference sequence
    "cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
    "variantPointer" : { Reference(Observation) } // Pointer to observed variant information
  }],
  "observedSeq" : "<string>", // Observed sequence
  "quality" : [{ // Sequence quality
    "standardSequence" : { CodeableConcept }, // Standard sequence for comparison
    "start" : <integer>, // Start position (inclusive) of the sequence
    "end" : <integer>, // End position (exclusive) of the sequence
    "score" : { Quantity }, // Quality score
    "method" : { CodeableConcept }, // Method for quality
    "truthTP" : <decimal>, // True positives from the perspective of the truth data
    "queryTP" : <decimal>, // True positives from the perspective of the query data
    "truthFN" : <decimal>, // False negatives
    "queryFP" : <decimal>, // False positives
    "gtFP" : <decimal>, // False positives where the non-REF alleles in the Truth and Query Call Sets match
    "precision" : <decimal>, // Precision
    "recall" : <decimal>, // Recall
    "fScore" : <decimal> // F-score
  }],
  "readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
  "repository" : [{ // External repository
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Name of the repository
    "variantId" : "<string>", // Id of the variant
    "readId" : "<string>" // Id of the read
  }],
  "pointer" : [{ Reference(Sequence) }], // Pointer to next atomic sequence
  "structureVariant" : [{ // 
    "precisionOfBoundaries" : "<string>", // Precision of boundaries
    "reportedaCGHRatio" : <decimal>, // Structural Variant reported aCGH ratio
    "length" : <integer>, // Structural Variant Length
    "outer" : { // 
      "start" : <integer>, // Structural Variant Outer Start-End
      "end" : <integer> // Structural Variant Outer Start-End
    },
    "inner" : { // 
      "start" : <integer>, // Structural Variant Inner Start-End
      "end" : <integer> // Structural Variant Inner Start-End
    }
  }]
}

Turtle Template

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


[ a fhir:Sequence;
  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:Sequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence
  fhir:Sequence.type [ code ]; # 1..1 AA | DNA | RNA
  fhir:Sequence.coordinateSystem [ integer ]; # 1..1 Numbering used for sequence (0-based or 1-based)
  fhir:Sequence.patient [ Reference(Patient) ]; # 0..1 Who and/or what this is about
  fhir:Sequence.specimen [ Reference(Specimen) ]; # 0..1 Specimen used for sequencing
  fhir:Sequence.device [ Reference(Device) ]; # 0..1 The method for sequencing
  fhir:Sequence.quantity [ Quantity ]; # 0..1 Quantity of the sequence
  fhir:Sequence.referenceSeq [ # 0..1 Reference sequence
    fhir:Sequence.referenceSeq.chromosome [ CodeableConcept ]; # 0..1 Chromosome containing genetic finding
    fhir:Sequence.referenceSeq.genomeBuild [ string ]; # 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    fhir:Sequence.referenceSeq.referenceSeqId [ CodeableConcept ]; # 1..1 Reference identifier
    fhir:Sequence.referenceSeq.referenceSeqPointer [ Reference(Sequence) ]; # 0..1 A Pointer to another Sequence entity as refence sequence
    fhir:Sequence.referenceSeq.referenceSeqString [ string ]; # 0..1 A Reference Sequence string
    fhir:Sequence.referenceSeq.strand [ integer ]; # 1..1 Strand of DNA
    fhir:Sequence.referenceSeq.windowStart [ integer ]; # 1..1 Start position (inclusive) of the window on the  reference sequence
    fhir:Sequence.referenceSeq.windowEnd [ integer ]; # 1..1 End position (exclusive) of the window on the reference sequence
  ];
  fhir:Sequence.variant [ # 0..* Sequence variant
    fhir:Sequence.variant.start [ integer ]; # 0..1 Start position (inclusive) of the variant on the  reference sequence
    fhir:Sequence.variant.end [ integer ]; # 0..1 End position (exclusive) of the variant on the reference sequence
    fhir:Sequence.variant.observedAllele [ string ]; # 0..1 Allele that was observed
    fhir:Sequence.variant.referenceAllele [ string ]; # 0..1 Allele of reference sequence
    fhir:Sequence.variant.cigar [ string ]; # 0..1 Extended CIGAR string for aligning the sequence with reference bases
    fhir:Sequence.variant.variantPointer [ Reference(Observation) ]; # 0..1 Pointer to observed variant information
  ], ...;
  fhir:Sequence.observedSeq [ string ]; # 0..1 Observed sequence
  fhir:Sequence.quality [ # 0..* Sequence quality
    fhir:Sequence.quality.standardSequence [ CodeableConcept ]; # 0..1 Standard sequence for comparison
    fhir:Sequence.quality.start [ integer ]; # 0..1 Start position (inclusive) of the sequence
    fhir:Sequence.quality.end [ integer ]; # 0..1 End position (exclusive) of the sequence
    fhir:Sequence.quality.score [ Quantity ]; # 0..1 Quality score
    fhir:Sequence.quality.method [ CodeableConcept ]; # 0..1 Method for quality
    fhir:Sequence.quality.truthTP [ decimal ]; # 0..1 True positives from the perspective of the truth data
    fhir:Sequence.quality.queryTP [ decimal ]; # 0..1 True positives from the perspective of the query data
    fhir:Sequence.quality.truthFN [ decimal ]; # 0..1 False negatives
    fhir:Sequence.quality.queryFP [ decimal ]; # 0..1 False positives
    fhir:Sequence.quality.gtFP [ decimal ]; # 0..1 False positives where the non-REF alleles in the Truth and Query Call Sets match
    fhir:Sequence.quality.precision [ decimal ]; # 0..1 Precision
    fhir:Sequence.quality.recall [ decimal ]; # 0..1 Recall
    fhir:Sequence.quality.fScore [ decimal ]; # 0..1 F-score
  ], ...;
  fhir:Sequence.readCoverage [ integer ]; # 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence
  fhir:Sequence.repository [ # 0..* External repository
    fhir:Sequence.repository.url [ uri ]; # 0..1 URI of the repository
    fhir:Sequence.repository.name [ string ]; # 0..1 Name of the repository
    fhir:Sequence.repository.variantId [ string ]; # 0..1 Id of the variant
    fhir:Sequence.repository.readId [ string ]; # 0..1 Id of the read
  ], ...;
  fhir:Sequence.pointer [ Reference(Sequence) ], ... ; # 0..* Pointer to next atomic sequence
  fhir:Sequence.structureVariant [ # 0..* 
    fhir:Sequence.structureVariant.precisionOfBoundaries [ string ]; # 0..1 Precision of boundaries
    fhir:Sequence.structureVariant.reportedaCGHRatio [ decimal ]; # 0..1 Structural Variant reported aCGH ratio
    fhir:Sequence.structureVariant.length [ integer ]; # 0..1 Structural Variant Length
    fhir:Sequence.structureVariant.outer [ # 0..1 
      fhir:Sequence.structureVariant.outer.start [ integer ]; # 0..1 Structural Variant Outer Start-End
      fhir:Sequence.structureVariant.outer.end [ integer ]; # 0..1 Structural Variant Outer Start-End
    ];
    fhir:Sequence.structureVariant.inner [ # 0..1 
      fhir:Sequence.structureVariant.inner.start [ integer ]; # 0..1 Structural Variant Inner Start-End
      fhir:Sequence.structureVariant.inner.end [ integer ]; # 0..1 Structural Variant Inner Start-End
    ];
  ], ...;
]

Changes since DSTU2

This resource did not exist in Release 2

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣDomainResourceInformation about a biological sequence
... identifier Σ0..*IdentifierUnique ID for this particular sequence
... type Σ1..1codeAA | DNA | RNA
sequenceType (Example)
... coordinateSystem Σ1..1integerNumbering used for sequence (0-based or 1-based)
... patient Σ0..1Reference(Patient)Who and/or what this is about
... specimen Σ0..1Reference(Specimen)Specimen used for sequencing
... device Σ0..1Reference(Device)The method for sequencing
... quantity Σ0..1QuantityQuantity of the sequence
... referenceSeq Σ0..1BackboneElementReference sequence
.... chromosome Σ0..1CodeableConceptChromosome containing genetic finding
chromosome-human (Example)
.... genomeBuild Σ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ1..1CodeableConceptReference identifier
ENSEMBL (Example)
.... referenceSeqPointer Σ0..1Reference(Sequence)A Pointer to another Sequence entity as refence sequence
.... referenceSeqString Σ0..1stringA Reference Sequence string
.... strand Σ1..1integerStrand of DNA
.... windowStart Σ1..1integerStart position (inclusive) of the window on the reference sequence
.... windowEnd Σ1..1integerEnd position (exclusive) of the window on the reference sequence
... variant Σ0..*BackboneElementSequence variant
.... start Σ0..1integerStart position (inclusive) of the variant on the reference sequence
.... end Σ0..1integerEnd position (exclusive) of the variant on the reference sequence
.... observedAllele Σ0..1stringAllele that was observed
.... referenceAllele Σ0..1stringAllele of reference sequence
.... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
.... variantPointer Σ0..1Reference(Observation)Pointer to observed variant information
... observedSeq Σ0..1stringObserved sequence
... quality Σ0..*BackboneElementSequence quality
.... standardSequence Σ0..1CodeableConceptStandard sequence for comparison
.... start Σ0..1integerStart position (inclusive) of the sequence
.... end Σ0..1integerEnd position (exclusive) of the sequence
.... score Σ0..1QuantityQuality score
.... method Σ0..1CodeableConceptMethod for quality
.... truthTP Σ0..1decimalTrue positives from the perspective of the truth data
.... queryTP Σ0..1decimalTrue positives from the perspective of the query data
.... truthFN Σ0..1decimalFalse negatives
.... queryFP Σ0..1decimalFalse positives
.... gtFP Σ0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
.... precision Σ0..1decimalPrecision
.... recall Σ0..1decimalRecall
.... fScore Σ0..1decimalF-score
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository Σ0..*BackboneElementExternal repository
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... variantId Σ0..1stringId of the variant
.... readId Σ0..1stringId of the read
... pointer Σ0..*Reference(Sequence)Pointer to next atomic sequence
... structureVariant Σ0..*BackboneElement
.... precisionOfBoundaries Σ0..1stringPrecision of boundaries
.... reportedaCGHRatio Σ0..1decimalStructural Variant reported aCGH ratio
.... length Σ0..1integerStructural Variant Length
.... outer Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Outer Start-End
..... end Σ0..1integerStructural Variant Outer Start-End
.... inner Σ0..1BackboneElement
..... start Σ0..1integerStructural Variant Inner Start-End
..... end Σ0..1integerStructural Variant Inner Start-End

doco Documentation for this format

UML Diagram (Legend)

Sequence (DomainResource)A unique identifier for this particular sequence instanceidentifier : Identifier [0..*]Amino acid / cDNA transcript / RNA varianttype : code [1..1] « Type if a sequence -- DNA, RNA, or amino acid sequence (Strength=Example)sequenceType?? »Whether the sequence is numbered starting at 0 (0-based numbering or coordinates) or starting at 1 (1-based numbering). Values are "0" for 0-based numbering and "1" for one-basedcoordinateSystem : integer [1..1]The patient whose sequencing results are described by this resourcepatient : Reference [0..1] « Patient »Specimen used for sequencingspecimen : Reference [0..1] « Specimen »The method for sequencing, for example, chip informationdevice : Reference [0..1] « Device »Quantity of the sequencequantity : Quantity [0..1]Sequence that was observedobservedSeq : string [0..1]Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequencereadCoverage : integer [0..1]Pointer to next atomic sequence which at most contains one variantpointer : Reference [0..*] « Sequence »ReferenceSeqStructural 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] « Chromosome number for human (Strength=Example)chromosome-human?? »The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was usedgenomeBuild : string [0..1]Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequencesreferenceSeqId : CodeableConcept [1..1] « Reference identifier (Strength=Example)ENSEMBL?? »A Pointer to another Sequence entity as refence sequencereferenceSeqPointer : Reference [0..1] « Sequence »A Reference Sequence stringreferenceSeqString : string [0..1]Strand of DNA. Available values are "1" for the plus strand and "-1" for the minus strandstrand : integer [1..1]Start position (inclusive) of the window on the reference sequencewindowStart : integer [1..1]End position (exclusive) of the window on the reference sequencewindowEnd : integer [1..1]VariantStart position (inclusive) of the variant on the reference sequencestart : integer [0..1]End position (exclusive) of the variant on the reference sequenceend : integer [0..1]An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 (+) strandobservedAllele : string [0..1]An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). 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 (+) strandreferenceAllele : string [0..1]Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm)cigar : string [0..1]A pointer to an Observation containing variant informationvariantPointer : Reference [0..1] « Observation »QualityGold standard sequence used for comparing againststandardSequence : CodeableConcept [0..1]Start position (inclusive) of the sequencestart : integer [0..1]End position (exclusive) of the sequenceend : integer [0..1]The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685))score : Quantity [0..1]Method for qualitymethod : CodeableConcept [0..1]True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the eventtruthTP : decimal [0..1]True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the eventqueryTP : decimal [0..1]False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted heretruthFN : decimal [0..1]False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted herequeryFP : decimal [0..1]The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar)gtFP : decimal [0..1]QUERY.TP / (QUERY.TP + QUERY.FP)precision : decimal [0..1]TRUTH.TP / (TRUTH.TP + TRUTH.FN)recall : decimal [0..1]Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall)fScore : decimal [0..1]RepositoryURI of an external repository which contains further details about the genetics dataurl : uri [0..1]URI of an external repository which contains further details about the genetics dataname : string [0..1]Id of the variant in this external repositoryvariantId : string [0..1]Id of the read in this external repositoryreadId : string [0..1]StructureVariantPrecision of boundariesprecisionOfBoundaries : string [0..1]Structural Variant reported aCGH ratioreportedaCGHRatio : decimal [0..1]Structural Variant Lengthlength : integer [0..1]OuterStructural Variant Outer Start-Endstart : integer [0..1]Structural Variant Outer Start-Endend : integer [0..1]InnerStructural Variant Inner Start-Endstart : integer [0..1]Structural Variant Inner Start-Endend : integer [0..1]A reference sequence is a sequence that is used to represent an allele or variantreferenceSeq[0..1]A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of))variant[0..*]An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686))quality[0..*]Configurations of the external repositoryrepository[0..*]Structural variant outerouter[0..1]Structural variant innerinner[0..1]Structural variantstructureVariant[0..*]

XML Template

<Sequence 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]"/><!-- 1..1 AA | DNA | RNA -->
 <coordinateSystem value="[integer]"/><!-- 1..1 Numbering used for sequence (0-based or 1-based) -->
 <patient><!-- 0..1 Reference(Patient) Who and/or what this is about --></patient>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for sequencing --></specimen>
 <device><!-- 0..1 Reference(Device) The method for sequencing --></device>
 <quantity><!-- 0..1 Quantity Quantity of the sequence --></quantity>
 <referenceSeq>  <!-- 0..1 Reference sequence -->
  <chromosome><!-- 0..1 CodeableConcept Chromosome containing genetic finding --></chromosome>
  <genomeBuild value="[string]"/><!-- 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' -->
  <referenceSeqId><!-- 1..1 CodeableConcept Reference identifier --></referenceSeqId>
  <referenceSeqPointer><!-- 0..1 Reference(Sequence) A Pointer to another Sequence entity as refence sequence --></referenceSeqPointer>
  <referenceSeqString value="[string]"/><!-- 0..1 A Reference Sequence string -->
  <strand value="[integer]"/><!-- 1..1 Strand of DNA -->
  <windowStart value="[integer]"/><!-- 1..1 Start position (inclusive) of the window on the  reference sequence -->
  <windowEnd value="[integer]"/><!-- 1..1 End position (exclusive) of the window on the reference sequence -->
 </referenceSeq>
 <variant>  <!-- 0..* Sequence variant -->
  <start value="[integer]"/><!-- 0..1 Start position (inclusive) of the variant on the  reference sequence -->
  <end value="[integer]"/><!-- 0..1 End position (exclusive) of the variant on the reference sequence -->
  <observedAllele value="[string]"/><!-- 0..1 Allele that was observed -->
  <referenceAllele value="[string]"/><!-- 0..1 Allele of reference sequence -->
  <cigar value="[string]"/><!-- 0..1 Extended CIGAR string for aligning the sequence with reference bases -->
  <variantPointer><!-- 0..1 Reference(Observation) Pointer to observed variant information --></variantPointer>
 </variant>
 <observedSeq value="[string]"/><!-- 0..1 Observed sequence -->
 <quality>  <!-- 0..* Sequence quality -->
  <standardSequence><!-- 0..1 CodeableConcept Standard sequence for comparison --></standardSequence>
  <start value="[integer]"/><!-- 0..1 Start position (inclusive) of the sequence -->
  <end value="[integer]"/><!-- 0..1 End position (exclusive) of the sequence -->
  <score><!-- 0..1 Quantity Quality score --></score>
  <method><!-- 0..1 CodeableConcept Method for quality --></method>
  <truthTP value="[decimal]"/><!-- 0..1 True positives from the perspective of the truth data -->
  <queryTP value="[decimal]"/><!-- 0..1 True positives from the perspective of the query data -->
  <truthFN value="[decimal]"/><!-- 0..1 False negatives -->
  <queryFP value="[decimal]"/><!-- 0..1 False positives -->
  <gtFP value="[decimal]"/><!-- 0..1 False positives where the non-REF alleles in the Truth and Query Call Sets match -->
  <precision value="[decimal]"/><!-- 0..1 Precision -->
  <recall value="[decimal]"/><!-- 0..1 Recall -->
  <fScore value="[decimal]"/><!-- 0..1 F-score -->
 </quality>
 <readCoverage value="[integer]"/><!-- 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence -->
 <repository>  <!-- 0..* External repository -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Name of the repository -->
  <variantId value="[string]"/><!-- 0..1 Id of the variant -->
  <readId value="[string]"/><!-- 0..1 Id of the read -->
 </repository>
 <pointer><!-- 0..* Reference(Sequence) Pointer to next atomic sequence --></pointer>
 <structureVariant>  <!-- 0..* -->
  <precisionOfBoundaries value="[string]"/><!-- 0..1 Precision of boundaries -->
  <reportedaCGHRatio value="[decimal]"/><!-- 0..1 Structural Variant reported aCGH ratio -->
  <length value="[integer]"/><!-- 0..1 Structural Variant Length -->
  <outer> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Outer Start-End -->
  </outer>
  <inner> 
   <start value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
   <end value="[integer]"/><!-- 0..1 Structural Variant Inner Start-End -->
  </inner>
 </structureVariant>
</Sequence>

JSON Template

{doco
  "resourceType" : "Sequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence
  "type" : "<code>", // R!  AA | DNA | RNA
  "coordinateSystem" : <integer>, // R!  Numbering used for sequence (0-based or 1-based)
  "patient" : { Reference(Patient) }, // Who and/or what this is about
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "quantity" : { Quantity }, // Quantity of the sequence
  "referenceSeq" : { // Reference sequence
    "chromosome" : { CodeableConcept }, // Chromosome containing genetic finding
    "genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    "referenceSeqId" : { CodeableConcept }, // R!  Reference identifier
    "referenceSeqPointer" : { Reference(Sequence) }, // A Pointer to another Sequence entity as refence sequence
    "referenceSeqString" : "<string>", // A Reference Sequence string
    "strand" : <integer>, // R!  Strand of DNA
    "windowStart" : <integer>, // R!  Start position (inclusive) of the window on the  reference sequence
    "windowEnd" : <integer> // R!  End position (exclusive) of the window on the reference sequence
  },
  "variant" : [{ // Sequence variant
    "start" : <integer>, // Start position (inclusive) of the variant on the  reference sequence
    "end" : <integer>, // End position (exclusive) of the variant on the reference sequence
    "observedAllele" : "<string>", // Allele that was observed
    "referenceAllele" : "<string>", // Allele of reference sequence
    "cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
    "variantPointer" : { Reference(Observation) } // Pointer to observed variant information
  }],
  "observedSeq" : "<string>", // Observed sequence
  "quality" : [{ // Sequence quality
    "standardSequence" : { CodeableConcept }, // Standard sequence for comparison
    "start" : <integer>, // Start position (inclusive) of the sequence
    "end" : <integer>, // End position (exclusive) of the sequence
    "score" : { Quantity }, // Quality score
    "method" : { CodeableConcept }, // Method for quality
    "truthTP" : <decimal>, // True positives from the perspective of the truth data
    "queryTP" : <decimal>, // True positives from the perspective of the query data
    "truthFN" : <decimal>, // False negatives
    "queryFP" : <decimal>, // False positives
    "gtFP" : <decimal>, // False positives where the non-REF alleles in the Truth and Query Call Sets match
    "precision" : <decimal>, // Precision
    "recall" : <decimal>, // Recall
    "fScore" : <decimal> // F-score
  }],
  "readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
  "repository" : [{ // External repository
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Name of the repository
    "variantId" : "<string>", // Id of the variant
    "readId" : "<string>" // Id of the read
  }],
  "pointer" : [{ Reference(Sequence) }], // Pointer to next atomic sequence
  "structureVariant" : [{ // 
    "precisionOfBoundaries" : "<string>", // Precision of boundaries
    "reportedaCGHRatio" : <decimal>, // Structural Variant reported aCGH ratio
    "length" : <integer>, // Structural Variant Length
    "outer" : { // 
      "start" : <integer>, // Structural Variant Outer Start-End
      "end" : <integer> // Structural Variant Outer Start-End
    },
    "inner" : { // 
      "start" : <integer>, // Structural Variant Inner Start-End
      "end" : <integer> // Structural Variant Inner Start-End
    }
  }]
}

Turtle Template

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


[ a fhir:Sequence;
  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:Sequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence
  fhir:Sequence.type [ code ]; # 1..1 AA | DNA | RNA
  fhir:Sequence.coordinateSystem [ integer ]; # 1..1 Numbering used for sequence (0-based or 1-based)
  fhir:Sequence.patient [ Reference(Patient) ]; # 0..1 Who and/or what this is about
  fhir:Sequence.specimen [ Reference(Specimen) ]; # 0..1 Specimen used for sequencing
  fhir:Sequence.device [ Reference(Device) ]; # 0..1 The method for sequencing
  fhir:Sequence.quantity [ Quantity ]; # 0..1 Quantity of the sequence
  fhir:Sequence.referenceSeq [ # 0..1 Reference sequence
    fhir:Sequence.referenceSeq.chromosome [ CodeableConcept ]; # 0..1 Chromosome containing genetic finding
    fhir:Sequence.referenceSeq.genomeBuild [ string ]; # 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    fhir:Sequence.referenceSeq.referenceSeqId [ CodeableConcept ]; # 1..1 Reference identifier
    fhir:Sequence.referenceSeq.referenceSeqPointer [ Reference(Sequence) ]; # 0..1 A Pointer to another Sequence entity as refence sequence
    fhir:Sequence.referenceSeq.referenceSeqString [ string ]; # 0..1 A Reference Sequence string
    fhir:Sequence.referenceSeq.strand [ integer ]; # 1..1 Strand of DNA
    fhir:Sequence.referenceSeq.windowStart [ integer ]; # 1..1 Start position (inclusive) of the window on the  reference sequence
    fhir:Sequence.referenceSeq.windowEnd [ integer ]; # 1..1 End position (exclusive) of the window on the reference sequence
  ];
  fhir:Sequence.variant [ # 0..* Sequence variant
    fhir:Sequence.variant.start [ integer ]; # 0..1 Start position (inclusive) of the variant on the  reference sequence
    fhir:Sequence.variant.end [ integer ]; # 0..1 End position (exclusive) of the variant on the reference sequence
    fhir:Sequence.variant.observedAllele [ string ]; # 0..1 Allele that was observed
    fhir:Sequence.variant.referenceAllele [ string ]; # 0..1 Allele of reference sequence
    fhir:Sequence.variant.cigar [ string ]; # 0..1 Extended CIGAR string for aligning the sequence with reference bases
    fhir:Sequence.variant.variantPointer [ Reference(Observation) ]; # 0..1 Pointer to observed variant information
  ], ...;
  fhir:Sequence.observedSeq [ string ]; # 0..1 Observed sequence
  fhir:Sequence.quality [ # 0..* Sequence quality
    fhir:Sequence.quality.standardSequence [ CodeableConcept ]; # 0..1 Standard sequence for comparison
    fhir:Sequence.quality.start [ integer ]; # 0..1 Start position (inclusive) of the sequence
    fhir:Sequence.quality.end [ integer ]; # 0..1 End position (exclusive) of the sequence
    fhir:Sequence.quality.score [ Quantity ]; # 0..1 Quality score
    fhir:Sequence.quality.method [ CodeableConcept ]; # 0..1 Method for quality
    fhir:Sequence.quality.truthTP [ decimal ]; # 0..1 True positives from the perspective of the truth data
    fhir:Sequence.quality.queryTP [ decimal ]; # 0..1 True positives from the perspective of the query data
    fhir:Sequence.quality.truthFN [ decimal ]; # 0..1 False negatives
    fhir:Sequence.quality.queryFP [ decimal ]; # 0..1 False positives
    fhir:Sequence.quality.gtFP [ decimal ]; # 0..1 False positives where the non-REF alleles in the Truth and Query Call Sets match
    fhir:Sequence.quality.precision [ decimal ]; # 0..1 Precision
    fhir:Sequence.quality.recall [ decimal ]; # 0..1 Recall
    fhir:Sequence.quality.fScore [ decimal ]; # 0..1 F-score
  ], ...;
  fhir:Sequence.readCoverage [ integer ]; # 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence
  fhir:Sequence.repository [ # 0..* External repository
    fhir:Sequence.repository.url [ uri ]; # 0..1 URI of the repository
    fhir:Sequence.repository.name [ string ]; # 0..1 Name of the repository
    fhir:Sequence.repository.variantId [ string ]; # 0..1 Id of the variant
    fhir:Sequence.repository.readId [ string ]; # 0..1 Id of the read
  ], ...;
  fhir:Sequence.pointer [ Reference(Sequence) ], ... ; # 0..* Pointer to next atomic sequence
  fhir:Sequence.structureVariant [ # 0..* 
    fhir:Sequence.structureVariant.precisionOfBoundaries [ string ]; # 0..1 Precision of boundaries
    fhir:Sequence.structureVariant.reportedaCGHRatio [ decimal ]; # 0..1 Structural Variant reported aCGH ratio
    fhir:Sequence.structureVariant.length [ integer ]; # 0..1 Structural Variant Length
    fhir:Sequence.structureVariant.outer [ # 0..1 
      fhir:Sequence.structureVariant.outer.start [ integer ]; # 0..1 Structural Variant Outer Start-End
      fhir:Sequence.structureVariant.outer.end [ integer ]; # 0..1 Structural Variant Outer Start-End
    ];
    fhir:Sequence.structureVariant.inner [ # 0..1 
      fhir:Sequence.structureVariant.inner.start [ integer ]; # 0..1 Structural Variant Inner Start-End
      fhir:Sequence.structureVariant.inner.end [ integer ]; # 0..1 Structural Variant Inner Start-End
    ];
  ], ...;
]

Changes since DSTU2

This resource did not exist in Release 2

 

Alternate definitions: Master Definition (XML, JSON), XML Schema/Schematron (for ) + JSON Schema, ShEx (for Turtle)

10.4.3.1 Terminology Bindings

PathDefinitionTypeReference
Sequence.type Type if a sequence -- DNA, RNA, or amino acid sequenceExamplesequenceType
Sequence.referenceSeq.chromosome Chromosome number for humanExamplechromosome-human
Sequence.referenceSeq.referenceSeqId Reference identifierExampleENSEMBL

10.4.4 Search Parameters

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

NameTypeDescriptionPaths
chromosometokenChromosome of the sequenceSequence.referenceSeq.chromosome
coordinatecompositeGenomic coordinate of the sequence. For example, a search for sequence in region 1:123-345 can be represented as `coordinate=1$lt345$gt123`
endnumberEnd position (0-based exclusive) of the sequenceSequence.variant.end
patientreferenceThe subject that the observation is aboutSequence.patient
(Patient)
startnumberStart position (0-based inclusive) of the sequenceSequence.variant.start
typetokenThe type of the variant: Amino acid / cDNA transcript / RNA variant.Sequence.type