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FoundationShEx statement for sequence
PREFIX fhir: <http://hl7.org/fhir/>
PREFIX fhirvs: <http://hl7.org/fhir/ValueSet/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
BASE <http://hl7.org/fhir/shape/>
start=@<Sequence> AND {fhir:nodeRole [fhir:treeRoot]}
# Information about a biological sequence
<Sequence> CLOSED {
a [fhir:Sequence];
fhir:nodeRole [fhir:treeRoot]?;
fhir:Resource.id @<id>?; # Logical id of this artifact
fhir:Resource.meta @<Meta>?; # Metadata about the resource
fhir:Resource.implicitRules @<uri>?; # A set of rules under which this
# content was created
fhir:Resource.language @<code>?; # Language of the resource content
fhir:DomainResource.text @<Narrative>?; # Text summary of the resource, for
# human interpretation
fhir:DomainResource.contained @<Resource>*; # Contained, inline Resources
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:modifierExtension @<Extension>*; # Extensions that cannot be ignored
fhir:Sequence.identifier @<Identifier>*; # Unique ID for this particular
# sequence. This is a FHIR-defined
# id
fhir:Sequence.type @<code>?; # aa | dna | rna
fhir:Sequence.coordinateSystem @<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)
fhir:Sequence.patient @<Reference>?; # Who and/or what this is about
fhir:Sequence.specimen @<Reference>?; # Specimen used for sequencing
fhir:Sequence.device @<Reference>?; # The method for sequencing
fhir:Sequence.performer @<Reference>?; # Who should be responsible for test
# result
fhir:Sequence.quantity @<Quantity>?; # The number of copies of the
# seqeunce of interest. (RNASeq)
fhir:Sequence.referenceSeq @<Sequence.referenceSeq>?; # Reference sequence
fhir:Sequence.variant @<Sequence.variant>*; # Sequence variant
fhir:Sequence.observedSeq @<string>?; # Observed sequence
fhir:Sequence.quality @<Sequence.quality>*; # Sequence quality
fhir:Sequence.readCoverage @<integer>?; # Average number of reads
# representing a given nucleotide in
# the reconstructed sequence
fhir:Sequence.repository @<Sequence.repository>*; # External repository which contains
# detailed report related with
# observedSeq in this resource
fhir:Sequence.pointer @<Reference>*; # Pointer to next atomic sequence
fhir:index xsd:integer? # Relative position in a list
}
# Sequence quality
<Sequence.quality> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:modifierExtension @<Extension>*; # Extensions that cannot be ignored
fhir:Sequence.quality.type @<code> AND
{fhir:value @fhirvs:quality-type}; # indel | snp | unknown
fhir:Sequence.quality.standardSequence @<CodeableConcept>?; # Standard sequence for comparison
fhir:Sequence.quality.start @<integer>?; # Start position of the sequence
fhir:Sequence.quality.end @<integer>?; # End position of the sequence
fhir:Sequence.quality.score @<Quantity>?; # Quality score
fhir:Sequence.quality.method @<CodeableConcept>?; # Method for quality
fhir:Sequence.quality.truthTP @<decimal>?; # True positives from the
# perspective of the truth data
fhir:Sequence.quality.queryTP @<decimal>?; # True positives from the
# perspective of the query data
fhir:Sequence.quality.truthFN @<decimal>?; # False negatives
fhir:Sequence.quality.queryFP @<decimal>?; # False positives
fhir:Sequence.quality.gtFP @<decimal>?; # False positives where the non-REF
# alleles in the Truth and Query
# Call Sets match
fhir:Sequence.quality.precision @<decimal>?; # Precision
fhir:Sequence.quality.recall @<decimal>?; # Recall
fhir:Sequence.quality.fScore @<decimal>?; # F-score
fhir:index xsd:integer? # Relative position in a list
}
# External repository which contains detailed report related with observedSeq in this resource
<Sequence.repository> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:modifierExtension @<Extension>*; # Extensions that cannot be ignored
fhir:Sequence.repository.type @<code> AND
{fhir:value @fhirvs:repository-type}; # directlink | openapi | login |
# oauth | other
fhir:Sequence.repository.url @<uri>?; # URI of the repository
fhir:Sequence.repository.name @<string>?; # Name of the repository
fhir:Sequence.repository.datasetId @<string>?; # Id of the dataset that used to
# call for dataset in repository
fhir:Sequence.repository.variantsetId @<string>?; # Id of the variantset that used to
# call for variantset in repository
fhir:Sequence.repository.readsetId @<string>?; # Id of the read
fhir:index xsd:integer? # Relative position in a list
}
# Reference sequence
<Sequence.referenceSeq> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:modifierExtension @<Extension>*; # Extensions that cannot be ignored
fhir:Sequence.referenceSeq.chromosome @<CodeableConcept>?; # Chromosome containing genetic
# finding
fhir:Sequence.referenceSeq.genomeBuild @<string>?; # The Genome Build used for
# reference, following GRCh build
# versions e.g. 'GRCh 37'
fhir:Sequence.referenceSeq.referenceSeqId @<CodeableConcept>?; # Reference identifier
fhir:Sequence.referenceSeq.referenceSeqPointer @<Reference>?; # A Pointer to another Sequence
# entity as reference sequence
fhir:Sequence.referenceSeq.referenceSeqString @<string>?; # A Reference Sequence string
fhir:Sequence.referenceSeq.strand @<integer>?; # Directionality of DNA ( +1/-1)
fhir:Sequence.referenceSeq.windowStart @<integer>; # Start position of the window on
# the reference sequence
fhir:Sequence.referenceSeq.windowEnd @<integer>; # End position of the window on the
# reference sequence
fhir:index xsd:integer? # Relative position in a list
}
# Sequence variant
<Sequence.variant> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:modifierExtension @<Extension>*; # Extensions that cannot be ignored
fhir:Sequence.variant.start @<integer>?; # Start position of the variant on
# the reference sequence
fhir:Sequence.variant.end @<integer>?; # End position of the variant on the
# reference sequence
fhir:Sequence.variant.observedAllele @<string>?; # Allele that was observed
fhir:Sequence.variant.referenceAllele @<string>?; # Allele of reference sequence
fhir:Sequence.variant.cigar @<string>?; # Extended CIGAR string for aligning
# the sequence with reference bases
fhir:Sequence.variant.variantPointer @<Reference>?; # Pointer to observed variant
# information
fhir:index xsd:integer? # Relative position in a list
}
#---------------------- Data Types -------------------
# Metadata about a resource
<Meta> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Meta.versionId @<id>?; # Version specific identifier
fhir:Meta.lastUpdated @<instant>?; # When the resource version last
# changed
fhir:Meta.profile @<uri>*; # Profiles this resource claims to
# conform to
fhir:Meta.security @<Coding>*; # Security Labels applied to this
# resource
fhir:Meta.tag @<Coding>*; # Tags applied to this resource
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type code
<code> CLOSED {
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:string?; # Primitive value for code
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type string
<string> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:string MAXLENGTH 1048576?; # Primitive value for string
fhir:index xsd:integer? # Relative position in a list
}
# A reference from one resource to another
<Reference> CLOSED {
fhir:link IRI?;
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Reference.reference @<string>?; # Literal reference, Relative,
# internal or absolute URL
fhir:Reference.identifier @<Identifier>?; # Logical reference, when literal
# reference is not known
fhir:Reference.display @<string>?; # Text alternative for the resource
fhir:index xsd:integer? # Relative position in a list
}
# Base Resource
<Resource> {a .+;
fhir:Resource.id @<id>?; # Logical id of this artifact
fhir:Resource.meta @<Meta>?; # Metadata about the resource
fhir:Resource.implicitRules @<uri>?; # A set of rules under which this
# content was created
fhir:Resource.language @<code>?; # Language of the resource content
fhir:index xsd:integer?
}
# A measured or measurable amount
<Quantity> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Quantity.value @<decimal>?; # Numerical value (with implicit
# precision)
fhir:Quantity.comparator @<code> AND
{fhir:value @fhirvs:quantity-comparator}?; # < | <= | >= | > - how to
# understand the value
fhir:Quantity.unit @<string>?; # Unit representation
fhir:Quantity.system @<uri>?; # System that defines coded unit form
fhir:Quantity.code @<code>?; # Coded form of the unit
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type integer
<integer> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:int MININCLUSIVE "-2147483648"^^xsd:int MAXINCLUSIVE "2147483647"^^xsd:int?; # Primitive value for integer
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type uri
<uri> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:string?; # Primitive value for uri
fhir:index xsd:integer? # Relative position in a list
}
<Extension> {fhir:extension @<Extension>*;
fhir:index xsd:integer?
}
# An identifier intended for computation
<Identifier> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Identifier.use @<code> AND
{fhir:value @fhirvs:identifier-use}?; # usual | official | temp |
# secondary (If known)
fhir:Identifier.type @<CodeableConcept>?; # Description of identifier
fhir:Identifier.system @<uri>?; # The namespace for the identifier
fhir:Identifier.value @<string>?; # The value that is unique
fhir:Identifier.period @<Period>?; # Time period when id is/was valid
# for use
fhir:Identifier.assigner @<Reference>?; # Organization that issued id (may
# be just text)
fhir:index xsd:integer? # Relative position in a list
}
# A human-readable formatted text, including images
<Narrative> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Narrative.status @<code> AND
{fhir:value @fhirvs:narrative-status}; # generated | extensions |
# additional | empty
fhir:Narrative.div xsd:string; # Limited xhtml content
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type id
<id> CLOSED {
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:string?; # Primitive value for id
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type decimal
<decimal> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:decimal?; # Primitive value for decimal
fhir:index xsd:integer? # Relative position in a list
}
# Concept - reference to a terminology or just text
<CodeableConcept> CLOSED {
fhir:concept IRI*;
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:CodeableConcept.coding @<Coding>*; # Code defined by a terminology
# system
fhir:CodeableConcept.text @<string>?; # Plain text representation of the
# concept
fhir:index xsd:integer? # Relative position in a list
}
# Time range defined by start and end date/time
<Period> CLOSED {
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Period.start @<dateTime>?; # Starting time with inclusive
# boundary
fhir:Period.end @<dateTime>?; # End time with inclusive boundary,
# if not ongoing
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type instant
<instant> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:dateTime?; # Primitive value for instant
fhir:index xsd:integer? # Relative position in a list
}
# A reference to a code defined by a terminology system
<Coding> CLOSED {
fhir:concept IRI?;
fhir:Element.id @<string>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:Coding.system @<uri>?; # Identity of the terminology system
fhir:Coding.version @<string>?; # Version of the system - if relevant
fhir:Coding.code @<code>?; # Symbol in syntax defined by the
# system
fhir:Coding.display @<string>?; # Representation defined by the
# system
fhir:Coding.userSelected @<boolean>?; # If this coding was chosen directly
# by the user
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type dateTime
<dateTime> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:gYear OR xsd:gYearMonth OR xsd:date OR xsd:dateTime?; # Primitive value for dateTime
fhir:index xsd:integer? # Relative position in a list
}
# Primitive Type boolean
<boolean> CLOSED {
fhir:Element.id @<id>?; # xml:id (or equivalent in JSON)
fhir:extension @<Extension>*; # Additional Content defined by
# implementations
fhir:value xsd:boolean?; # Primitive value for boolean
fhir:index xsd:integer? # Relative position in a list
}
#---------------------- Reference Types -------------------
#---------------------- Value Sets ------------------------
# Type for quality report
fhirvs:quality-type ["indel" "snp" "unknown"]
# Identifies the purpose for this identifier, if known .
fhirvs:identifier-use ["usual" "official" "temp" "secondary"]
# Type for access of external uri
fhirvs:repository-type ["directlink" "openapi" "login" "oauth" "other"]
# The status of a resource narrative
fhirvs:narrative-status ["generated" "extensions" "additional" "empty"]
# How the Quantity should be understood and represented.
fhirvs:quantity-comparator ["<" "<=" ">=" ">"]
Usage note: every effort has been made to ensure that the ShEx files are correct and useful, but they are not a normative part of the specification.
© HL7.org 2011+. FHIR STU3 Candidate (v1.8.0-10605) generated on Mon, Dec 19, 2016 23:20-0500. QA Page
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