Genomicstudy.shex

ShEx statement for genomicstudy

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 <Task.shex>
IMPORT <Group.shex>
IMPORT <Device.shex>
IMPORT <string.shex>
IMPORT <Patient.shex>
IMPORT <dateTime.shex>
IMPORT <markdown.shex>
IMPORT <Resource.shex>
IMPORT <Specimen.shex>
IMPORT <Reference.shex>
IMPORT <Substance.shex>
IMPORT <Encounter.shex>
IMPORT <canonical.shex>
IMPORT <Procedure.shex>
IMPORT <Identifier.shex>
IMPORT <Annotation.shex>
IMPORT <Observation.shex>
IMPORT <Practitioner.shex>
IMPORT <Organization.shex>
IMPORT <DomainResource.shex>
IMPORT <ServiceRequest.shex>
IMPORT <CodeableConcept.shex>
IMPORT <BackboneElement.shex>
IMPORT <NutritionProduct.shex>
IMPORT <PractitionerRole.shex>
IMPORT <CodeableReference.shex>
IMPORT <DocumentReference.shex>
IMPORT <BiologicallyDerivedProduct.shex>
start=@<GenomicStudy> AND {fhir:nodeRole [fhir:treeRoot]}
# Genomic Study
<GenomicStudy> EXTENDS @<DomainResource> CLOSED { 
 a [fhir:GenomicStudy]?;
 fhir:nodeRole [fhir:treeRoot]?;
 fhir:identifier @<OneOrMore_Identifier>?; # Identifiers for this genomic study
 fhir:status @<code> AND
 	{fhir:v @fhirvs:genomicstudy-status}; # registered | available | cancelled 
 # | entered-in-error | unknown 
 fhir:type @<OneOrMore_CodeableConcept>?; # The type of the study (e.g., 
 # Familial variant segregation, 
 # Functional variation detection, or 
 # Gene expression profiling) 
 fhir:subject @<Reference> AND {fhir:link 
 			@<BiologicallyDerivedProduct> OR 
 			@<Group> OR 
 			@<NutritionProduct> OR 
 			@<Patient> OR 
 			@<Substance> ? }; # The primary subject of the genomic 
 # study 
 fhir:encounter @<Reference> AND {fhir:link 
 			@<Encounter> ? }?; # The healthcare event with which 
 # this genomics study is associated 
 fhir:startDate @<dateTime>?; # When the genomic study was started
 fhir:basedOn @<OneOrMore_Reference_ServiceRequest_OR_Task>?; # Event resources that the genomic 
 # study is based on 
 fhir:referrer @<Reference> AND {fhir:link 
 			@<Practitioner> OR 
 			@<PractitionerRole> ? }?; # Healthcare professional who 
 # requested or referred the genomic 
 # study 
 fhir:interpreter @<OneOrMore_Reference_Practitioner_OR_PractitionerRole>?; # Healthcare professionals who 
 # interpreted the genomic study 
 fhir:reason @<OneOrMore_CodeableReference>?; # Why the genomic study was performed
 fhir:instantiatesCanonical @<canonical>?; # The defined protocol that 
 # describes the study 
 fhir:instantiatesUri @<uri>?; # The URL pointing to an externally 
 # maintained protocol that describes 
 # the study 
 fhir:note @<OneOrMore_Annotation>?; # Comments related to the genomic 
 # study 
 fhir:description @<markdown>?; # Description of the genomic study
 fhir:analysis @<OneOrMore_GenomicStudy.analysis>?; # Genomic Analysis Event
} 
# Inputs for the analysis event
<GenomicStudy.analysis.input> EXTENDS @<BackboneElement> CLOSED { 
 fhir:file @<Reference> AND {fhir:link 
 			@<DocumentReference> ? }?; # File containing input data
 fhir:type @<CodeableConcept>?; # Type of input data (e.g., BAM, 
 # CRAM, or FASTA) 
 fhir:generatedBy @<Identifier> OR 
 			(@<Reference> AND {fhir:link @<GenomicStudy> }) ?; # The analysis event or other 
 # GenomicStudy that generated this 
 # input file 
} 
# Performer for the analysis event
<GenomicStudy.analysis.performer> EXTENDS @<BackboneElement> CLOSED { 
 fhir:actor @<Reference> AND {fhir:link 
 			@<Device> OR 
 			@<Organization> OR 
 			@<Practitioner> OR 
 			@<PractitionerRole> ? }?; # The organization, healthcare 
 # professional, or others who 
 # participated in performing this 
 # analysis 
 fhir:role @<CodeableConcept>?; # Role of the actor for this analysis
} 
# Devices used for the analysis (e.g., instruments, software), with settings and parameters
<GenomicStudy.analysis.device> EXTENDS @<BackboneElement> CLOSED { 
 fhir:device @<Reference> AND {fhir:link 
 			@<Device> ? }?; # Device used for the analysis
 fhir:function @<CodeableConcept>?; # Specific function for the device 
 # used for the analysis 
} 
# Outputs for the analysis event
<GenomicStudy.analysis.output> EXTENDS @<BackboneElement> CLOSED { 
 fhir:file @<Reference> AND {fhir:link 
 			@<DocumentReference> ? }?; # File containing output data
 fhir:type @<CodeableConcept>?; # Type of output data (e.g., VCF, 
 # MAF, or BAM) 
} 
# Genomic Analysis Event
<GenomicStudy.analysis> EXTENDS @<BackboneElement> CLOSED { 
 fhir:identifier @<OneOrMore_Identifier>?; # Identifiers for the analysis event
 fhir:methodType @<OneOrMore_CodeableConcept>?; # Type of the methods used in the 
 # analysis (e.g., FISH, Karyotyping, 
 # MSI) 
 fhir:changeType @<OneOrMore_CodeableConcept>?; # Type of the genomic changes 
 # studied in the analysis (e.g., 
 # DNA, RNA, or AA change) 
 fhir:genomeBuild @<CodeableConcept>?; # Genome build that is used in this 
 # analysis 
 fhir:instantiatesCanonical @<canonical>?; # The defined protocol that 
 # describes the analysis 
 fhir:instantiatesUri @<uri>?; # The URL pointing to an externally 
 # maintained protocol that describes 
 # the analysis 
 fhir:title @<string>?; # Name of the analysis event (human 
 # friendly) 
 fhir:focus @<OneOrMore_Reference_Resource>?; # What the genomic analysis is 
 # about, when it is not about the 
 # subject of record 
 fhir:specimen @<OneOrMore_Reference_Specimen>?; # The specimen used in the analysis 
 # event 
 fhir:date @<dateTime>?; # The date of the analysis event
 fhir:note @<OneOrMore_Annotation>?; # Any notes capture with the 
 # analysis event 
 fhir:protocolPerformed @<Reference> AND {fhir:link 
 			@<Procedure> OR 
 			@<Task> ? }?; # The protocol that was performed 
 # for the analysis event 
 fhir:regionsStudied @<OneOrMore_Reference_DocumentReference_OR_Observation>?; # The genomic regions to be studied 
 # in the analysis (BED file) 
 fhir:regionsCalled @<OneOrMore_Reference_DocumentReference_OR_Observation>?; # Genomic regions actually called in 
 # the analysis event (BED file) 
 fhir:input @<OneOrMore_GenomicStudy.analysis.input>?; # Inputs for the analysis event
 fhir:output @<OneOrMore_GenomicStudy.analysis.output>?; # Outputs for the analysis event
 fhir:performer @<OneOrMore_GenomicStudy.analysis.performer>?; # Performer for the analysis event
 fhir:device @<OneOrMore_GenomicStudy.analysis.device>?; # Devices used for the analysis 
 # (e.g., instruments, software), 
 # with settings and parameters 
} 
#---------------------- Cardinality Types (OneOrMore) -------------------
<OneOrMore_Identifier> CLOSED {
 rdf:first @<Identifier> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Identifier> 
}
<OneOrMore_CodeableConcept> CLOSED {
 rdf:first @<CodeableConcept> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_CodeableConcept> 
}
<OneOrMore_Reference_ServiceRequest_OR_Task> CLOSED {
 rdf:first @<Reference> AND {fhir:link 
			@<ServiceRequest> OR 
			@<Task> } ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Reference_ServiceRequest_OR_Task> 
}
<OneOrMore_Reference_Practitioner_OR_PractitionerRole> CLOSED {
 rdf:first @<Reference> AND {fhir:link 
			@<Practitioner> OR 
			@<PractitionerRole> } ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Reference_Practitioner_OR_PractitionerRole> 
}
<OneOrMore_CodeableReference> CLOSED {
 rdf:first @<CodeableReference> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_CodeableReference> 
}
<OneOrMore_Annotation> CLOSED {
 rdf:first @<Annotation> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Annotation> 
}
<OneOrMore_GenomicStudy.analysis> CLOSED {
 rdf:first @<GenomicStudy.analysis> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_GenomicStudy.analysis> 
}
<OneOrMore_Reference_Resource> CLOSED {
 rdf:first @<Reference> AND {fhir:link 
			@<Resource> } ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Reference_Resource> 
}
<OneOrMore_Reference_Specimen> CLOSED {
 rdf:first @<Reference> AND {fhir:link 
			@<Specimen> } ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Reference_Specimen> 
}
<OneOrMore_Reference_DocumentReference_OR_Observation> CLOSED {
 rdf:first @<Reference> AND {fhir:link 
			@<DocumentReference> OR 
			@<Observation> } ;
 rdf:rest [rdf:nil] OR @<OneOrMore_Reference_DocumentReference_OR_Observation> 
}
<OneOrMore_GenomicStudy.analysis.input> CLOSED {
 rdf:first @<GenomicStudy.analysis.input> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_GenomicStudy.analysis.input> 
}
<OneOrMore_GenomicStudy.analysis.output> CLOSED {
 rdf:first @<GenomicStudy.analysis.output> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_GenomicStudy.analysis.output> 
}
<OneOrMore_GenomicStudy.analysis.performer> CLOSED {
 rdf:first @<GenomicStudy.analysis.performer> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_GenomicStudy.analysis.performer> 
}
<OneOrMore_GenomicStudy.analysis.device> CLOSED {
 rdf:first @<GenomicStudy.analysis.device> ;
 rdf:rest [rdf:nil] OR @<OneOrMore_GenomicStudy.analysis.device> 
}
#---------------------- Value Sets ------------------------
# The status of the GenomicStudy.
fhirvs:genomicstudy-status ["registered" "available" "cancelled" "entered-in-error" "unknown"]