10.6 Resource MolecularSequence - Content

Work Group

Raw data describing a biological sequence.

The Clinical Genomics committee has identified overlaps and redundancies between content in the MolecularSequence resource and content in Observation profiles in the evolving Implementation Guide for Clinical Genomics Reporting found here . The committee is considering options for modifying the resource and anticipates potential changes being brought forward in an upcoming ballot.

10.6.1 Scope and Usage

The MolecularSequence resource is designed to describe an atomic sequence which contains the alignment sequencing test result and multiple variations. 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 MolecularSequence resource avoids large genomic payloads in a manner analogous to how the FHIR ImagingStudy resource references large images maintained in other systems. For use cases, details on how this resource interact with other Clinical Genomics resources or profiles, please refer to implementation guidance document here.

10.6.1.1 Genetic Standards and Resources include:

Variant Databases: dbSNP , ClinVar , and COSMIC
Reference Sequences: RefSeq and ENSEMBL

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

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

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.

10.6.2 Boundaries and Relationships

Focus of the resource is to provide sequencing alignment data immediately relevant to what the interpretation on clinical decision-making originates from. 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 MolecularSequence 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 MolecularSequence resource can be referenced by the Condition resource to provide specific genetic data to support assertions. This is analogous to how Condition references other resources, such as AllergyIntolerance, Procedure, and Questionnaire resources.

10.6.3 References

This resource is referenced by itself and Observation.

This resource does not implement any patterns.

Structure

Name	Flags	Card.	Type	Description & Constraints
MolecularSequence	Σ I TU		DomainResource	Information about a biological sequence + Rule: Only 0 and 1 are valid for coordinateSystem Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence. This is a FHIR-defined id
type	Σ	0..1	code	aa \| dna \| rna sequenceType (Required)
coordinateSystem	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
patient	Σ	0..1	Reference(Patient)	Who and/or what this is about
specimen	Σ	0..1	Reference(Specimen)	Specimen used for sequencing
device	Σ	0..1	Reference(Device)	The method for sequencing
performer	Σ	0..1	Reference(Organization)	Who should be responsible for test result
quantity	Σ	0..1	Quantity	The number of copies of the sequence of interest. (RNASeq)
referenceSeq	Σ I	0..1	BackboneElement	A sequence used as reference + Rule: GenomeBuild 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. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
chromosome	Σ	0..1	CodeableConcept	Chromosome containing genetic finding chromosome-human (Example)
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	Σ	0..1	code	sense \| antisense orientationType (Required)
referenceSeqId	Σ	0..1	CodeableConcept	Reference identifier E n s e m b l (Example)
referenceSeqPointer	Σ	0..1	Reference(MolecularSequence)	A pointer to another MolecularSequence entity as reference sequence
referenceSeqString	Σ	0..1	string	A string to represent reference sequence
strand	Σ	0..1	code	watson \| crick strandType (Required)
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
windowEnd	Σ	0..1	integer	End position of the window on the reference sequence
variant	Σ	0..*	BackboneElement	Variant in sequence
start	Σ	0..1	integer	Start position of the variant on the reference sequence
end	Σ	0..1	integer	End position of the variant on the reference sequence
observedAllele	Σ	0..1	string	Allele that was observed
referenceAllele	Σ	0..1	string	Allele in the reference sequence
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
variantPointer	Σ	0..1	Reference(Observation)	Pointer to observed variant information
observedSeq	Σ	0..1	string	Sequence that was observed
quality	Σ	0..*	BackboneElement	An set of value as quality of sequence
type	Σ	1..1	code	indel \| snp \| unknown qualityType (Required)
standardSequence	Σ	0..1	CodeableConcept	Standard sequence for comparison F d a- standard sequence (Example)
start	Σ	0..1	integer	Start position of the sequence
end	Σ	0..1	integer	End position of the sequence
score	Σ	0..1	Quantity	Quality score for the comparison
method	Σ	0..1	CodeableConcept	Method to get quality F d a- method (Example)
truthTP	Σ	0..1	decimal	True positives from the perspective of the truth data
queryTP	Σ	0..1	decimal	True positives from the perspective of the query data
truthFN	Σ	0..1	decimal	False negatives
queryFP	Σ	0..1	decimal	False positives
gtFP	Σ	0..1	decimal	False positives where the non-REF alleles in the Truth and Query Call Sets match
precision	Σ	0..1	decimal	Precision of comparison
recall	Σ	0..1	decimal	Recall of comparison
fScore	Σ	0..1	decimal	F-score
roc	Σ	0..1	BackboneElement	Receiver Operator Characteristic (ROC) Curve
score	Σ	0..*	integer	Genotype quality score
numTP	Σ	0..*	integer	Roc score true positive numbers
numFP	Σ	0..*	integer	Roc score false positive numbers
numFN	Σ	0..*	integer	Roc score false negative numbers
precision	Σ	0..*	decimal	Precision of the GQ score
sensitivity	Σ	0..*	decimal	Sensitivity of the GQ score
fMeasure	Σ	0..*	decimal	FScore of the GQ score
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type	Σ	1..1	code	directlink \| openapi \| login \| oauth \| other repositoryType (Required)
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Repository's name
datasetId	Σ	0..1	string	Id of the dataset that used to call for dataset in repository
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference(MolecularSequence)	Pointer to next atomic sequence
structureVariant	Σ	0..*	BackboneElement	Structural variant
variantType	Σ	0..1	CodeableConcept	Structural variant change type LOINC LL379-9 answerlist (Required)
exact	Σ	0..1	boolean	Does the structural variant have base pair resolution breakpoints?
length	Σ	0..1	integer	Structural variant length
outer	Σ	0..1	BackboneElement	Structural variant outer
start	Σ	0..1	integer	Structural variant outer start
end	Σ	0..1	integer	Structural variant outer end
inner	Σ	0..1	BackboneElement	Structural variant inner
start	Σ	0..1	integer	Structural variant inner start
end	Σ	0..1	integer	Structural variant inner end
Documentation for this format

UML Diagram (Legend)

XML Template

<MolecularSequence xmlns="http://hl7.org/fhir"> 
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence. This is a FHIR-defined id --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <coordinateSystem value="[integer]"/><!-- 1..1 Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) -->
 <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>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <quantity><!-- 0..1 Quantity The number of copies of the sequence of interest.  (RNASeq) --></quantity>
 <referenceSeq>  <!-- 0..1 A sequence used as reference -->
  <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' -->
  <orientation value="[code]"/><!-- 0..1 sense | antisense -->
  <referenceSeqId><!-- 0..1 CodeableConcept Reference identifier --></referenceSeqId>
  <referenceSeqPointer><!-- 0..1 Reference(MolecularSequence) A pointer to another MolecularSequence entity as reference sequence --></referenceSeqPointer>
  <referenceSeqString value="[string]"/><!-- 0..1 A string to represent reference sequence -->
  <strand value="[code]"/><!-- 0..1 watson | crick -->
  <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 -->
 </referenceSeq>
 <variant>  <!-- 0..* Variant in sequence -->
  <start value="[integer]"/><!-- 0..1 Start position of the variant on the  reference sequence -->
  <end value="[integer]"/><!-- 0..1 End position of the variant on the reference sequence -->
  <observedAllele value="[string]"/><!-- 0..1 Allele that was observed -->
  <referenceAllele value="[string]"/><!-- 0..1 Allele in the 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 Sequence that was observed -->
 <quality>  <!-- 0..* An set of value as quality of sequence -->
  <type value="[code]"/><!-- 1..1 indel | snp | unknown -->
  <standardSequence><!-- 0..1 CodeableConcept Standard sequence for comparison --></standardSequence>
  <start value="[integer]"/><!-- 0..1 Start position of the sequence -->
  <end value="[integer]"/><!-- 0..1 End position of the sequence -->
  <score><!-- 0..1 Quantity Quality score for the comparison --></score>
  <method><!-- 0..1 CodeableConcept Method to get 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 of comparison -->
  <recall value="[decimal]"/><!-- 0..1 Recall of comparison -->
  <fScore value="[decimal]"/><!-- 0..1 F-score -->
  <roc>  <!-- 0..1 Receiver Operator Characteristic (ROC) Curve -->
   <score value="[integer]"/><!-- 0..* Genotype quality score -->
   <numTP value="[integer]"/><!-- 0..* Roc score true positive numbers -->
   <numFP value="[integer]"/><!-- 0..* Roc score false positive numbers -->
   <numFN value="[integer]"/><!-- 0..* Roc score false negative numbers -->
   <precision value="[decimal]"/><!-- 0..* Precision of the GQ score -->
   <sensitivity value="[decimal]"/><!-- 0..* Sensitivity of the GQ score -->
   <fMeasure value="[decimal]"/><!-- 0..* FScore of the GQ score -->
  </roc>
 </quality>
 <readCoverage value="[integer]"/><!-- 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence -->
 <repository>  <!-- 0..* External repository which contains detailed report related with observedSeq in this resource -->
  <type value="[code]"/><!-- 1..1 directlink | openapi | login | oauth | other -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Repository's name -->
  <datasetId value="[string]"/><!-- 0..1 Id of the dataset that used to call for dataset in repository -->
  <variantsetId value="[string]"/><!-- 0..1 Id of the variantset that used to call for variantset in repository -->
  <readsetId value="[string]"/><!-- 0..1 Id of the read -->
 </repository>
 <pointer><!-- 0..* Reference(MolecularSequence) Pointer to next atomic sequence --></pointer>
 <structureVariant>  <!-- 0..* Structural variant -->
  <variantType><!-- 0..1 CodeableConcept Structural variant change type  --></variantType>
  <exact value="[boolean]"/><!-- 0..1 Does the structural variant have base pair resolution breakpoints? -->
  <length value="[integer]"/><!-- 0..1 Structural variant length -->
  <outer>  <!-- 0..1 Structural variant outer -->
   <start value="[integer]"/><!-- 0..1 Structural variant outer start -->
   <end value="[integer]"/><!-- 0..1 Structural variant outer end -->
  </outer>
  <inner>  <!-- 0..1 Structural variant inner -->
   <start value="[integer]"/><!-- 0..1 Structural variant inner start -->
   <end value="[integer]"/><!-- 0..1 Structural variant inner end -->
  </inner>
 </structureVariant>
</MolecularSequence>

JSON Template

{
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence. This is a FHIR-defined id
  "type" : "<code>", // aa | dna | rna
  "coordinateSystem" : <integer>, // R!  Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
  "patient" : { Reference(Patient) }, // Who and/or what this is about
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "quantity" : { Quantity }, // The number of copies of the sequence of interest.  (RNASeq)
  "referenceSeq" : { // A sequence used as reference
    "chromosome" : { CodeableConcept }, // Chromosome containing genetic finding
    "genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    "orientation" : "<code>", // sense | antisense
    "referenceSeqId" : { CodeableConcept }, // Reference identifier
    "referenceSeqPointer" : { Reference(MolecularSequence) }, // A pointer to another MolecularSequence entity as reference sequence
    "referenceSeqString" : "<string>", // A string to represent reference sequence
    "strand" : "<code>", // watson | crick
    "windowStart" : <integer>, // Start position of the window on the  reference sequence
    "windowEnd" : <integer> // End position of the window on the reference sequence
  },
  "variant" : [{ // Variant in sequence
    "start" : <integer>, // Start position of the variant on the  reference sequence
    "end" : <integer>, // End position of the variant on the reference sequence
    "observedAllele" : "<string>", // Allele that was observed
    "referenceAllele" : "<string>", // Allele in the reference sequence
    "cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
    "variantPointer" : { Reference(Observation) } // Pointer to observed variant information
  }],
  "observedSeq" : "<string>", // Sequence that was observed
  "quality" : [{ // An set of value as quality of sequence
    "type" : "<code>", // R!  indel | snp | unknown
    "standardSequence" : { CodeableConcept }, // Standard sequence for comparison
    "start" : <integer>, // Start position of the sequence
    "end" : <integer>, // End position of the sequence
    "score" : { Quantity }, // Quality score for the comparison
    "method" : { CodeableConcept }, // Method to get 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 of comparison
    "recall" : <decimal>, // Recall of comparison
    "fScore" : <decimal>, // F-score
    "roc" : { // Receiver Operator Characteristic (ROC) Curve
      "score" : [<integer>], // Genotype quality score
      "numTP" : [<integer>], // Roc score true positive numbers
      "numFP" : [<integer>], // Roc score false positive numbers
      "numFN" : [<integer>], // Roc score false negative numbers
      "precision" : [<decimal>], // Precision of the GQ score
      "sensitivity" : [<decimal>], // Sensitivity of the GQ score
      "fMeasure" : [<decimal>] // FScore of the GQ score
    }
  }],
  "readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
  "repository" : [{ // External repository which contains detailed report related with observedSeq in this resource
    "type" : "<code>", // R!  directlink | openapi | login | oauth | other
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Repository's name
    "datasetId" : "<string>", // Id of the dataset that used to call for dataset in repository
    "variantsetId" : "<string>", // Id of the variantset that used to call for variantset in repository
    "readsetId" : "<string>" // Id of the read
  }],
  "pointer" : [{ Reference(MolecularSequence) }], // Pointer to next atomic sequence
  "structureVariant" : [{ // Structural variant
    "variantType" : { CodeableConcept }, // Structural variant change type 
    "exact" : <boolean>, // Does the structural variant have base pair resolution breakpoints?
    "length" : <integer>, // Structural variant length
    "outer" : { // Structural variant outer
      "start" : <integer>, // Structural variant outer start
      "end" : <integer> // Structural variant outer end
    },
    "inner" : { // Structural variant inner
      "start" : <integer>, // Structural variant inner start
      "end" : <integer> // Structural variant inner end
    }
  }]
}

Turtle Template

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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:MolecularSequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence. This is a FHIR-defined id
  fhir:MolecularSequence.type [ code ]; # 0..1 aa | dna | rna
  fhir:MolecularSequence.coordinateSystem [ integer ]; # 1..1 Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
  fhir:MolecularSequence.patient [ Reference(Patient) ]; # 0..1 Who and/or what this is about
  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.quantity [ Quantity ]; # 0..1 The number of copies of the sequence of interest.  (RNASeq)
  fhir:MolecularSequence.referenceSeq [ # 0..1 A sequence used as reference
    fhir:MolecularSequence.referenceSeq.chromosome [ CodeableConcept ]; # 0..1 Chromosome containing genetic finding
    fhir:MolecularSequence.referenceSeq.genomeBuild [ string ]; # 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    fhir:MolecularSequence.referenceSeq.orientation [ code ]; # 0..1 sense | antisense
    fhir:MolecularSequence.referenceSeq.referenceSeqId [ CodeableConcept ]; # 0..1 Reference identifier
    fhir:MolecularSequence.referenceSeq.referenceSeqPointer [ Reference(MolecularSequence) ]; # 0..1 A pointer to another MolecularSequence entity as reference sequence
    fhir:MolecularSequence.referenceSeq.referenceSeqString [ string ]; # 0..1 A string to represent reference sequence
    fhir:MolecularSequence.referenceSeq.strand [ code ]; # 0..1 watson | crick
    fhir:MolecularSequence.referenceSeq.windowStart [ integer ]; # 0..1 Start position of the window on the  reference sequence
    fhir:MolecularSequence.referenceSeq.windowEnd [ integer ]; # 0..1 End position of the window on the reference sequence
  ];
  fhir:MolecularSequence.variant [ # 0..* Variant in sequence
    fhir:MolecularSequence.variant.start [ integer ]; # 0..1 Start position of the variant on the  reference sequence
    fhir:MolecularSequence.variant.end [ integer ]; # 0..1 End position of the variant on the reference sequence
    fhir:MolecularSequence.variant.observedAllele [ string ]; # 0..1 Allele that was observed
    fhir:MolecularSequence.variant.referenceAllele [ string ]; # 0..1 Allele in the reference sequence
    fhir:MolecularSequence.variant.cigar [ string ]; # 0..1 Extended CIGAR string for aligning the sequence with reference bases
    fhir:MolecularSequence.variant.variantPointer [ Reference(Observation) ]; # 0..1 Pointer to observed variant information
  ], ...;
  fhir:MolecularSequence.observedSeq [ string ]; # 0..1 Sequence that was observed
  fhir:MolecularSequence.quality [ # 0..* An set of value as quality of sequence
    fhir:MolecularSequence.quality.type [ code ]; # 1..1 indel | snp | unknown
    fhir:MolecularSequence.quality.standardSequence [ CodeableConcept ]; # 0..1 Standard sequence for comparison
    fhir:MolecularSequence.quality.start [ integer ]; # 0..1 Start position of the sequence
    fhir:MolecularSequence.quality.end [ integer ]; # 0..1 End position of the sequence
    fhir:MolecularSequence.quality.score [ Quantity ]; # 0..1 Quality score for the comparison
    fhir:MolecularSequence.quality.method [ CodeableConcept ]; # 0..1 Method to get quality
    fhir:MolecularSequence.quality.truthTP [ decimal ]; # 0..1 True positives from the perspective of the truth data
    fhir:MolecularSequence.quality.queryTP [ decimal ]; # 0..1 True positives from the perspective of the query data
    fhir:MolecularSequence.quality.truthFN [ decimal ]; # 0..1 False negatives
    fhir:MolecularSequence.quality.queryFP [ decimal ]; # 0..1 False positives
    fhir:MolecularSequence.quality.gtFP [ decimal ]; # 0..1 False positives where the non-REF alleles in the Truth and Query Call Sets match
    fhir:MolecularSequence.quality.precision [ decimal ]; # 0..1 Precision of comparison
    fhir:MolecularSequence.quality.recall [ decimal ]; # 0..1 Recall of comparison
    fhir:MolecularSequence.quality.fScore [ decimal ]; # 0..1 F-score
    fhir:MolecularSequence.quality.roc [ # 0..1 Receiver Operator Characteristic (ROC) Curve
      fhir:MolecularSequence.quality.roc.score [ integer ], ... ; # 0..* Genotype quality score
      fhir:MolecularSequence.quality.roc.numTP [ integer ], ... ; # 0..* Roc score true positive numbers
      fhir:MolecularSequence.quality.roc.numFP [ integer ], ... ; # 0..* Roc score false positive numbers
      fhir:MolecularSequence.quality.roc.numFN [ integer ], ... ; # 0..* Roc score false negative numbers
      fhir:MolecularSequence.quality.roc.precision [ decimal ], ... ; # 0..* Precision of the GQ score
      fhir:MolecularSequence.quality.roc.sensitivity [ decimal ], ... ; # 0..* Sensitivity of the GQ score
      fhir:MolecularSequence.quality.roc.fMeasure [ decimal ], ... ; # 0..* FScore of the GQ score
    ];
  ], ...;
  fhir:MolecularSequence.readCoverage [ integer ]; # 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence
  fhir:MolecularSequence.repository [ # 0..* External repository which contains detailed report related with observedSeq in this resource
    fhir:MolecularSequence.repository.type [ code ]; # 1..1 directlink | openapi | login | oauth | other
    fhir:MolecularSequence.repository.url [ uri ]; # 0..1 URI of the repository
    fhir:MolecularSequence.repository.name [ string ]; # 0..1 Repository's name
    fhir:MolecularSequence.repository.datasetId [ string ]; # 0..1 Id of the dataset that used to call for dataset in repository
    fhir:MolecularSequence.repository.variantsetId [ string ]; # 0..1 Id of the variantset that used to call for variantset in repository
    fhir:MolecularSequence.repository.readsetId [ string ]; # 0..1 Id of the read
  ], ...;
  fhir:MolecularSequence.pointer [ Reference(MolecularSequence) ], ... ; # 0..* Pointer to next atomic sequence
  fhir:MolecularSequence.structureVariant [ # 0..* Structural variant
    fhir:MolecularSequence.structureVariant.variantType [ CodeableConcept ]; # 0..1 Structural variant change type
    fhir:MolecularSequence.structureVariant.exact [ boolean ]; # 0..1 Does the structural variant have base pair resolution breakpoints?
    fhir:MolecularSequence.structureVariant.length [ integer ]; # 0..1 Structural variant length
    fhir:MolecularSequence.structureVariant.outer [ # 0..1 Structural variant outer
      fhir:MolecularSequence.structureVariant.outer.start [ integer ]; # 0..1 Structural variant outer start
      fhir:MolecularSequence.structureVariant.outer.end [ integer ]; # 0..1 Structural variant outer end
    ];
    fhir:MolecularSequence.structureVariant.inner [ # 0..1 Structural variant inner
      fhir:MolecularSequence.structureVariant.inner.start [ integer ]; # 0..1 Structural variant inner start
      fhir:MolecularSequence.structureVariant.inner.end [ integer ]; # 0..1 Structural variant inner end
    ];
  ], ...;
]

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|4.1.0

MolecularSequence.referenceSeq.orientation

Change value set from http://hl7.org/fhir/ValueSet/orientation-type|4.0.0 to http://hl7.org/fhir/ValueSet/orientation-type|4.1.0

MolecularSequence.referenceSeq.strand

Change value set from http://hl7.org/fhir/ValueSet/strand-type|4.0.0 to http://hl7.org/fhir/ValueSet/strand-type|4.1.0

MolecularSequence.quality.type

Change value set from http://hl7.org/fhir/ValueSet/quality-type|4.0.0 to http://hl7.org/fhir/ValueSet/quality-type|4.1.0

MolecularSequence.repository.type

Change value set from http://hl7.org/fhir/ValueSet/repository-type|4.0.0 to http://hl7.org/fhir/ValueSet/repository-type|4.1.0

MolecularSequence.structureVariant.variantType

Change value set from http://loinc.org/vs/LL379-9|4.0.0 to http://loinc.org/vs/LL379-9|4.1.0

See the Full Difference for further information

This analysis is available as XML or JSON.

See R3 <--> R4 Conversion Maps (status = 14 tests that all execute ok. All tests pass round-trip testing and all r3 resources are valid.)

Structure

Name	Flags	Card.	Type	Description & Constraints
MolecularSequence	Σ I TU		DomainResource	Information about a biological sequence + Rule: Only 0 and 1 are valid for coordinateSystem Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
identifier	Σ	0..*	Identifier	Unique ID for this particular sequence. This is a FHIR-defined id
type	Σ	0..1	code	aa \| dna \| rna sequenceType (Required)
coordinateSystem	Σ	1..1	integer	Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
patient	Σ	0..1	Reference(Patient)	Who and/or what this is about
specimen	Σ	0..1	Reference(Specimen)	Specimen used for sequencing
device	Σ	0..1	Reference(Device)	The method for sequencing
performer	Σ	0..1	Reference(Organization)	Who should be responsible for test result
quantity	Σ	0..1	Quantity	The number of copies of the sequence of interest. (RNASeq)
referenceSeq	Σ I	0..1	BackboneElement	A sequence used as reference + Rule: GenomeBuild 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. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
chromosome	Σ	0..1	CodeableConcept	Chromosome containing genetic finding chromosome-human (Example)
genomeBuild	Σ	0..1	string	The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
orientation	Σ	0..1	code	sense \| antisense orientationType (Required)
referenceSeqId	Σ	0..1	CodeableConcept	Reference identifier E n s e m b l (Example)
referenceSeqPointer	Σ	0..1	Reference(MolecularSequence)	A pointer to another MolecularSequence entity as reference sequence
referenceSeqString	Σ	0..1	string	A string to represent reference sequence
strand	Σ	0..1	code	watson \| crick strandType (Required)
windowStart	Σ	0..1	integer	Start position of the window on the reference sequence
windowEnd	Σ	0..1	integer	End position of the window on the reference sequence
variant	Σ	0..*	BackboneElement	Variant in sequence
start	Σ	0..1	integer	Start position of the variant on the reference sequence
end	Σ	0..1	integer	End position of the variant on the reference sequence
observedAllele	Σ	0..1	string	Allele that was observed
referenceAllele	Σ	0..1	string	Allele in the reference sequence
cigar	Σ	0..1	string	Extended CIGAR string for aligning the sequence with reference bases
variantPointer	Σ	0..1	Reference(Observation)	Pointer to observed variant information
observedSeq	Σ	0..1	string	Sequence that was observed
quality	Σ	0..*	BackboneElement	An set of value as quality of sequence
type	Σ	1..1	code	indel \| snp \| unknown qualityType (Required)
standardSequence	Σ	0..1	CodeableConcept	Standard sequence for comparison F d a- standard sequence (Example)
start	Σ	0..1	integer	Start position of the sequence
end	Σ	0..1	integer	End position of the sequence
score	Σ	0..1	Quantity	Quality score for the comparison
method	Σ	0..1	CodeableConcept	Method to get quality F d a- method (Example)
truthTP	Σ	0..1	decimal	True positives from the perspective of the truth data
queryTP	Σ	0..1	decimal	True positives from the perspective of the query data
truthFN	Σ	0..1	decimal	False negatives
queryFP	Σ	0..1	decimal	False positives
gtFP	Σ	0..1	decimal	False positives where the non-REF alleles in the Truth and Query Call Sets match
precision	Σ	0..1	decimal	Precision of comparison
recall	Σ	0..1	decimal	Recall of comparison
fScore	Σ	0..1	decimal	F-score
roc	Σ	0..1	BackboneElement	Receiver Operator Characteristic (ROC) Curve
score	Σ	0..*	integer	Genotype quality score
numTP	Σ	0..*	integer	Roc score true positive numbers
numFP	Σ	0..*	integer	Roc score false positive numbers
numFN	Σ	0..*	integer	Roc score false negative numbers
precision	Σ	0..*	decimal	Precision of the GQ score
sensitivity	Σ	0..*	decimal	Sensitivity of the GQ score
fMeasure	Σ	0..*	decimal	FScore of the GQ score
readCoverage	Σ	0..1	integer	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	Σ	0..*	BackboneElement	External repository which contains detailed report related with observedSeq in this resource
type	Σ	1..1	code	directlink \| openapi \| login \| oauth \| other repositoryType (Required)
url	Σ	0..1	uri	URI of the repository
name	Σ	0..1	string	Repository's name
datasetId	Σ	0..1	string	Id of the dataset that used to call for dataset in repository
variantsetId	Σ	0..1	string	Id of the variantset that used to call for variantset in repository
readsetId	Σ	0..1	string	Id of the read
pointer	Σ	0..*	Reference(MolecularSequence)	Pointer to next atomic sequence
structureVariant	Σ	0..*	BackboneElement	Structural variant
variantType	Σ	0..1	CodeableConcept	Structural variant change type LOINC LL379-9 answerlist (Required)
exact	Σ	0..1	boolean	Does the structural variant have base pair resolution breakpoints?
length	Σ	0..1	integer	Structural variant length
outer	Σ	0..1	BackboneElement	Structural variant outer
start	Σ	0..1	integer	Structural variant outer start
end	Σ	0..1	integer	Structural variant outer end
inner	Σ	0..1	BackboneElement	Structural variant inner
start	Σ	0..1	integer	Structural variant inner start
end	Σ	0..1	integer	Structural variant inner end
Documentation for this format

UML Diagram (Legend)

XML Template

<MolecularSequence xmlns="http://hl7.org/fhir"> 
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier Unique ID for this particular sequence. This is a FHIR-defined id --></identifier>
 <type value="[code]"/><!-- 0..1 aa | dna | rna -->
 <coordinateSystem value="[integer]"/><!-- 1..1 Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) -->
 <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>
 <performer><!-- 0..1 Reference(Organization) Who should be responsible for test result --></performer>
 <quantity><!-- 0..1 Quantity The number of copies of the sequence of interest.  (RNASeq) --></quantity>
 <referenceSeq>  <!-- 0..1 A sequence used as reference -->
  <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' -->
  <orientation value="[code]"/><!-- 0..1 sense | antisense -->
  <referenceSeqId><!-- 0..1 CodeableConcept Reference identifier --></referenceSeqId>
  <referenceSeqPointer><!-- 0..1 Reference(MolecularSequence) A pointer to another MolecularSequence entity as reference sequence --></referenceSeqPointer>
  <referenceSeqString value="[string]"/><!-- 0..1 A string to represent reference sequence -->
  <strand value="[code]"/><!-- 0..1 watson | crick -->
  <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 -->
 </referenceSeq>
 <variant>  <!-- 0..* Variant in sequence -->
  <start value="[integer]"/><!-- 0..1 Start position of the variant on the  reference sequence -->
  <end value="[integer]"/><!-- 0..1 End position of the variant on the reference sequence -->
  <observedAllele value="[string]"/><!-- 0..1 Allele that was observed -->
  <referenceAllele value="[string]"/><!-- 0..1 Allele in the 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 Sequence that was observed -->
 <quality>  <!-- 0..* An set of value as quality of sequence -->
  <type value="[code]"/><!-- 1..1 indel | snp | unknown -->
  <standardSequence><!-- 0..1 CodeableConcept Standard sequence for comparison --></standardSequence>
  <start value="[integer]"/><!-- 0..1 Start position of the sequence -->
  <end value="[integer]"/><!-- 0..1 End position of the sequence -->
  <score><!-- 0..1 Quantity Quality score for the comparison --></score>
  <method><!-- 0..1 CodeableConcept Method to get 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 of comparison -->
  <recall value="[decimal]"/><!-- 0..1 Recall of comparison -->
  <fScore value="[decimal]"/><!-- 0..1 F-score -->
  <roc>  <!-- 0..1 Receiver Operator Characteristic (ROC) Curve -->
   <score value="[integer]"/><!-- 0..* Genotype quality score -->
   <numTP value="[integer]"/><!-- 0..* Roc score true positive numbers -->
   <numFP value="[integer]"/><!-- 0..* Roc score false positive numbers -->
   <numFN value="[integer]"/><!-- 0..* Roc score false negative numbers -->
   <precision value="[decimal]"/><!-- 0..* Precision of the GQ score -->
   <sensitivity value="[decimal]"/><!-- 0..* Sensitivity of the GQ score -->
   <fMeasure value="[decimal]"/><!-- 0..* FScore of the GQ score -->
  </roc>
 </quality>
 <readCoverage value="[integer]"/><!-- 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence -->
 <repository>  <!-- 0..* External repository which contains detailed report related with observedSeq in this resource -->
  <type value="[code]"/><!-- 1..1 directlink | openapi | login | oauth | other -->
  <url value="[uri]"/><!-- 0..1 URI of the repository -->
  <name value="[string]"/><!-- 0..1 Repository's name -->
  <datasetId value="[string]"/><!-- 0..1 Id of the dataset that used to call for dataset in repository -->
  <variantsetId value="[string]"/><!-- 0..1 Id of the variantset that used to call for variantset in repository -->
  <readsetId value="[string]"/><!-- 0..1 Id of the read -->
 </repository>
 <pointer><!-- 0..* Reference(MolecularSequence) Pointer to next atomic sequence --></pointer>
 <structureVariant>  <!-- 0..* Structural variant -->
  <variantType><!-- 0..1 CodeableConcept Structural variant change type  --></variantType>
  <exact value="[boolean]"/><!-- 0..1 Does the structural variant have base pair resolution breakpoints? -->
  <length value="[integer]"/><!-- 0..1 Structural variant length -->
  <outer>  <!-- 0..1 Structural variant outer -->
   <start value="[integer]"/><!-- 0..1 Structural variant outer start -->
   <end value="[integer]"/><!-- 0..1 Structural variant outer end -->
  </outer>
  <inner>  <!-- 0..1 Structural variant inner -->
   <start value="[integer]"/><!-- 0..1 Structural variant inner start -->
   <end value="[integer]"/><!-- 0..1 Structural variant inner end -->
  </inner>
 </structureVariant>
</MolecularSequence>

JSON Template

{
  "resourceType" : "MolecularSequence",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // Unique ID for this particular sequence. This is a FHIR-defined id
  "type" : "<code>", // aa | dna | rna
  "coordinateSystem" : <integer>, // R!  Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
  "patient" : { Reference(Patient) }, // Who and/or what this is about
  "specimen" : { Reference(Specimen) }, // Specimen used for sequencing
  "device" : { Reference(Device) }, // The method for sequencing
  "performer" : { Reference(Organization) }, // Who should be responsible for test result
  "quantity" : { Quantity }, // The number of copies of the sequence of interest.  (RNASeq)
  "referenceSeq" : { // A sequence used as reference
    "chromosome" : { CodeableConcept }, // Chromosome containing genetic finding
    "genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    "orientation" : "<code>", // sense | antisense
    "referenceSeqId" : { CodeableConcept }, // Reference identifier
    "referenceSeqPointer" : { Reference(MolecularSequence) }, // A pointer to another MolecularSequence entity as reference sequence
    "referenceSeqString" : "<string>", // A string to represent reference sequence
    "strand" : "<code>", // watson | crick
    "windowStart" : <integer>, // Start position of the window on the  reference sequence
    "windowEnd" : <integer> // End position of the window on the reference sequence
  },
  "variant" : [{ // Variant in sequence
    "start" : <integer>, // Start position of the variant on the  reference sequence
    "end" : <integer>, // End position of the variant on the reference sequence
    "observedAllele" : "<string>", // Allele that was observed
    "referenceAllele" : "<string>", // Allele in the reference sequence
    "cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
    "variantPointer" : { Reference(Observation) } // Pointer to observed variant information
  }],
  "observedSeq" : "<string>", // Sequence that was observed
  "quality" : [{ // An set of value as quality of sequence
    "type" : "<code>", // R!  indel | snp | unknown
    "standardSequence" : { CodeableConcept }, // Standard sequence for comparison
    "start" : <integer>, // Start position of the sequence
    "end" : <integer>, // End position of the sequence
    "score" : { Quantity }, // Quality score for the comparison
    "method" : { CodeableConcept }, // Method to get 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 of comparison
    "recall" : <decimal>, // Recall of comparison
    "fScore" : <decimal>, // F-score
    "roc" : { // Receiver Operator Characteristic (ROC) Curve
      "score" : [<integer>], // Genotype quality score
      "numTP" : [<integer>], // Roc score true positive numbers
      "numFP" : [<integer>], // Roc score false positive numbers
      "numFN" : [<integer>], // Roc score false negative numbers
      "precision" : [<decimal>], // Precision of the GQ score
      "sensitivity" : [<decimal>], // Sensitivity of the GQ score
      "fMeasure" : [<decimal>] // FScore of the GQ score
    }
  }],
  "readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
  "repository" : [{ // External repository which contains detailed report related with observedSeq in this resource
    "type" : "<code>", // R!  directlink | openapi | login | oauth | other
    "url" : "<uri>", // URI of the repository
    "name" : "<string>", // Repository's name
    "datasetId" : "<string>", // Id of the dataset that used to call for dataset in repository
    "variantsetId" : "<string>", // Id of the variantset that used to call for variantset in repository
    "readsetId" : "<string>" // Id of the read
  }],
  "pointer" : [{ Reference(MolecularSequence) }], // Pointer to next atomic sequence
  "structureVariant" : [{ // Structural variant
    "variantType" : { CodeableConcept }, // Structural variant change type 
    "exact" : <boolean>, // Does the structural variant have base pair resolution breakpoints?
    "length" : <integer>, // Structural variant length
    "outer" : { // Structural variant outer
      "start" : <integer>, // Structural variant outer start
      "end" : <integer> // Structural variant outer end
    },
    "inner" : { // Structural variant inner
      "start" : <integer>, // Structural variant inner start
      "end" : <integer> // Structural variant inner end
    }
  }]
}

Turtle Template

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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:MolecularSequence.identifier [ Identifier ], ... ; # 0..* Unique ID for this particular sequence. This is a FHIR-defined id
  fhir:MolecularSequence.type [ code ]; # 0..1 aa | dna | rna
  fhir:MolecularSequence.coordinateSystem [ integer ]; # 1..1 Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
  fhir:MolecularSequence.patient [ Reference(Patient) ]; # 0..1 Who and/or what this is about
  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.quantity [ Quantity ]; # 0..1 The number of copies of the sequence of interest.  (RNASeq)
  fhir:MolecularSequence.referenceSeq [ # 0..1 A sequence used as reference
    fhir:MolecularSequence.referenceSeq.chromosome [ CodeableConcept ]; # 0..1 Chromosome containing genetic finding
    fhir:MolecularSequence.referenceSeq.genomeBuild [ string ]; # 0..1 The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
    fhir:MolecularSequence.referenceSeq.orientation [ code ]; # 0..1 sense | antisense
    fhir:MolecularSequence.referenceSeq.referenceSeqId [ CodeableConcept ]; # 0..1 Reference identifier
    fhir:MolecularSequence.referenceSeq.referenceSeqPointer [ Reference(MolecularSequence) ]; # 0..1 A pointer to another MolecularSequence entity as reference sequence
    fhir:MolecularSequence.referenceSeq.referenceSeqString [ string ]; # 0..1 A string to represent reference sequence
    fhir:MolecularSequence.referenceSeq.strand [ code ]; # 0..1 watson | crick
    fhir:MolecularSequence.referenceSeq.windowStart [ integer ]; # 0..1 Start position of the window on the  reference sequence
    fhir:MolecularSequence.referenceSeq.windowEnd [ integer ]; # 0..1 End position of the window on the reference sequence
  ];
  fhir:MolecularSequence.variant [ # 0..* Variant in sequence
    fhir:MolecularSequence.variant.start [ integer ]; # 0..1 Start position of the variant on the  reference sequence
    fhir:MolecularSequence.variant.end [ integer ]; # 0..1 End position of the variant on the reference sequence
    fhir:MolecularSequence.variant.observedAllele [ string ]; # 0..1 Allele that was observed
    fhir:MolecularSequence.variant.referenceAllele [ string ]; # 0..1 Allele in the reference sequence
    fhir:MolecularSequence.variant.cigar [ string ]; # 0..1 Extended CIGAR string for aligning the sequence with reference bases
    fhir:MolecularSequence.variant.variantPointer [ Reference(Observation) ]; # 0..1 Pointer to observed variant information
  ], ...;
  fhir:MolecularSequence.observedSeq [ string ]; # 0..1 Sequence that was observed
  fhir:MolecularSequence.quality [ # 0..* An set of value as quality of sequence
    fhir:MolecularSequence.quality.type [ code ]; # 1..1 indel | snp | unknown
    fhir:MolecularSequence.quality.standardSequence [ CodeableConcept ]; # 0..1 Standard sequence for comparison
    fhir:MolecularSequence.quality.start [ integer ]; # 0..1 Start position of the sequence
    fhir:MolecularSequence.quality.end [ integer ]; # 0..1 End position of the sequence
    fhir:MolecularSequence.quality.score [ Quantity ]; # 0..1 Quality score for the comparison
    fhir:MolecularSequence.quality.method [ CodeableConcept ]; # 0..1 Method to get quality
    fhir:MolecularSequence.quality.truthTP [ decimal ]; # 0..1 True positives from the perspective of the truth data
    fhir:MolecularSequence.quality.queryTP [ decimal ]; # 0..1 True positives from the perspective of the query data
    fhir:MolecularSequence.quality.truthFN [ decimal ]; # 0..1 False negatives
    fhir:MolecularSequence.quality.queryFP [ decimal ]; # 0..1 False positives
    fhir:MolecularSequence.quality.gtFP [ decimal ]; # 0..1 False positives where the non-REF alleles in the Truth and Query Call Sets match
    fhir:MolecularSequence.quality.precision [ decimal ]; # 0..1 Precision of comparison
    fhir:MolecularSequence.quality.recall [ decimal ]; # 0..1 Recall of comparison
    fhir:MolecularSequence.quality.fScore [ decimal ]; # 0..1 F-score
    fhir:MolecularSequence.quality.roc [ # 0..1 Receiver Operator Characteristic (ROC) Curve
      fhir:MolecularSequence.quality.roc.score [ integer ], ... ; # 0..* Genotype quality score
      fhir:MolecularSequence.quality.roc.numTP [ integer ], ... ; # 0..* Roc score true positive numbers
      fhir:MolecularSequence.quality.roc.numFP [ integer ], ... ; # 0..* Roc score false positive numbers
      fhir:MolecularSequence.quality.roc.numFN [ integer ], ... ; # 0..* Roc score false negative numbers
      fhir:MolecularSequence.quality.roc.precision [ decimal ], ... ; # 0..* Precision of the GQ score
      fhir:MolecularSequence.quality.roc.sensitivity [ decimal ], ... ; # 0..* Sensitivity of the GQ score
      fhir:MolecularSequence.quality.roc.fMeasure [ decimal ], ... ; # 0..* FScore of the GQ score
    ];
  ], ...;
  fhir:MolecularSequence.readCoverage [ integer ]; # 0..1 Average number of reads representing a given nucleotide in the reconstructed sequence
  fhir:MolecularSequence.repository [ # 0..* External repository which contains detailed report related with observedSeq in this resource
    fhir:MolecularSequence.repository.type [ code ]; # 1..1 directlink | openapi | login | oauth | other
    fhir:MolecularSequence.repository.url [ uri ]; # 0..1 URI of the repository
    fhir:MolecularSequence.repository.name [ string ]; # 0..1 Repository's name
    fhir:MolecularSequence.repository.datasetId [ string ]; # 0..1 Id of the dataset that used to call for dataset in repository
    fhir:MolecularSequence.repository.variantsetId [ string ]; # 0..1 Id of the variantset that used to call for variantset in repository
    fhir:MolecularSequence.repository.readsetId [ string ]; # 0..1 Id of the read
  ], ...;
  fhir:MolecularSequence.pointer [ Reference(MolecularSequence) ], ... ; # 0..* Pointer to next atomic sequence
  fhir:MolecularSequence.structureVariant [ # 0..* Structural variant
    fhir:MolecularSequence.structureVariant.variantType [ CodeableConcept ]; # 0..1 Structural variant change type
    fhir:MolecularSequence.structureVariant.exact [ boolean ]; # 0..1 Does the structural variant have base pair resolution breakpoints?
    fhir:MolecularSequence.structureVariant.length [ integer ]; # 0..1 Structural variant length
    fhir:MolecularSequence.structureVariant.outer [ # 0..1 Structural variant outer
      fhir:MolecularSequence.structureVariant.outer.start [ integer ]; # 0..1 Structural variant outer start
      fhir:MolecularSequence.structureVariant.outer.end [ integer ]; # 0..1 Structural variant outer end
    ];
    fhir:MolecularSequence.structureVariant.inner [ # 0..1 Structural variant inner
      fhir:MolecularSequence.structureVariant.inner.start [ integer ]; # 0..1 Structural variant inner start
      fhir:MolecularSequence.structureVariant.inner.end [ integer ]; # 0..1 Structural variant inner end
    ];
  ], ...;
]

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|4.1.0

MolecularSequence.referenceSeq.orientation

Change value set from http://hl7.org/fhir/ValueSet/orientation-type|4.0.0 to http://hl7.org/fhir/ValueSet/orientation-type|4.1.0

MolecularSequence.referenceSeq.strand

Change value set from http://hl7.org/fhir/ValueSet/strand-type|4.0.0 to http://hl7.org/fhir/ValueSet/strand-type|4.1.0

MolecularSequence.quality.type

Change value set from http://hl7.org/fhir/ValueSet/quality-type|4.0.0 to http://hl7.org/fhir/ValueSet/quality-type|4.1.0

MolecularSequence.repository.type

Change value set from http://hl7.org/fhir/ValueSet/repository-type|4.0.0 to http://hl7.org/fhir/ValueSet/repository-type|4.1.0

MolecularSequence.structureVariant.variantType

Change value set from http://loinc.org/vs/LL379-9|4.0.0 to http://loinc.org/vs/LL379-9|4.1.0

See the Full Difference for further information

This analysis is available as XML or JSON.

See R3 <--> R4 Conversion Maps (status = 14 tests that all execute ok. All tests pass round-trip testing and all r3 resources are valid.)

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

10.6.4.1 Terminology Bindings

Path	Definition	Type	Reference
MolecularSequence.type	Type if a sequence -- DNA, RNA, or amino acid sequence.	Required	sequenceType
MolecularSequence.referenceSeq.chromosome	Chromosome number for human.	Example	chromosome-human
MolecularSequence.referenceSeq.orientation	Type for orientation.	Required	orientationType
MolecularSequence.referenceSeq.referenceSeqId	Reference identifier.	Example	ENSEMBL
MolecularSequence.referenceSeq.strand	Type for strand.	Required	strandType
MolecularSequence.quality.type	Type for quality report.	Required	qualityType
MolecularSequence.quality.standardSequence	Reference identifier of the sequence that used to mark the quality of tested samples.	Example	FDA-StandardSequence
MolecularSequence.quality.method	The method used to evaluate the numerical quality of the observed sequence.	Example	FDA-Method
MolecularSequence.repository.type	Type for access of external URI.	Required	repositoryType
MolecularSequence.structureVariant.variantType	DNA change type.	Required	http://loinc.org/vs/LL379-9

Path

Definition

Type

Reference

MolecularSequence.type

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

Required

sequenceType

MolecularSequence.referenceSeq.chromosome

Chromosome number for human.

Example

chromosome-human

MolecularSequence.referenceSeq.orientation

Type for orientation.

Required

orientationType

MolecularSequence.referenceSeq.referenceSeqId

Reference identifier.

Example

ENSEMBL

MolecularSequence.referenceSeq.strand

Type for strand.

Required

strandType

MolecularSequence.quality.type

Type for quality report.

Required

qualityType

MolecularSequence.quality.standardSequence

Reference identifier of the sequence that used to mark the quality of tested samples.

Example

FDA-StandardSequence

MolecularSequence.quality.method

The method used to evaluate the numerical quality of the observed sequence.

Example

FDA-Method

MolecularSequence.repository.type

Type for access of external URI.

Required

repositoryType

MolecularSequence.structureVariant.variantType

DNA change type.

Required

http://loinc.org/vs/LL379-9

10.6.4.2 Constraints

Level

Location

Description

Expression

msq-3

Rule

(base)

Only 0 and 1 are valid for coordinateSystem

coordinateSystem = 1 or coordinateSystem = 0

msq-5

Rule

MolecularSequence.referenceSeq

GenomeBuild and chromosome must be both contained if either one of them is contained

(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())

msq-6

Rule

MolecularSequence.referenceSeq

Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;

(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1

10.6.5 Notes:

10.6.5.1 MolecularSequence Coordinate System

When saving the variant information, the nucleic acid will be numbered with order. Some files are using 0-based coordinates (e.g. BCD file format) while some files are using 1-based coordinates (e.g. VCF file format). The element coordinateSystem in MolecularSequence resource contains this information.

MolecularSequence.coordinateSystem constraints within two possible values: 0 for 0-based system, which will mark the sequence from number 0, while 1 for 1-based system, which will begin marking the first position with number 1. The significant difference between two system is the end position. In 0-based system, the end position is exclusive, which means the last position will not be contained in the sequence window while in 1-based system, the end position is inclusive , which means the last position is included in the sequence window. Note both systems has an inclusive start position.

For example, ACGTGCAT will be numbered from 1 to 8 in 1-based system and will be numbered from 0 to 8 in 0-based system to mark flanks (i.e. place between two Nucleotide). So the interval [3,5] in 1-based system is GTG while interval [2,5) in 0-based system is same segment GTG.

10.6.5.2 Choice of Strand

There are lots of definition concerning with the Directionality of DNA or RNA. Here we are using referenceSeq.orientation and referenceSeq.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').

10.6.5.3 String usage for reference sequence and observed sequence

We hope that string of observedSeq can be constrained more than just any normal string but with notation tables. Here we present what the nucleotide acid string should be constrained within the range:

A --> adenosine	M --> A C (amino)	U --> uridine	H --> A C T	V --> G C A
C --> cytidine	S --> G C (strong)	D --> G A T	K --> G T (keto)
G --> guanine	W --> A T (weak)	R --> G A (purine)	N --> A G C T (any)
T --> thymidine	B --> G T C	Y --> T C (pyrimidine)	- --> gap of indeterminate length

while the amino acid string should be constrained within the range:

A alanine	P proline	B aspartate or asparagine	Q glutamine
C cystine	R arginine	D aspartate	S serine
E glutamate	T threonine	F phenylalanine	U selenocysteine
G glycine	V valine	H histidine	W tryptophan
I isoleucine	Y tyrosine	K lysine	Z glutamate or glutamine
L leucine	X any	M methionine	* translation stop
N asparagine	- gap of indeterminate length

10.6.6 Search Parameters

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

Name	Type	Description	Expression	In Common
chromosome	token	Chromosome number of the reference sequence	MolecularSequence.referenceSeq.chromosome
chromosome-variant-coordinate	composite	Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.	On MolecularSequence.variant: chromosome: %resource.referenceSeq.chromosome variant-start: start variant-end: end
chromosome-window-coordinate	composite	Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.	On MolecularSequence.referenceSeq: chromosome: chromosome window-start: windowStart window-end: windowEnd
identifier	token	The unique identity for a particular sequence	MolecularSequence.identifier
patient	reference	The subject that the observation is about	MolecularSequence.patient (Patient)
referenceseqid	token	Reference Sequence of the sequence	MolecularSequence.referenceSeq.referenceSeqId
referenceseqid-variant-coordinate	composite	Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.	On MolecularSequence.variant: referenceseqid: %resource.referenceSeq.referenceSeqId variant-start: start variant-end: end
referenceseqid-window-coordinate	composite	Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.	On MolecularSequence.referenceSeq: referenceseqid: referenceSeqId window-start: windowStart window-end: windowEnd
type	token	Amino Acid Sequence/ DNA Sequence / RNA Sequence	MolecularSequence.type
variant-end	number	End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.	MolecularSequence.variant.end
variant-start	number	Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.	MolecularSequence.variant.start
window-end	number	End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.	MolecularSequence.referenceSeq.windowEnd
window-start	number	Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.	MolecularSequence.referenceSeq.windowStart