Evidence.shex

ShEx statement for evidence

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 <boolean.shex>
IMPORT <decimal.shex>
IMPORT <markdown.shex>
IMPORT <Citation.shex>
IMPORT <dateTime.shex>
IMPORT <Quantity.shex>
IMPORT <Reference.shex>
IMPORT <Identifier.shex>
IMPORT <Annotation.shex>
IMPORT <unsignedInt.shex>
IMPORT <UsageContext.shex>
IMPORT <ContactDetail.shex>
IMPORT <DomainResource.shex>
IMPORT <SimpleQuantity.shex>
IMPORT <RelatedArtifact.shex>
IMPORT <CodeableConcept.shex>
IMPORT <BackboneElement.shex>

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

# Single evidence bit
<Evidence> EXTENDS @<DomainResource> CLOSED {   
    a [fhir:Evidence]?;fhir:nodeRole [fhir:treeRoot]?;

    fhir:url @<uri>?;                       # Canonical identifier for this 
                                            # evidence, represented as a 
                                            # globally unique URI 
    fhir:identifier @<OneOrMore_Identifier>?;  # Additional identifier for the 
                                            # summary 
    fhir:version @<string>?;                # Business version of this summary
    fhir:versionAlgorithm @<string>  OR 
    			@<Coding>  ?;  # How to compare versions
    fhir:name @<string>?;                   # Name for this summary (machine 
                                            # friendly) 
    fhir:title @<string>?;                  # Name for this summary (human 
                                            # friendly) 
    fhir:citeAs (@<Reference>  AND {fhir:link @<Citation> })  OR 
    			@<markdown>  ?;  # Citation for this evidence
    fhir:status @<code> AND
    	{fhir:v @fhirvs:publication-status};  # draft | active | retired | unknown
    fhir:experimental @<boolean>?;          # For testing purposes, not real 
                                            # usage 
    fhir:date @<dateTime>?;                 # Date last changed
    fhir:approvalDate @<date>?;             # When the summary was approved by 
                                            # publisher 
    fhir:lastReviewDate @<date>?;           # When the summary was last reviewed 
                                            # by the publisher 
    fhir:publisher @<string>?;              # Name of the publisher/steward 
                                            # (organization or individual) 
    fhir:contact @<OneOrMore_ContactDetail>?;  # Contact details for the publisher
    fhir:author @<OneOrMore_ContactDetail>?;  # Who authored the content
    fhir:editor @<OneOrMore_ContactDetail>?;  # Who edited the content
    fhir:reviewer @<OneOrMore_ContactDetail>?;  # Who reviewed the content
    fhir:endorser @<OneOrMore_ContactDetail>?;  # Who endorsed the content
    fhir:useContext @<OneOrMore_UsageContext>?;  # The context that the content is 
                                            # intended to support 
    fhir:purpose @<markdown>?;              # Why this Evidence is defined
    fhir:copyright @<markdown>?;            # Use and/or publishing restrictions
    fhir:copyrightLabel @<string>?;         # Copyright holder and year(s)
    fhir:relatedArtifact @<OneOrMore_RelatedArtifact>?;  # Link or citation to artifact 
                                            # associated with the summary 
    fhir:description @<markdown>?;          # Description of the particular 
                                            # summary 
    fhir:assertion @<markdown>?;            # Declarative description of the 
                                            # Evidence 
    fhir:note @<OneOrMore_Annotation>?;     # Footnotes and/or explanatory notes
    fhir:variableDefinition @<OneOrMore_Evidence.variableDefinition>;  # Evidence variable such as 
                                            # population, exposure, or outcome 
    fhir:synthesisType @<CodeableConcept>?;  # The method to combine studies
    fhir:studyDesign @<OneOrMore_CodeableConcept>?;  # The design of the study that 
                                            # produced this evidence 
    fhir:statistic @<OneOrMore_Evidence.statistic>?;  # Values and parameters for a single 
                                            # statistic 
    fhir:certainty @<OneOrMore_Evidence.certainty>?;  # Certainty or quality of the 
                                            # evidence 
}  

# Values and parameters for a single statistic
<Evidence.statistic> EXTENDS @<BackboneElement> CLOSED {   
    fhir:description @<markdown>?;          # Description of content
    fhir:note @<OneOrMore_Annotation>?;     # Footnotes and/or explanatory notes
    fhir:statisticType @<CodeableConcept>?;  # Type of statistic, e.g., relative 
                                            # risk 
    fhir:category @<CodeableConcept>?;      # Associated category for 
                                            # categorical variable 
    fhir:quantity @<Quantity>?;             # Statistic value
    fhir:numberOfEvents @<unsignedInt>?;    # The number of events associated 
                                            # with the statistic 
    fhir:numberAffected @<unsignedInt>?;    # The number of participants affected
    fhir:sampleSize @<Evidence.statistic.sampleSize>?;  # Number of samples in the statistic
    fhir:attributeEstimate @<OneOrMore_Evidence.statistic.attributeEstimate>?;  # An attribute of the Statistic
    fhir:modelCharacteristic @<OneOrMore_Evidence.statistic.modelCharacteristic>?;  # An aspect of the statistical model
}  

# Number of samples in the statistic
<Evidence.statistic.sampleSize> EXTENDS @<BackboneElement> CLOSED {   
    fhir:description @<markdown>?;          # Textual description of sample size 
                                            # for statistic 
    fhir:note @<OneOrMore_Annotation>?;     # Footnote or explanatory note about 
                                            # the sample size 
    fhir:numberOfStudies @<unsignedInt>?;   # Number of contributing studies
    fhir:numberOfParticipants @<unsignedInt>?;  # Cumulative number of participants
    fhir:knownDataCount @<unsignedInt>?;    # Number of participants with known 
                                            # results for measured variables 
}  

# Certainty or quality of the evidence
<Evidence.certainty> EXTENDS @<BackboneElement> CLOSED {   
    fhir:description @<markdown>?;          # Textual description of certainty
    fhir:note @<OneOrMore_Annotation>?;     # Footnotes and/or explanatory notes
    fhir:type @<CodeableConcept>?;          # Aspect of certainty being rated
    fhir:rating @<CodeableConcept>?;        # Assessment or judgement of the 
                                            # aspect 
    fhir:rater @<string>?;                  # Individual or group who did the 
                                            # rating 
    fhir:subcomponent @<OneOrMore_Evidence.certainty>?;  # A domain or subdomain of certainty
}  

# A nested attribute estimate; which is the attribute estimate of an attribute estimate
<Evidence.statistic.attributeEstimate.attributeEstimatenull> CLOSED {   
}  

# Evidence variable such as population, exposure, or outcome
<Evidence.variableDefinition> EXTENDS @<BackboneElement> CLOSED {   
    fhir:description @<markdown>?;          # A text description or summary of 
                                            # the variable 
    fhir:note @<OneOrMore_Annotation>?;     # Footnotes and/or explanatory notes
    fhir:variableRole @<code> AND
    	{fhir:v @fhirvs:variable-role};  # population | exposure | outcome | 
                                            # covariate 
    fhir:roleSubtype @<CodeableConcept>?;   # subgroup | variable-A | variable-B 
                                            # | variable-AB | confounder | 
                                            # collider | mediator | 
                                            # effect-modifier 
    fhir:comparatorCategory @<string>?;     # The reference value used for 
                                            # comparison 
    fhir:observed @<Reference> AND {fhir:link 
    			@<EvidenceVariable> OR 
    			@<Group> ? }?;  # Definition of the actual variable 
                                            # related to the statistic(s) 
    fhir:intended @<Reference> AND {fhir:link 
    			@<EvidenceVariable> OR 
    			@<Group> ? }?;  # Definition of the intended 
                                            # variable related to the Evidence 
    fhir:directnessMatch @<CodeableConcept>?;  # low | moderate | high | exact
}  

# An aspect of the statistical model
<Evidence.statistic.modelCharacteristic> EXTENDS @<BackboneElement> CLOSED {   
    fhir:code @<CodeableConcept>;           # Model specification
    fhir:value @<SimpleQuantity>  OR 
    			@<Range>  OR 
    			@<CodeableConcept>  ?;  # The specific value (when paired 
                                            # with code) 
    fhir:intended @<boolean>?;              # The plan for analysis
    fhir:applied @<boolean>?;               # The analysis that was applied
    fhir:variable @<OneOrMore_Evidence.statistic.modelCharacteristic.variable>?;  # A variable adjusted for in the 
                                            # adjusted analysis 
    fhir:attribute @<OneOrMore_Evidence.statistic.attributeEstimate>?;  # An attribute of the statistic used 
                                            # as a model characteristic 
}  

# An attribute of the Statistic
<Evidence.statistic.attributeEstimate> EXTENDS @<BackboneElement> CLOSED {   
    fhir:description @<markdown>?;          # Textual description of the 
                                            # attribute estimate 
    fhir:note @<OneOrMore_Annotation>?;     # Footnote or explanatory note about 
                                            # the estimate 
    fhir:type @<CodeableConcept>?;          # The type of attribute estimate, 
                                            # e.g., confidence interval or p 
                                            # value 
    fhir:quantity @<Quantity>?;             # The singular quantity of the 
                                            # attribute estimate, for attribute 
                                            # estimates represented as single 
                                            # values; also used to report unit 
                                            # of measure 
    fhir:level @<decimal>?;                 # Level of confidence interval, 
                                            # e.g., 0.95 for 95% confidence 
                                            # interval 
    fhir:range @<Range>?;                   # Lower and upper bound values of 
                                            # the attribute estimate 
    fhir:attributeEstimate @<OneOrMore_Evidence.statistic.attributeEstimate>?;  # A nested attribute estimate; which 
                                            # is the attribute estimate of an 
                                            # attribute estimate 
}  

# A domain or subdomain of certainty
<Evidence.certainty.subcomponentnull> CLOSED {   
}  

# A variable adjusted for in the adjusted analysis
<Evidence.statistic.modelCharacteristic.variable> EXTENDS @<BackboneElement> CLOSED {   
    fhir:variableDefinition @<Reference> AND {fhir:link 
    			@<EvidenceVariable> OR 
    			@<Group> ? };  # Description of the variable
    fhir:handling @<code> AND
    	{fhir:v @fhirvs:variable-handling}?;  # continuous | dichotomous | ordinal 
                                            # | polychotomous 
    fhir:valueCategory @<OneOrMore_CodeableConcept>?;  # Description for grouping of 
                                            # ordinal or polychotomous variables 
    fhir:valueQuantity @<OneOrMore_Quantity>?;  # Discrete value for grouping of 
                                            # ordinal or polychotomous variables 
    fhir:valueRange @<OneOrMore_Range>?;    # Range of values for grouping of 
                                            # ordinal or polychotomous variables 
}  

#---------------------- Cardinality Types (OneOrMore) -------------------
<OneOrMore_Identifier> CLOSED {
    rdf:first @<Identifier>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Identifier> 
}
<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_RelatedArtifact> CLOSED {
    rdf:first @<RelatedArtifact>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_RelatedArtifact> 
}
<OneOrMore_Annotation> CLOSED {
    rdf:first @<Annotation>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Annotation> 
}
<OneOrMore_Evidence.variableDefinition> CLOSED {
    rdf:first @<Evidence.variableDefinition>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Evidence.variableDefinition> 
}
<OneOrMore_CodeableConcept> CLOSED {
    rdf:first @<CodeableConcept>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_CodeableConcept> 
}
<OneOrMore_Evidence.statistic> CLOSED {
    rdf:first @<Evidence.statistic>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Evidence.statistic> 
}
<OneOrMore_Evidence.certainty> CLOSED {
    rdf:first @<Evidence.certainty>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Evidence.certainty> 
}
<OneOrMore_Evidence.statistic.attributeEstimate> CLOSED {
    rdf:first @<Evidence.statistic.attributeEstimate>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Evidence.statistic.attributeEstimate> 
}
<OneOrMore_Evidence.statistic.modelCharacteristic> CLOSED {
    rdf:first @<Evidence.statistic.modelCharacteristic>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Evidence.statistic.modelCharacteristic> 
}
<OneOrMore_Evidence.statistic.modelCharacteristic.variable> CLOSED {
    rdf:first @<Evidence.statistic.modelCharacteristic.variable>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Evidence.statistic.modelCharacteristic.variable> 
}
<OneOrMore_Quantity> CLOSED {
    rdf:first @<Quantity>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Quantity> 
}
<OneOrMore_Range> CLOSED {
    rdf:first @<Range>  ;
    rdf:rest [rdf:nil] OR @<OneOrMore_Range> 
}

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

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

# The handling of the variable in statistical analysis for exposures or outcomes (E.g. Dichotomous, Continuous, Descriptive).
fhirvs:variable-handling ["continuous" "dichotomous" "ordinal" "polychotomous"]

# The role that the variable plays.
fhirvs:variable-role ["population" "exposure" "outcome" "covariate"]