http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1

description: Raw data describing a biological sequence.
derivation: specialization
name: MolecularSequence
type: MolecularSequence
elements:
  patient: {short: Who and/or what this is about, isSummary: true, index: 3}
  structureVariant:
    short: Structural variant
    array: true
    isSummary: true
    index: 58
    elements:
      variantType:
        short: Structural variant change type
        binding: {strength: required, valueSet: 'http://loinc.org/vs/LL379-9|4.0.1'}
        isSummary: true
        index: 59
      exact: {short: 'Does the structural variant have base pair resolution breakpoints?', isSummary: true, index: 60}
      length: {short: Structural variant length, isSummary: true, index: 61}
      outer:
        short: Structural variant outer
        isSummary: true
        index: 62
        elements:
          start: {short: Structural variant outer start, isSummary: true, index: 63}
          end: {short: Structural variant outer end, isSummary: true, index: 64}
      inner:
        short: Structural variant inner
        isSummary: true
        index: 65
        elements:
          start: {short: Structural variant inner start, isSummary: true, index: 66}
          end: {short: Structural variant inner end, isSummary: true, index: 67}
  repository:
    short: External repository which contains detailed report related with observedSeq in this resource
    array: true
    isSummary: true
    index: 50
    elements:
      type:
        short: directlink | openapi | login | oauth | other
        binding: {strength: required, valueSet: 'http://hl7.org/fhir/ValueSet/repository-type|4.0.1'}
        isSummary: true
        index: 51
      url: {short: URI of the repository, isSummary: true, index: 52}
      name: {short: Repository's name, isSummary: true, index: 53}
      datasetId: {short: Id of the dataset that used to call for dataset in repository, isSummary: true, index: 54}
      variantsetId: {short: Id of the variantset that used to call for variantset in repository, isSummary: true, index: 55}
      readsetId: {short: Id of the read, isSummary: true, index: 56}
    required: [type]
  variant:
    short: Variant in sequence
    array: true
    isSummary: true
    index: 18
    elements:
      start: {short: Start position of the variant on the  reference sequence, isSummary: true, index: 19}
      end: {short: End position of the variant on the reference sequence, isSummary: true, index: 20}
      observedAllele: {short: Allele that was observed, isSummary: true, index: 21}
      referenceAllele: {short: Allele in the reference sequence, isSummary: true, index: 22}
      cigar: {short: Extended CIGAR string for aligning the sequence with reference bases, isSummary: true, index: 23}
      variantPointer: {short: Pointer to observed variant information, isSummary: true, index: 24}
  specimen: {short: Specimen used for sequencing, isSummary: true, index: 4}
  type:
    short: aa | dna | rna
    binding: {strength: required, valueSet: 'http://hl7.org/fhir/ValueSet/sequence-type|4.0.1'}
    isSummary: true
    index: 1
  pointer: {short: Pointer to next atomic sequence, array: true, isSummary: true, index: 57}
  observedSeq: {short: Sequence that was observed, isSummary: true, index: 25}
  identifier: {short: Unique ID for this particular sequence. This is a FHIR-defined id, array: true, isSummary: true, index: 0}
  quality:
    short: An set of value as quality of sequence
    array: true
    isSummary: true
    index: 26
    elements:
      truthTP: {short: True positives from the perspective of the truth data, isSummary: true, index: 33}
      fScore: {short: F-score, isSummary: true, index: 40}
      truthFN: {short: False negatives, isSummary: true, index: 35}
      queryFP: {short: False positives, isSummary: true, index: 36}
      method:
        short: Method to get quality
        binding: {strength: example, valueSet: 'http://hl7.org/fhir/ValueSet/sequence-quality-method'}
        isSummary: true
        index: 32
      precision: {short: Precision of comparison, isSummary: true, index: 38}
      start: {short: Start position of the sequence, isSummary: true, index: 29}
      queryTP: {short: True positives from the perspective of the query data, isSummary: true, index: 34}
      type:
        short: indel | snp | unknown
        binding: {strength: required, valueSet: 'http://hl7.org/fhir/ValueSet/quality-type|4.0.1'}
        isSummary: true
        index: 27
      recall: {short: Recall of comparison, isSummary: true, index: 39}
      roc:
        short: Receiver Operator Characteristic (ROC) Curve
        isSummary: true
        index: 41
        elements:
          score: {short: Genotype quality score, array: true, isSummary: true, index: 42}
          numTP: {short: Roc score true positive numbers, array: true, isSummary: true, index: 43}
          numFP: {short: Roc score false positive numbers, array: true, isSummary: true, index: 44}
          numFN: {short: Roc score false negative numbers, array: true, isSummary: true, index: 45}
          precision: {short: Precision of the GQ score, array: true, isSummary: true, index: 46}
          sensitivity: {short: Sensitivity of the GQ score, array: true, isSummary: true, index: 47}
          fMeasure: {short: FScore of the GQ score, array: true, isSummary: true, index: 48}
      score: {short: Quality score for the comparison, isSummary: true, index: 31}
      end: {short: End position of the sequence, isSummary: true, index: 30}
      standardSequence:
        short: Standard sequence for comparison
        binding: {strength: example, valueSet: 'http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence'}
        isSummary: true
        index: 28
      gtFP: {short: False positives where the non-REF alleles in the Truth and Query Call Sets match, isSummary: true, index: 37}
    required: [type]
  device: {short: The method for sequencing, isSummary: true, index: 5}
  quantity: {short: The number of copies of the sequence of interest.  (RNASeq), isSummary: true, index: 7}
  coordinateSystem: {short: '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)', isSummary: true, index: 2}
  referenceSeq:
    constraint:
      msq-6: {human: 'Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer;  4. referenceSeqString;', severity: error, expression: (genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1}
      msq-5: {human: GenomeBuild and chromosome must be both contained if either one of them is contained, severity: error, expression: (chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())}
    short: A sequence used as reference
    isSummary: true
    index: 8
    elements:
      chromosome:
        short: Chromosome containing genetic finding
        binding: {strength: example, valueSet: 'http://hl7.org/fhir/ValueSet/chromosome-human'}
        isSummary: true
        index: 9
      referenceSeqId:
        short: Reference identifier
        binding: {strength: example, valueSet: 'http://hl7.org/fhir/ValueSet/sequence-referenceSeq'}
        isSummary: true
        index: 12
      windowEnd: {short: End position of the window on the reference sequence, isSummary: true, index: 17}
      strand:
        short: watson | crick
        binding: {strength: required, valueSet: 'http://hl7.org/fhir/ValueSet/strand-type|4.0.1'}
        isSummary: true
        index: 15
      genomeBuild: {short: 'The Genome Build used for reference, following GRCh build versions e.g. ''GRCh 37''', isSummary: true, index: 10}
      orientation:
        short: sense | antisense
        binding: {strength: required, valueSet: 'http://hl7.org/fhir/ValueSet/orientation-type|4.0.1'}
        isSummary: true
        index: 11
      referenceSeqPointer: {short: A pointer to another MolecularSequence entity as reference sequence, isSummary: true, index: 13}
      referenceSeqString: {short: A string to represent reference sequence, isSummary: true, index: 14}
      windowStart: {short: Start position of the window on the  reference sequence, isSummary: true, index: 16}
  performer: {short: Who should be responsible for test result, isSummary: true, index: 6}
  readCoverage: {short: Average number of reads representing a given nucleotide in the reconstructed sequence, isSummary: true, index: 49}
class: resource
kind: resource
url: http://hl7.org/fhir/StructureDefinition/MolecularSequence
base: http://hl7.org/fhir/StructureDefinition/DomainResource
version: 4.0.1
required: [coordinateSystem]