PREFIX fhir: PREFIX fhirvs: PREFIX xsd: BASE start=@ AND {fhir:nodeRole [fhir:treeRoot]} # Information about a biological sequence CLOSED { a [fhir:MolecularSequence]; fhir:nodeRole [fhir:treeRoot]?; fhir:Resource.id id?; # Logical id of this artifact fhir:Resource.meta @?; # Metadata about the resource fhir:Resource.implicitRules @?; # A set of rules under which this # content was created fhir:Resource.language @?; # Language of the resource content fhir:DomainResource.text @?; # Text summary of the resource, for # human interpretation fhir:DomainResource.contained @*; # Contained, inline Resources fhir:DomainResource.extension @*; # Additional content defined by # implementations fhir:DomainResource.modifierExtension @*; # Extensions that cannot be ignored fhir:MolecularSequence.identifier @*; # Unique ID for this particular # sequence. This is a FHIR-defined # id fhir:MolecularSequence.type @ AND {fhir:value @fhirvs:sequence-type}?; # aa | dna | rna fhir:MolecularSequence.coordinateSystem @; # 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 @?; # Who and/or what this is about fhir:MolecularSequence.specimen @?; # Specimen used for sequencing fhir:MolecularSequence.device @?; # The method for sequencing fhir:MolecularSequence.performer @?; # Who should be responsible for test # result fhir:MolecularSequence.quantity @?; # The number of copies of the # sequence of interest. (RNASeq) fhir:MolecularSequence.referenceSeq @?; # A sequence used as reference fhir:MolecularSequence.variant @*; # Variant in sequence fhir:MolecularSequence.observedSeq @?; # Sequence that was observed fhir:MolecularSequence.quality @*; # An set of value as quality of # sequence fhir:MolecularSequence.readCoverage @?; # Average number of reads # representing a given nucleotide in # the reconstructed sequence fhir:MolecularSequence.repository @*; # External repository which contains # detailed report related with # observedSeq in this resource fhir:MolecularSequence.pointer @*; # Pointer to next atomic sequence fhir:MolecularSequence.structureVariant @*; # Structural variant fhir:index xsd:integer? # Relative position in a list } # Variant in sequence CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.variant.start @?; # Start position of the variant on # the reference sequence fhir:MolecularSequence.variant.end @?; # End position of the variant on the # reference sequence fhir:MolecularSequence.variant.observedAllele @?; # Allele that was observed fhir:MolecularSequence.variant.referenceAllele @?; # Allele in the reference sequence fhir:MolecularSequence.variant.cigar @?; # Extended CIGAR string for aligning # the sequence with reference bases fhir:MolecularSequence.variant.variantPointer @?; # Pointer to observed variant # information fhir:index xsd:integer? # Relative position in a list } # External repository which contains detailed report related with observedSeq in this resource CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.repository.type @ AND {fhir:value @fhirvs:repository-type}; # directlink | openapi | login | # oauth | other fhir:MolecularSequence.repository.url @?; # URI of the repository fhir:MolecularSequence.repository.name @?; # Repository's name fhir:MolecularSequence.repository.datasetId @?; # Id of the dataset that used to # call for dataset in repository fhir:MolecularSequence.repository.variantsetId @?; # Id of the variantset that used to # call for variantset in repository fhir:MolecularSequence.repository.readsetId @?; # Id of the read fhir:index xsd:integer? # Relative position in a list } # Structural variant CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.structureVariant.variantType @?; # Structural variant change type fhir:MolecularSequence.structureVariant.exact @?; # Does the structural variant have # base pair resolution breakpoints? fhir:MolecularSequence.structureVariant.length @?; # Structural variant length fhir:MolecularSequence.structureVariant.outer @?; # Structural variant outer fhir:MolecularSequence.structureVariant.inner @?; # Structural variant inner fhir:index xsd:integer? # Relative position in a list } # An set of value as quality of sequence CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.quality.type @ AND {fhir:value @fhirvs:quality-type}; # indel | snp | unknown fhir:MolecularSequence.quality.standardSequence @?; # Standard sequence for comparison fhir:MolecularSequence.quality.start @?; # Start position of the sequence fhir:MolecularSequence.quality.end @?; # End position of the sequence fhir:MolecularSequence.quality.score @?; # Quality score for the comparison fhir:MolecularSequence.quality.method @?; # Method to get quality fhir:MolecularSequence.quality.truthTP @?; # True positives from the # perspective of the truth data fhir:MolecularSequence.quality.queryTP @?; # True positives from the # perspective of the query data fhir:MolecularSequence.quality.truthFN @?; # False negatives fhir:MolecularSequence.quality.queryFP @?; # False positives fhir:MolecularSequence.quality.gtFP @?; # False positives where the non-REF # alleles in the Truth and Query # Call Sets match fhir:MolecularSequence.quality.precision @?; # Precision of comparison fhir:MolecularSequence.quality.recall @?; # Recall of comparison fhir:MolecularSequence.quality.fScore @?; # F-score fhir:MolecularSequence.quality.roc @?; # Receiver Operator Characteristic # (ROC) Curve fhir:index xsd:integer? # Relative position in a list } # A sequence used as reference CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.referenceSeq.chromosome @?; # Chromosome containing genetic # finding fhir:MolecularSequence.referenceSeq.genomeBuild @?; # The Genome Build used for # reference, following GRCh build # versions e.g. 'GRCh 37' fhir:MolecularSequence.referenceSeq.orientation @ AND {fhir:value @fhirvs:orientation-type}?; # sense | antisense fhir:MolecularSequence.referenceSeq.referenceSeqId @?; # Reference identifier fhir:MolecularSequence.referenceSeq.referenceSeqPointer @?; # A pointer to another # MolecularSequence entity as # reference sequence fhir:MolecularSequence.referenceSeq.referenceSeqString @?; # A string to represent reference # sequence fhir:MolecularSequence.referenceSeq.strand @ AND {fhir:value @fhirvs:strand-type}?; # watson | crick fhir:MolecularSequence.referenceSeq.windowStart @?; # Start position of the window on # the reference sequence fhir:MolecularSequence.referenceSeq.windowEnd @?; # End position of the window on the # reference sequence fhir:index xsd:integer? # Relative position in a list } # Structural variant inner CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.structureVariant.inner.start @?; # Structural variant inner start fhir:MolecularSequence.structureVariant.inner.end @?; # Structural variant inner end fhir:index xsd:integer? # Relative position in a list } # Receiver Operator Characteristic (ROC) Curve CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.quality.roc.score @*; # Genotype quality score fhir:MolecularSequence.quality.roc.numTP @*; # Roc score true positive numbers fhir:MolecularSequence.quality.roc.numFP @*; # Roc score false positive numbers fhir:MolecularSequence.quality.roc.numFN @*; # Roc score false negative numbers fhir:MolecularSequence.quality.roc.precision @*; # Precision of the GQ score fhir:MolecularSequence.quality.roc.sensitivity @*; # Sensitivity of the GQ score fhir:MolecularSequence.quality.roc.fMeasure @*; # FScore of the GQ score fhir:index xsd:integer? # Relative position in a list } # Structural variant outer CLOSED { fhir:Element.id string?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:BackboneElement.modifierExtension @*; # Extensions that cannot be ignored # even if unrecognized fhir:MolecularSequence.structureVariant.outer.start @?; # Structural variant outer start fhir:MolecularSequence.structureVariant.outer.end @?; # Structural variant outer end fhir:index xsd:integer? # Relative position in a list } #---------------------- Data Types ------------------- # Metadata about a resource CLOSED { fhir:Element.id id?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:Meta.versionId @?; # Version specific identifier fhir:Meta.lastUpdated @?; # When the resource version last # changed fhir:Meta.source @?; # Identifies where the resource # comes from fhir:Meta.profile @*; # Profiles this resource claims to # conform to fhir:Meta.security @*; # Security Labels applied to this # resource fhir:Meta.tag @*; # Tags applied to this resource fhir:index xsd:integer? # Relative position in a list } # Primitive Type code CLOSED { fhir:Element.id string?; # xml:id (or equivalent in JSON) fhir:Element.extension @*; # Additional content defined by # implementations fhir:value code?; # Primitive value for code fhir:index xsd:integer? # Relative position in a list } # Primitive Type string CLOSED { fhir:Element.id string?; # xml:id (or equivalent in JSON) fhir:Element.extension @*; # Additional content defined by # implementations fhir:value string MAXLENGTH 1048576?; # Primitive value for string fhir:index xsd:integer? # Relative position in a list } # A reference from one resource to another CLOSED { fhir:link IRI?; fhir:Element.id id?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:Reference.reference @?; # Literal reference, Relative, # internal or absolute URL fhir:Reference.type @?; # Type the reference refers to (e.g. # "Patient") fhir:Reference.identifier @?; # Logical reference, when literal # reference is not known fhir:Reference.display @?; # Text alternative for the resource fhir:index xsd:integer? # Relative position in a list } # Base Resource {a .+; fhir:Resource.id id?; # Logical id of this artifact fhir:Resource.meta @?; # Metadata about the resource fhir:Resource.implicitRules @?; # A set of rules under which this # content was created fhir:Resource.language @?; # Language of the resource content fhir:index xsd:integer? } # A measured or measurable amount CLOSED { fhir:Element.id id?; # Unique id for inter-element # referencing fhir:Element.extension @*; # Additional content defined by # implementations fhir:Quantity.value @?; # Numerical value (with implicit # precision) fhir:Quantity.comparator @ AND {fhir:value @fhirvs:quantity-comparator}?; # < | <= | >= | > - how to # understand the value fhir:Quantity.unit @?; # Unit representation fhir:Quantity.system @?; # System that defines coded unit form fhir:Quantity.code @?; # Coded form of the unit fhir:index xsd:integer? # Relative position in a list } # Primitive Type integer CLOSED { fhir:Element.id string?; # xml:id (or equivalent in JSON) fhir:Element.extension @*; # Additional content defined by # implementations fhir:value integer MININCLUSIVE -2147483648 MAXINCLUSIVE 2147483647?; # Primitive value for integer fhir:index xsd:integer? # Relative position in a list } # Primitive Type uri CLOSED { fhir:Element.id string?; # xml:id (or equivalent in JSON) fhir:Element.extension @*; # Additional content defined by # implementations fhir:value uri?; # Primitive value for uri fhir:index xsd:integer? # Relative position in a list } # Optional Extensions Element CLOSED { fhir:Element.id id?; fhir:Element.extension @*; fhir:Extension.url uri; ( fhir:Extension.valueBase64Binary @ | fhir:Extension.valueBoolean @ | fhir:Extension.valueCanonical @ | fhir:Extension.valueCode @ | fhir:Extension.valueDate @ | fhir:Extension.valueDateTime @ | fhir:Extension.valueDecimal @ | fhir:Extension.valueId @ | fhir:Extension.valueInstant @ | fhir:Extension.valueInteger @ | fhir:Extension.valueMarkdown @ | fhir:Extension.valueOid @ | fhir:Extension.valuePositiveInt @ | fhir:Extension.valueString @ | fhir:Extension.valueTime @