Observation.shex

ShEx statement for observation

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=<Observation> AND {fhir:nodeRole [fhir:treeRoot]}


# Measurements and simple assertions
<Observation> CLOSED {
    a [fhir:Observation];
    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:Observation.identifier @<Identifier>*;  # Unique Id for this particular 
                                            # observation 
    fhir:Observation.status @<code> AND
    	{fhir:value @fhirvs:observation-status};  # registered | preliminary | final | 
                                            # amended + 
    fhir:Observation.category @<CodeableConcept>*;  # Classification of  type of 
                                            # observation 
    fhir:Observation.code @<CodeableConcept>;  # Type of observation (code / type)
    fhir:Observation.subject                # Who and/or what this is about
    (   @<PatientReference> OR
        @<GroupReference> OR
        @<DeviceReference> OR
        @<LocationReference>
    )?;
    fhir:Observation.encounter @<EncounterReference>?;  # Healthcare event during which this 
                                            # observation is made 
    (                                       # Clinically relevant 
                                            # time/time-period for observation 
        fhir:Observation.effectiveDateTime @<dateTime>  |
        fhir:Observation.effectivePeriod @<Period> 
    )?;
    fhir:Observation.issued @<instant>?;    # Date/Time this was made available
    fhir:Observation.performer              # Who is responsible for the 
                                            # observation 
    (   @<PractitionerReference> OR
        @<OrganizationReference> OR
        @<PatientReference> OR
        @<RelatedPersonReference>
    )*;
    (                                       # Actual result
        fhir:Observation.valueQuantity @<Quantity>  |
        fhir:Observation.valueCodeableConcept @<CodeableConcept>  |
        fhir:Observation.valueString @<string>  |
        fhir:Observation.valueRange @<Range>  |
        fhir:Observation.valueRatio @<Ratio>  |
        fhir:Observation.valueSampledData @<SampledData>  |
        fhir:Observation.valueAttachment @<Attachment>  |
        fhir:Observation.valueTime @<time>  |
        fhir:Observation.valueDateTime @<dateTime>  |
        fhir:Observation.valuePeriod @<Period> 
    )?;
    fhir:Observation.dataAbsentReason @<CodeableConcept>?;  # Why the result is missing
    fhir:Observation.interpretation @<CodeableConcept>?;  # High, low, normal, etc.
    fhir:Observation.comment @<string>?;    # Comments about result
    fhir:Observation.bodySite @<CodeableConcept>?;  # Observed body part
    fhir:Observation.method @<CodeableConcept>?;  # How it was done
    fhir:Observation.specimen @<SpecimenReference>?;  # Specimen used for this observation
    fhir:Observation.device                 # (Measurement) Device
    (   @<DeviceReference> OR
        @<DeviceMetricReference>
    )?;
    fhir:Observation.referenceRange @<Observation.referenceRange>*;  # Provides guide for interpretation
    fhir:Observation.related @<Observation.related>*;  # Resource related to this 
                                            # observation 
    fhir:Observation.component @<Observation.component>*;  # Component results
    fhir:index xsd:integer?                 # Relative position in a list
}

# Component results
<Observation.component> 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:Observation.component.code @<CodeableConcept>;  # Type of component observation 
                                            # (code / type) 
    (                                       # Actual component result
        fhir:Observation.component.valueQuantity @<Quantity>  |
        fhir:Observation.component.valueCodeableConcept @<CodeableConcept>  |
        fhir:Observation.component.valueString @<string>  |
        fhir:Observation.component.valueRange @<Range>  |
        fhir:Observation.component.valueRatio @<Ratio>  |
        fhir:Observation.component.valueSampledData @<SampledData>  |
        fhir:Observation.component.valueAttachment @<Attachment>  |
        fhir:Observation.component.valueTime @<time>  |
        fhir:Observation.component.valueDateTime @<dateTime>  |
        fhir:Observation.component.valuePeriod @<Period> 
    )?;
    fhir:Observation.component.dataAbsentReason @<CodeableConcept>?;  # Why the component result is missing
    fhir:Observation.component.interpretation @<CodeableConcept>?;  # High, low, normal, etc.
    fhir:Observation.component.referenceRange @<Observation.referenceRange>*;  # Provides guide for interpretation 
                                            # of component result 
    fhir:index xsd:integer?                 # Relative position in a list
}

# Provides guide for interpretation
<Observation.referenceRange> 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:Observation.referenceRange.low @<SimpleQuantity>?;  # Low Range, if relevant
    fhir:Observation.referenceRange.high @<SimpleQuantity>?;  # High Range, if relevant
    fhir:Observation.referenceRange.meaning @<CodeableConcept>*;  # Reference range qualifier
    fhir:Observation.referenceRange.age @<Range>?;  # Applicable age range, if relevant
    fhir:Observation.referenceRange.text @<string>?;  # Text based reference range in an 
                                            # observation 
    fhir:index xsd:integer?                 # Relative position in a list
}

# Resource related to this observation
<Observation.related> 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:Observation.related.type @<code> AND
    	{fhir:value @fhirvs:observation-relationshiptypes}?;  # has-member | derived-from | 
                                            # sequel-to | replaces | 
                                            # qualified-by | interfered-by 
    fhir:Observation.related.target         # Resource that is related to this 
                                            # one 
    (   @<ObservationReference> OR
        @<QuestionnaireResponseReference> OR
        @<SequenceReference>
    );
    fhir:index xsd:integer?                 # Relative position in a list
}

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

# Primitive Type dateTime
<dateTime> CLOSED {
    fhir: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
}

# 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: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
}

# 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 fixed quantity (no comparator)
<SimpleQuantity> 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.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: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 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
}

# Content in a format defined elsewhere
<Attachment> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir: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
}

# Set of values bounded by low and high
<Range> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir: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
}

# Primitive Type uri
<uri> CLOSED {
    fhir: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
}

# Primitive Type instant
<instant> CLOSED {
    fhir: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
}

<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 @<OrganizationReference>?;  # 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
}

# A series of measurements taken by a device
<SampledData> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir: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: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 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 time
<time> CLOSED {
    fhir:id @<id>?;                         # xml:id (or equivalent in JSON)
    fhir:extension @<Extension>*;           # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:time?;                   # Primitive value for time
    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
}

# 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 positiveInt
<positiveInt> CLOSED {
    fhir:extension @<Extension>*;           # Additional Content defined by 
                                            # implementations 
    fhir:value xsd:positiveInteger?;        # Primitive value for positiveInt
    fhir:index xsd:integer?                 # Relative position in a list
}

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

# Primitive Type unsignedInt
<unsignedInt> CLOSED {
    fhir: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 decimal
<decimal> CLOSED {
    fhir: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
}

# Primitive Type boolean
<boolean> CLOSED {
    fhir: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 -------------------

<GroupReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Group> OR CLOSED {a fhir:Group}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<OrganizationReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Organization> OR CLOSED {a fhir:Organization}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<DeviceReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Device> OR CLOSED {a fhir:Device}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<PatientReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Patient> OR CLOSED {a fhir:Patient}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<SequenceReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Sequence> OR CLOSED {a fhir:Sequence}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<DeviceMetricReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<DeviceMetric> OR CLOSED {a fhir:DeviceMetric}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<QuestionnaireResponseReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<QuestionnaireResponse> OR CLOSED {a fhir:QuestionnaireResponse}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<RelatedPersonReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<RelatedPerson> OR CLOSED {a fhir:RelatedPerson}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<PractitionerReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Practitioner> OR CLOSED {a fhir:Practitioner}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<SpecimenReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Specimen> OR CLOSED {a fhir:Specimen}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<ObservationReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Observation> OR CLOSED {a fhir:Observation}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<EncounterReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Encounter> OR CLOSED {a fhir:Encounter}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

<LocationReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<Location> OR CLOSED {a fhir:Location}?;
    fhir:Reference.reference @<string>?;
    fhir:Reference.display @<string>?;
    fhir:index xsd:integer?
}

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

# Codes providing the status of an observation.
@fhirvs:observation-status = ["registered" "preliminary" "final" "amended" "cancelled" "entered-in-error" "unknown"]

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

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

# Codes specifying how two observations are related.
@fhirvs:observation-relationshiptypes = ["has-member" "derived-from" "sequel-to" "replaces" "qualified-by" "interfered-by"]

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