Specimen.shex

ShEx statement for specimen

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


# Sample for analysis
<Specimen> CLOSED {
    a [fhir:Specimen];
    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:Specimen.identifier @<Identifier>*;  # External Identifier
    fhir:Specimen.accessionIdentifier @<Identifier>?;  # Identifier assigned by the lab
    fhir:Specimen.status @<code> AND
    	{fhir:value @fhirvs:specimen-status}?;  # available | unavailable | 
                                            # unsatisfactory | entered-in-error 
    fhir:Specimen.type @<CodeableConcept>?;  # Kind of material that forms the 
                                            # specimen 
    fhir:Specimen.subject                   # Where the specimen came from. This 
                                            # may be from the patient(s) or from 
                                            # the environment or a device 
    (   @<PatientReference> OR
        @<GroupReference> OR
        @<DeviceReference> OR
        @<SubstanceReference>
    );
    fhir:Specimen.receivedTime @<dateTime>?;  # The time when specimen was 
                                            # received for processing 
    fhir:Specimen.parent @<SpecimenReference>*;  # Specimen from which this specimen 
                                            # originated 
    fhir:Specimen.request                   # Why the specimen was collected
    (   @<DiagnosticRequestReference> OR
        @<ProcedureRequestReference>
    )*;
    fhir:Specimen.collection @<Specimen.collection>?;  # Collection details
    fhir:Specimen.treatment @<Specimen.treatment>*;  # Treatment and processing step 
                                            # details 
    fhir:Specimen.container @<Specimen.container>*;  # Direct container of specimen 
                                            # (tube/slide, etc.) 
    fhir:Specimen.note @<Annotation>*;      # Comments
    fhir:index xsd:integer?                 # Relative position in a list
}

# Collection details
<Specimen.collection> 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:Specimen.collection.collector @<PractitionerReference>?;  # Who collected the specimen
    (                                       # Collection time
        fhir:Specimen.collection.collectedDateTime @<dateTime>  |
        fhir:Specimen.collection.collectedPeriod @<Period> 
    )?;
    fhir:Specimen.collection.quantity @<SimpleQuantity>?;  # The quantity of specimen collected
    fhir:Specimen.collection.method @<CodeableConcept>?;  # Technique used to perform 
                                            # collection 
    fhir:Specimen.collection.bodySite @<CodeableConcept>?;  # Anatomical collection site
    fhir:index xsd:integer?                 # Relative position in a list
}

# Treatment and processing step details
<Specimen.treatment> 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:Specimen.treatment.description @<string>?;  # Textual description of procedure
    fhir:Specimen.treatment.procedure @<CodeableConcept>?;  # Indicates the treatment or 
                                            # processing step  applied to the 
                                            # specimen 
    fhir:Specimen.treatment.additive @<SubstanceReference>*;  # Material used in the processing 
                                            # step 
    (                                       # Date and time of specimen treatment
        fhir:Specimen.treatment.timeDateTime @<dateTime>  |
        fhir:Specimen.treatment.timePeriod @<Period> 
    )?;
    fhir:index xsd:integer?                 # Relative position in a list
}

# Direct container of specimen (tube/slide, etc.)
<Specimen.container> 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:Specimen.container.identifier @<Identifier>*;  # Id for the container
    fhir:Specimen.container.description @<string>?;  # Textual description of the 
                                            # container 
    fhir:Specimen.container.type @<CodeableConcept>?;  # Kind of container directly 
                                            # associated with specimen 
    fhir:Specimen.container.capacity @<SimpleQuantity>?;  # Container volume or size
    fhir:Specimen.container.specimenQuantity @<SimpleQuantity>?;  # Quantity of specimen within 
                                            # container 
    (                                       # Additive associated with container
        fhir:Specimen.container.additiveCodeableConcept @<CodeableConcept>  |
        fhir:Specimen.container.additiveReference @<SubstanceReference> 
    )?;
    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
}

# 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
}

# Text node with attribution
<Annotation> CLOSED {
    fhir:Element.id @<string>?;             # xml:id (or equivalent in JSON)
    fhir:extension @<Extension>*;           # Additional Content defined by 
                                            # implementations 
    (                                       # Individual responsible for the 
                                            # annotation 
        fhir:Annotation.authorReference @<PractitionerReference>  |
        fhir:Annotation.authorReference @<PatientReference>  |
        fhir:Annotation.authorReference @<RelatedPersonReference>  |
        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
}

<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
}

# 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
}

# 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
}

# 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
}

# 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 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 -------------------

<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?
}

<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?
}

<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?
}

<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?
}

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

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

<DiagnosticRequestReference> CLOSED {
    fhir:Element.id @<id>?;
    fhir:extension @<Extension>*;
    fhir:link @<DiagnosticRequest> OR CLOSED {a fhir:DiagnosticRequest}?;
    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?
}

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

# Codes providing the status/availability of a specimen.
@fhirvs:specimen-status = ["available" "unavailable" "unsatisfactory" "entered-in-error"]

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

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