Specimendefinition.shex

ShEx statement for specimendefinition

PREFIX fhir: <http://hl7.org/fhir/> 
PREFIX fhirvs: <http://hl7.org/fhir/ValueSet/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

IMPORT <uri.shex>
IMPORT <code.shex>
IMPORT <date.shex>
IMPORT <Group.shex>
IMPORT <Range.shex>
IMPORT <string.shex>
IMPORT <Coding.shex>
IMPORT <Period.shex>
IMPORT <boolean.shex>
IMPORT <dateTime.shex>
IMPORT <markdown.shex>
IMPORT <Duration.shex>
IMPORT <Quantity.shex>
IMPORT <canonical.shex>
IMPORT <Reference.shex>
IMPORT <Identifier.shex>
IMPORT <UsageContext.shex>
IMPORT <ContactDetail.shex>
IMPORT <DomainResource.shex>
IMPORT <SimpleQuantity.shex>
IMPORT <CodeableConcept.shex>
IMPORT <BackboneElement.shex>
IMPORT <SubstanceDefinition.shex>

start=@<SpecimenDefinition> AND {fhir:nodeRole [fhir:treeRoot]}

# Kind of specimen
<SpecimenDefinition> EXTENDS @<DomainResource> CLOSED {   
    a [fhir:SpecimenDefinition]?;fhir:nodeRole [fhir:treeRoot]?;

    fhir:url @<uri>?;                       # Logical canonical URL to reference 
                                            # this SpecimenDefinition (globally 
                                            # unique) 
    fhir:identifier @<Identifier>?;         # Business identifier
    fhir:version @<string>?;                # Business version of the 
                                            # SpecimenDefinition 
    fhir:versionAlgorithm @<string>  OR 
    			@<Coding>  ?;  # How to compare versions
    fhir:name @<string>?;                   # Name for this {{title}} (computer 
                                            # friendly) 
    fhir:title @<string>?;                  # Name for this SpecimenDefinition 
                                            # (Human friendly) 
    fhir:derivedFromCanonical @<OneOrMore_canonical>?;  # Based on FHIR definition of 
                                            # another SpecimenDefinition 
    fhir:derivedFromUri @<OneOrMore_uri>?;  # Based on external definition
    fhir:status @<code> AND
    	{fhir:v @fhirvs:publication-status};  # draft | active | retired | unknown
    fhir:experimental @<boolean>?;          # If this SpecimenDefinition is not 
                                            # for real usage 
    fhir:subject @<CodeableConcept>  OR 
    			(@<Reference>  AND {fhir:link @<Group> })  ?;  # Type of subject for specimen 
                                            # collection 
    fhir:date @<dateTime>?;                 # Date status first applied
    fhir:publisher @<string>?;              # The name of the individual or 
                                            # organization that published the 
                                            # SpecimenDefinition 
    fhir:contact @<OneOrMore_ContactDetail>?;  # Contact details for the publisher
    fhir:description @<markdown>?;          # Natural language description of 
                                            # the SpecimenDefinition 
    fhir:useContext @<OneOrMore_UsageContext>?;  # Content intends to support these 
                                            # contexts 
    fhir:jurisdiction @<OneOrMore_CodeableConcept>?;  # Intended jurisdiction for this 
                                            # SpecimenDefinition (if applicable) 
    fhir:purpose @<markdown>?;              # Why this SpecimenDefinition is 
                                            # defined 
    fhir:copyright @<markdown>?;            # Use and/or publishing restrictions
    fhir:copyrightLabel @<string>?;         # Copyright holder and year(s)
    fhir:approvalDate @<date>?;             # When SpecimenDefinition was 
                                            # approved by publisher 
    fhir:lastReviewDate @<date>?;           # The date on which the asset 
                                            # content was last reviewed by the 
                                            # publisher 
    fhir:effectivePeriod @<Period>?;        # The effective date range for the 
                                            # SpecimenDefinition 
    fhir:typeCollected @<CodeableConcept>?;  # Kind of material to collect
    fhir:patientPreparation @<OneOrMore_CodeableConcept>?;  # Patient preparation for collection
    fhir:timeAspect @<string>?;             # Time aspect for collection
    fhir:collection @<OneOrMore_CodeableConcept>?;  # Specimen collection procedure
    fhir:typeTested @<OneOrMore_SpecimenDefinition.typeTested>?;  # Specimen in container intended for 
                                            # testing by lab 
}  

# Specimen in container intended for testing by lab
<SpecimenDefinition.typeTested> EXTENDS @<BackboneElement> CLOSED {   
    fhir:isDerived @<boolean>?;             # Primary or secondary specimen
    fhir:type @<CodeableConcept>?;          # Type of intended specimen
    fhir:preference @<code> AND
    	{fhir:v @fhirvs:specimen-contained-preference};  # preferred | alternate
    fhir:container @<SpecimenDefinition.typeTested.container>?;  # The specimen's container
    fhir:requirement @<markdown>?;          # Requirements for specimen delivery 
                                            # and special handling 
    fhir:retentionTime @<Duration>?;        # The usual time for retaining this 
                                            # kind of specimen 
    fhir:singleUse @<boolean>?;             # Specimen for single use only
    fhir:rejectionCriterion @<OneOrMore_CodeableConcept>?;  # Criterion specified for specimen 
                                            # rejection 
    fhir:handling @<OneOrMore_SpecimenDefinition.typeTested.handling>?;  # Specimen handling before testing
    fhir:testingDestination @<OneOrMore_CodeableConcept>?;  # Where the specimen will be tested
}  

# The specimen's container
<SpecimenDefinition.typeTested.container> EXTENDS @<BackboneElement> CLOSED {   
    fhir:material @<CodeableConcept>?;      # The material type used for the 
                                            # container 
    fhir:type @<CodeableConcept>?;          # Kind of container associated with 
                                            # the kind of specimen 
    fhir:cap @<CodeableConcept>?;           # Color of container cap
    fhir:description @<markdown>?;          # The description of the kind of 
                                            # container 
    fhir:capacity @<Quantity>?;             # The capacity of this kind of 
                                            # container 
    fhir:minimumVolume @<SimpleQuantity>  OR 
    			@<string>  ?;  # Minimum volume
    fhir:additive @<OneOrMore_SpecimenDefinition.typeTested.container.additive>?;  # Additive associated with container
    fhir:preparation @<markdown>?;          # Special processing applied to the 
                                            # container for this specimen type 
}  

# Additive associated with container
<SpecimenDefinition.typeTested.container.additive> EXTENDS @<BackboneElement> CLOSED {   
    fhir:additive @<CodeableConcept>  OR 
    			(@<Reference>  AND {fhir:link @<SubstanceDefinition> })  ;  # Additive associated with container
}  

# Specimen handling before testing
<SpecimenDefinition.typeTested.handling> EXTENDS @<BackboneElement> CLOSED {   
    fhir:temperatureQualifier @<CodeableConcept>?;  # Qualifies the interval of 
                                            # temperature 
    fhir:temperatureRange @<Range>?;        # Temperature range for these 
                                            # handling instructions 
    fhir:maxDuration @<Duration>?;          # Maximum preservation time
    fhir:instruction @<markdown>?;          # Preservation instruction
}  

#---------------------- Cardinality Types (OneOrMore) -------------------
<OneOrMore_canonical> CLOSED {
    rdf:first @<canonical>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_canonical> 
}
<OneOrMore_uri> CLOSED {
    rdf:first @<uri>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_uri> 
}
<OneOrMore_ContactDetail> CLOSED {
    rdf:first @<ContactDetail>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_ContactDetail> 
}
<OneOrMore_UsageContext> CLOSED {
    rdf:first @<UsageContext>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_UsageContext> 
}
<OneOrMore_CodeableConcept> CLOSED {
    rdf:first @<CodeableConcept>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_CodeableConcept> 
}
<OneOrMore_SpecimenDefinition.typeTested> CLOSED {
    rdf:first @<SpecimenDefinition.typeTested>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SpecimenDefinition.typeTested> 
}
<OneOrMore_SpecimenDefinition.typeTested.handling> CLOSED {
    rdf:first @<SpecimenDefinition.typeTested.handling>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SpecimenDefinition.typeTested.handling> 
}
<OneOrMore_SpecimenDefinition.typeTested.container.additive> CLOSED {
    rdf:first @<SpecimenDefinition.typeTested.container.additive>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_SpecimenDefinition.typeTested.container.additive> 
}

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

# The lifecycle status of an artifact.
fhirvs:publication-status ["draft" "active" "retired" "unknown"]

# Degree of preference of a type of conditioned specimen.
fhirvs:specimen-contained-preference ["preferred" "alternate"]