Sequence.shex

ShEx 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:DomainResource.extension @<Extension>*;  # Additional Content defined by 
                                            # implementations 
    fhir:DomainResource.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>?;  # A sequence used as reference
    fhir:Sequence.variant @<Sequence.variant>*;  # Variant in sequence
    fhir:Sequence.observedSeq @<string>?;   # Sequence that was observed
    fhir:Sequence.quality @<Sequence.quality>*;  # An set of value as quality of 
                                            # sequence 
    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
}

# An set of value as quality of sequence
<Sequence.quality> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:BackboneElement.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 for the comparison
    fhir:Sequence.quality.method @<CodeableConcept>?;  # Method to get 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 of comparison
    fhir:Sequence.quality.recall @<decimal>?;  # Recall of comparison
    fhir:Sequence.quality.fScore @<decimal>?;  # F-score
    fhir:index xsd:integer?                 # Relative position in a list
}

# Variant in sequence
<Sequence.variant> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:BackboneElement.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 in the 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
}

# 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:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:BackboneElement.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>?;  # Repository's name
    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
}

# A sequence used as reference
<Sequence.referenceSeq> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:BackboneElement.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 string to represent reference 
                                            # sequence 
    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
}

#---------------------- Data Types -------------------

# Metadata about a resource
<Meta> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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 @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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:Element.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:Element.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 @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:integer MININCLUSIVE "-2147483648"^^xsd:integer MAXINCLUSIVE "2147483647"^^xsd:integer?;  # Primitive value for integer
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type uri
<uri> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:string?;                 # Primitive value for uri
    fhir:index xsd:integer?                 # Relative position in a list
}

# Optional Extensions Element
<Extension> CLOSED {
    fhir:Element.id @<string>?; 
    fhir:Element.extension @<Extension>*; 
    fhir:Extension.url @<uri>; 
    ( 
        fhir:Extension.valueBase64Binary @<base64Binary>  |
        fhir:Extension.valueBoolean @<boolean>  |
        fhir:Extension.valueCode @<code>  |
        fhir:Extension.valueDate @<date>  |
        fhir:Extension.valueDateTime @<dateTime>  |
        fhir:Extension.valueDecimal @<decimal>  |
        fhir:Extension.valueId @<id>  |
        fhir:Extension.valueInstant @<instant>  |
        fhir:Extension.valueInteger @<integer>  |
        fhir:Extension.valueMarkdown @<markdown>  |
        fhir:Extension.valueOid @<oid>  |
        fhir:Extension.valuePositiveInt @<positiveInt>  |
        fhir:Extension.valueString @<string>  |
        fhir:Extension.valueTime @<time>  |
        fhir:Extension.valueUnsignedInt @<unsignedInt>  |
        fhir:Extension.valueUri @<uri>  |
        fhir:Extension.valueAddress @<Address>  |
        fhir:Extension.valueAge @<Age>  |
        fhir:Extension.valueAnnotation @<Annotation>  |
        fhir:Extension.valueAttachment @<Attachment>  |
        fhir:Extension.valueCodeableConcept @<CodeableConcept>  |
        fhir:Extension.valueCoding @<Coding>  |
        fhir:Extension.valueContactPoint @<ContactPoint>  |
        fhir:Extension.valueCount @<Count>  |
        fhir:Extension.valueDistance @<Distance>  |
        fhir:Extension.valueDuration @<Duration>  |
        fhir:Extension.valueHumanName @<HumanName>  |
        fhir:Extension.valueIdentifier @<Identifier>  |
        fhir:Extension.valueMoney @<Money>  |
        fhir:Extension.valuePeriod @<Period>  |
        fhir:Extension.valueQuantity @<Quantity>  |
        fhir:Extension.valueRange @<Range>  |
        fhir:Extension.valueRatio @<Ratio>  |
        fhir:Extension.valueReference @<Reference>  |
        fhir:Extension.valueSampledData @<SampledData>  |
        fhir:Extension.valueSignature @<Signature>  |
        fhir:Extension.valueTiming @<Timing>  |
        fhir:Extension.valueMeta @<Meta> 
    )?;
    fhir:index xsd:integer?                 # Relative position in a list
}

# An identifier intended for computation
<Identifier> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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 
                                            # value 
    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:Element.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:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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 @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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 {
    a NONLITERAL*;
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# Primitive Type date
<date> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:gYear OR xsd:gYearMonth OR xsd:date?;  # Primitive value for date
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type dateTime
<dateTime> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# An address expressed using postal conventions (as opposed to GPS or other location definition formats)
<Address> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Address.use @<code> AND
    	{fhir:value @fhirvs:address-use}?;  # home | work | temp | old - purpose 
                                            # of this address 
    fhir:Address.type @<code> AND
    	{fhir:value @fhirvs:address-type}?;  # postal | physical | both
    fhir:Address.text @<string>?;           # Text representation of the address
    fhir:Address.line @<string>*;           # Street name, number, direction & 
                                            # P.O. Box etc. 
    fhir:Address.city @<string>?;           # Name of city, town etc.
    fhir:Address.district @<string>?;       # District name (aka county)
    fhir:Address.state @<string>?;          # Sub-unit of country (abbreviations 
                                            # ok) 
    fhir:Address.postalCode @<string>?;     # Postal code for area
    fhir:Address.country @<string>?;        # Country (e.g. can be ISO 3166 2 or 
                                            # 3 letter code) 
    fhir:Address.period @<Period>?;         # Time period when address was/is in 
                                            # use 
    fhir:index xsd:integer?                 # Relative position in a list
}

# Content in a format defined elsewhere
<Attachment> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Attachment.contentType @<code>?;   # Mime type of the content, with 
                                            # charset etc. 
    fhir:Attachment.language @<code>?;      # Human language of the content 
                                            # (BCP-47) 
    fhir:Attachment.data @<base64Binary>?;  # Data inline, base64ed
    fhir:Attachment.url @<uri>?;            # Uri where the data can be found
    fhir:Attachment.size @<unsignedInt>?;   # Number of bytes of content (if url 
                                            # provided) 
    fhir:Attachment.hash @<base64Binary>?;  # Hash of the data (sha-1, base64ed)
    fhir:Attachment.title @<string>?;       # Label to display in place of the 
                                            # data 
    fhir:Attachment.creation @<dateTime>?;  # Date attachment was first created
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type oid
<oid> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:string?;                 # Primitive value for oid
    fhir:index xsd:integer?                 # Relative position in a list
}

# A measured or measurable amount
<Count> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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 instant
<instant> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:dateTime?;               # Primitive value for instant
    fhir:index xsd:integer?                 # Relative position in a list
}

# Details of a Technology mediated contact point (phone, fax, email, etc.)
<ContactPoint> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:ContactPoint.system @<code> AND
    	{fhir:value @fhirvs:contact-point-system}?;  # phone | fax | email | pager | url 
                                            # | sms | other 
    fhir:ContactPoint.value @<string>?;     # The actual contact point details
    fhir:ContactPoint.use @<code> AND
    	{fhir:value @fhirvs:contact-point-use}?;  # home | work | temp | old | mobile 
                                            # - purpose of this contact point 
    fhir:ContactPoint.rank @<positiveInt>?;  # Specify preferred order of use (1 
                                            # = highest) 
    fhir:ContactPoint.period @<Period>?;    # Time period when the contact point 
                                            # was/is in use 
    fhir:index xsd:integer?                 # Relative position in a list
}

# Name of a human - parts and usage
<HumanName> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:HumanName.use @<code> AND
    	{fhir:value @fhirvs:name-use}?;  # usual | official | temp | nickname 
                                            # | anonymous | old | maiden 
    fhir:HumanName.text @<string>?;         # Text representation of the full 
                                            # name 
    fhir:HumanName.family @<string>?;       # Family name (often called 
                                            # 'Surname') 
    fhir:HumanName.given @<string>*;        # Given names (not always 'first'). 
                                            # Includes middle names 
    fhir:HumanName.prefix @<string>*;       # Parts that come before the name
    fhir:HumanName.suffix @<string>*;       # Parts that come after the name
    fhir:HumanName.period @<Period>?;       # Time period when name was/is in use
    fhir:index xsd:integer?                 # Relative position in a list
}

# An amount of economic utility in some recognized currency
<Money> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# A reference to a code defined by a terminology system
<Coding> CLOSED {
    a NONLITERAL?;
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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 markdown
<markdown> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:string?;                 # Primitive value for markdown
    fhir:index xsd:integer?                 # Relative position in a list
}

# A series of measurements taken by a device
<SampledData> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:SampledData.origin @<SimpleQuantity>;  # Zero value and units
    fhir:SampledData.period @<decimal>;     # Number of milliseconds between 
                                            # samples 
    fhir:SampledData.factor @<decimal>?;    # Multiply data by this before 
                                            # adding to origin 
    fhir:SampledData.lowerLimit @<decimal>?;  # Lower limit of detection
    fhir:SampledData.upperLimit @<decimal>?;  # Upper limit of detection
    fhir:SampledData.dimensions @<positiveInt>;  # Number of sample points at each 
                                            # time point 
    fhir:SampledData.data @<string>;        # Decimal values with spaces, or "E" 
                                            # | "U" | "L" 
    fhir:index xsd:integer?                 # Relative position in a list
}

# A ratio of two Quantity values - a numerator and a denominator
<Ratio> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Ratio.numerator @<Quantity>?;      # Numerator value
    fhir:Ratio.denominator @<Quantity>?;    # Denominator value
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type positiveInt
<positiveInt> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:positiveInteger?;        # Primitive value for positiveInt
    fhir:index xsd:integer?                 # Relative position in a list
}

# A duration of time during which an organism (or a process) has existed
<Age> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# A length - a value with a unit that is a physical distance
<Distance> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# Time range defined by start and end date/time
<Period> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# A length of time
<Duration> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.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
}

# Set of values bounded by low and high
<Range> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Range.low @<SimpleQuantity>?;      # Low limit
    fhir:Range.high @<SimpleQuantity>?;     # High limit
    fhir:index xsd:integer?                 # Relative position in a list
}

# Text node with attribution
<Annotation> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    (                                       # Individual responsible for the 
                                            # annotation 
        fhir:Annotation.authorReference @<Reference>  |
        fhir:Annotation.authorReference @<Reference>  |
        fhir:Annotation.authorReference @<Reference>  |
        fhir:Annotation.authorString @<string> 
    )?;
    fhir:Annotation.time @<dateTime>?;      # When the annotation was made
    fhir:Annotation.text @<string>;         # The annotation  - text content
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type boolean
<boolean> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:boolean?;                # Primitive value for boolean
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type base64Binary
<base64Binary> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:base64Binary?;           # Primitive value for base64Binary
    fhir:index xsd:integer?                 # Relative position in a list
}

# A digital Signature - XML DigSig, JWT, Graphical image of signature, etc.
<Signature> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Signature.type @<Coding>+;         # Indication of the reason the 
                                            # entity signed the object(s) 
    fhir:Signature.when @<instant>;         # When the signature was created
    (                                       # Who signed
        fhir:Signature.whoUri @<uri>  |
        fhir:Signature.whoReference @<Reference>  |
        fhir:Signature.whoReference @<Reference>  |
        fhir:Signature.whoReference @<Reference>  |
        fhir:Signature.whoReference @<Reference>  |
        fhir:Signature.whoReference @<Reference> 
    );
    (                                       # The party represented
        fhir:Signature.onBehalfOfUri @<uri>  |
        fhir:Signature.onBehalfOfReference @<Reference>  |
        fhir:Signature.onBehalfOfReference @<Reference>  |
        fhir:Signature.onBehalfOfReference @<Reference>  |
        fhir:Signature.onBehalfOfReference @<Reference>  |
        fhir:Signature.onBehalfOfReference @<Reference> 
    )?;
    fhir:Signature.contentType @<code>?;    # The technical format of the 
                                            # signature 
    fhir:Signature.blob @<base64Binary>?;   # The actual signature content (XML 
                                            # DigSig. JWT, picture, etc.) 
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type unsignedInt
<unsignedInt> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:nonNegativeInteger?;     # Primitive value for unsignedInt
    fhir:index xsd:integer?                 # Relative position in a list
}

# Primitive Type time
<time> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:time?;                   # Primitive value for time
    fhir:index xsd:integer?                 # Relative position in a list
}

# A timing schedule that specifies an event that may occur multiple times
<Timing> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Timing.event @<dateTime>*;         # When the event occurs
    fhir:Timing.repeat @<Timing.repeat>?;   # When the event is to occur
    fhir:Timing.code @<CodeableConcept>?;   # BID | TID | QID | AM | PM | QD | 
                                            # QOD | Q4H | Q6H + 
    fhir:index xsd:integer?                 # Relative position in a list
}

# A fixed quantity (no comparator)
<SimpleQuantity> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    fhir:Quantity.value @<decimal>?;        # Numerical value (with implicit 
                                            # precision) 
    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
}

# When the event is to occur
<Timing.repeat> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:Element.extension @<Extension>*;   # Additional Content defined by 
                                            # implementations 
    (                                       # Length/Range of lengths, or (Start 
                                            # and/or end) limits 
        fhir:Timing.repeat.boundsDuration @<Duration>  |
        fhir:Timing.repeat.boundsRange @<Range>  |
        fhir:Timing.repeat.boundsPeriod @<Period> 
    )?;
    fhir:Timing.repeat.count @<integer>?;   # Number of times to repeat
    fhir:Timing.repeat.countMax @<integer>?;  # Maximum number of times to repeat
    fhir:Timing.repeat.duration @<decimal>?;  # How long when it happens
    fhir:Timing.repeat.durationMax @<decimal>?;  # How long when it happens (Max)
    fhir:Timing.repeat.durationUnit @<code> AND
    	{fhir:value @fhirvs:units-of-time}?;  # s | min | h | d | wk | mo | a - 
                                            # unit of time (UCUM) 
    fhir:Timing.repeat.frequency @<integer>?;  # Event occurs frequency times per 
                                            # period 
    fhir:Timing.repeat.frequencyMax @<integer>?;  # Event occurs up to frequencyMax 
                                            # times per period 
    fhir:Timing.repeat.period @<decimal>?;  # Event occurs frequency times per 
                                            # period 
    fhir:Timing.repeat.periodMax @<decimal>?;  # Upper limit of period (3-4 hours)
    fhir:Timing.repeat.periodUnit @<code> AND
    	{fhir:value @fhirvs:units-of-time}?;  # s | min | h | d | wk | mo | a - 
                                            # unit of time (UCUM) 
    fhir:Timing.repeat.dayOfWeek @<code> AND
    	{fhir:value @fhirvs:days-of-week}*;  # mon | tue | wed | thu | fri | sat 
                                            # | sun 
    fhir:Timing.repeat.timeOfDay @<time>*;  # Time of day for action
    fhir:Timing.repeat.when @<code> AND
    	{fhir:value @fhirvs:event-timing}*;  # Regular life events the event is 
                                            # tied to 
    fhir:Timing.repeat.offset @<unsignedInt>?;  # Minutes from event (before or 
                                            # after) 
    fhir:index xsd:integer?                 # Relative position in a list
}

#---------------------- Reference Types -------------------

#---------------------- Value Sets ------------------------

# The status of a resource narrative
fhirvs:narrative-status ["generated" "extensions" "additional" "empty"]

# Use of contact point
fhirvs:contact-point-use ["home" "work" "temp" "old" "mobile"]

# The days of the week.
fhirvs:days-of-week ["mon" "tue" "wed" "thu" "fri" "sat" "sun"]

# Type for quality report
fhirvs:quality-type ["indel" "snp" "unknown"]

# Type for access of external URI
fhirvs:repository-type ["directlink" "openapi" "login" "oauth" "other"]

# How the Quantity should be understood and represented.
fhirvs:quantity-comparator ["<" "<=" ">=" ">"]

# The type of an address (physical / postal)
fhirvs:address-type ["postal" "physical" "both"]

# Real world event relating to the schedule.
fhirvs:event-timing ["MORN" "AFT" "EVE" "NIGHT" "PHS" "HS" "WAKE" "C" "CM" "CD" "CV" "AC" "ACM" "ACD" "ACV" "PC" "PCM" "PCD" "PCV"]

# Identifies the purpose for this identifier, if known .
fhirvs:identifier-use ["usual" "official" "temp" "secondary"]

# A unit of time (units from UCUM).
fhirvs:units-of-time ["s" "min" "h" "d" "wk" "mo" "a"]

# The use of an address
fhirvs:address-use ["home" "work" "temp" "old"]

# The use of a human name
fhirvs:name-use ["usual" "official" "temp" "nickname" "anonymous" "old" "maiden"]

# Telecommunications form for contact point
fhirvs:contact-point-system ["phone" "fax" "email" "pager" "url" "sms" "other"]