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 @