Generated Narrative: StructureDefinition ext-R5-GenomicStudy Name Flags Card. Type Description & Constraints Extension 0..* Extension(4.0.1) Genomic Study #xD; Slices for extension 1..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:status 1..1 Extension registered | available | cancelled | entered-in-error | unknown #xD; url 1..1 uri "status" #xD; value[x] 0..1 code registered | available | cancelled | entered-in-error | unknown Binding: R5_genomicstudy_status_for_R4 (0.0.1-snapshot-2) (required): The status of the GenomicStudy. #xD; extension:type 0..* Extension The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) #xD; url 1..1 uri "type" #xD; value[x] 0..1 CodeableConcept The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling) Binding: R5_genomicstudy_type_for_R4 (0.0.1-snapshot-2) (example): The type relevant to GenomicStudy. #xD; extension:encounter 0..1 Extension The healthcare event with which this genomics study is associated #xD; url 1..1 uri "encounter" #xD; value[x] 0..1 Reference() The healthcare event with which this genomics study is associated #xD; extension:startDate 0..1 Extension When the genomic study was started #xD; url 1..1 uri "startDate" #xD; value[x] 0..1 dateTime When the genomic study was started #xD; extension:basedOn 0..* Extension Event resources that the genomic study is based on #xD; url 1..1 uri "basedOn" #xD; value[x] 0..1 Reference() Event resources that the genomic study is based on #xD; extension:referrer 0..1 Extension Healthcare professional who requested or referred the genomic study #xD; url 1..1 uri "referrer" #xD; value[x] 0..1 Reference() Healthcare professional who requested or referred the genomic study #xD; extension:interpreter 0..* Extension Healthcare professionals who interpreted the genomic study #xD; url 1..1 uri "interpreter" #xD; value[x] 0..1 Reference() Healthcare professionals who interpreted the genomic study #xD; extension:reason 0..* Extension Why the genomic study was performed #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:concept 0..1 Extension Reference to a concept (by class) #xD; url 1..1 uri "concept" #xD; value[x] 0..1 CodeableConcept Reference to a concept (by class) #xD; extension:reference 0..1 Extension Reference to a resource (by instance) #xD; url 1..1 uri "reference" #xD; value[x] 0..1 Reference() Reference to a resource (by instance) #xD; extension:_datatype 0..1 (Complex) Data type name for GenomicStudy.reason from FHIR R5 URL: http://hl7.org/fhir/StructureDefinition/_datatype #xD; value[x] 1..1 string Value of extension Fixed Value: CodeableReference #xD; url 1..1 uri "reason" #xD; extension:instantiatesCanonical 0..1 Extension The defined protocol that describes the study #xD; url 1..1 uri "instantiatesCanonical" #xD; value[x] 0..1 canonical() The defined protocol that describes the study #xD; extension:instantiatesUri 0..1 Extension The URL pointing to an externally maintained protocol that describes the study #xD; url 1..1 uri "instantiatesUri" #xD; value[x] 0..1 uri The URL pointing to an externally maintained protocol that describes the study #xD; extension:note 0..* Extension Comments related to the genomic study #xD; url 1..1 uri "note" #xD; value[x] 0..1 Annotation Comments related to the genomic study #xD; extension:description 0..1 Extension Description of the genomic study #xD; url 1..1 uri "description" #xD; value[x] 0..1 markdown Description of the genomic study #xD; extension:analysis 0..* Extension Genomic Analysis Event #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:identifier 0..* Extension Identifiers for the analysis event #xD; url 1..1 uri "identifier" #xD; value[x] 0..1 Identifier Identifiers for the analysis event #xD; extension:methodType 0..* Extension Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) #xD; url 1..1 uri "methodType" #xD; value[x] 0..1 CodeableConcept Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI) Binding: R5_genomicstudy_methodtype_for_R4 (0.0.1-snapshot-2) (example): The method type of the GenomicStudy analysis. #xD; extension:changeType 0..* Extension Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) #xD; url 1..1 uri "changeType" #xD; value[x] 0..1 CodeableConcept Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change) Binding: R5_genomicstudy_changetype_for_R4 (0.0.1-snapshot-2) (example): The change type relevant to GenomicStudy analysis. #xD; extension:genomeBuild 0..1 Extension Genome build that is used in this analysis #xD; url 1..1 uri "genomeBuild" #xD; value[x] 0..1 CodeableConcept Genome build that is used in this analysis Binding: AccountStatus (extensible): Human reference sequence NCBI build ID #xD; extension:instantiatesCanonical 0..1 Extension The defined protocol that describes the analysis #xD; url 1..1 uri "instantiatesCanonical" #xD; value[x] 0..1 canonical() The defined protocol that describes the analysis #xD; extension:instantiatesUri 0..1 Extension The URL pointing to an externally maintained protocol that describes the analysis #xD; url 1..1 uri "instantiatesUri" #xD; value[x] 0..1 uri The URL pointing to an externally maintained protocol that describes the analysis #xD; extension:title 0..1 Extension Name of the analysis event (human friendly) #xD; url 1..1 uri "title" #xD; value[x] 0..1 string Name of the analysis event (human friendly) #xD; <a href="StructureDefinition-ext-R5-GenomicStudy-definitions.html#Extension.extension:analysis.extension:focus" title="Slice focus: The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.">extension:focus 0..* Extension What the genomic analysis is about, when it is not about the subject of record #xD; url 1..1 uri "focus" #xD; <a href="StructureDefinition-ext-R5-GenomicStudy-definitions.html#Extension.extension:analysis.extension:focus.value[x]" title="The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.">value[x] 0..1 Reference() What the genomic analysis is about, when it is not about the subject of record #xD; extension:specimen 0..* Extension The specimen used in the analysis event #xD; url 1..1 uri "specimen" #xD; value[x] 0..1 Reference() The specimen used in the analysis event #xD; extension:date 0..1 Extension The date of the analysis event #xD; url 1..1 uri "date" #xD; value[x] 0..1 dateTime The date of the analysis event #xD; extension:note 0..* Extension Any notes capture with the analysis event #xD; url 1..1 uri "note" #xD; value[x] 0..1 Annotation Any notes capture with the analysis event #xD; extension:protocolPerformed 0..1 Extension The protocol that was performed for the analysis event #xD; url 1..1 uri "protocolPerformed" #xD; value[x] 0..1 Reference() The protocol that was performed for the analysis event #xD; extension:regionsStudied 0..* Extension The genomic regions to be studied in the analysis (BED file) #xD; url 1..1 uri "regionsStudied" #xD; value[x] 0..1 Reference() The genomic regions to be studied in the analysis (BED file) #xD; extension:regionsCalled 0..* Extension Genomic regions actually called in the analysis event (BED file) #xD; url 1..1 uri "regionsCalled" #xD; value[x] 0..1 Reference() Genomic regions actually called in the analysis event (BED file) #xD; extension:input 0..* Extension Inputs for the analysis event #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:file 0..1 Extension File containing input data #xD; url 1..1 uri "file" #xD; value[x] 0..1 Reference() File containing input data #xD; extension:type 0..1 Extension Type of input data (e.g., BAM, CRAM, or FASTA) #xD; url 1..1 uri "type" #xD; value[x] 0..1 CodeableConcept Type of input data (e.g., BAM, CRAM, or FASTA) Binding: R5_genomicstudy_dataformat_for_R4 (0.0.1-snapshot-2) (example): The data format of the data file. #xD; extension:generatedBy[x] 0..1 Extension The analysis event or other GenomicStudy that generated this input file #xD; url 1..1 uri "generatedBy[x]" #xD; value[x] 0..1 The analysis event or other GenomicStudy that generated this input file #xD; valueIdentifier Identifier #xD; valueReference Reference(Any) #xD; url 1..1 uri "input" #xD; extension:output 0..* Extension Outputs for the analysis event #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:file 0..1 Extension File containing output data #xD; url 1..1 uri "file" #xD; value[x] 0..1 Reference() File containing output data #xD; extension:type 0..1 Extension Type of output data (e.g., VCF, MAF, or BAM) #xD; url 1..1 uri "type" #xD; value[x] 0..1 CodeableConcept Type of output data (e.g., VCF, MAF, or BAM) Binding: R5_genomicstudy_dataformat_for_R4 (0.0.1-snapshot-2) (example): The data format of the data file. #xD; url 1..1 uri "output" #xD; extension:performer 0..* Extension Performer for the analysis event #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:actor 0..1 Extension The organization, healthcare professional, or others who participated in performing this analysis #xD; url 1..1 uri "actor" #xD; value[x] 0..1 Reference() The organization, healthcare professional, or others who participated in performing this analysis #xD; extension:role 0..1 Extension Role of the actor for this analysis #xD; url 1..1 uri "role" #xD; value[x] 0..1 CodeableConcept Role of the actor for this analysis #xD; url 1..1 uri "performer" #xD; extension:device 0..* Extension Devices used for the analysis (e.g., instruments, software), with settings and parameters #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Closed by value:url #xD; extension:device 0..1 Extension Device used for the analysis #xD; url 1..1 uri "device" #xD; value[x] 0..1 Reference() Device used for the analysis #xD; extension:function 0..1 Extension Specific function for the device used for the analysis #xD; url 1..1 uri "function" #xD; value[x] 0..1 CodeableConcept Specific function for the device used for the analysis #xD; url 1..1 uri "device" #xD; url 1..1 uri "analysis" #xD; url 1..1 uri "http://hl7.org/fhir/5.0/StructureDefinition/extension-GenomicStudy" #xD; Documentation for this format
Cross-version Extension for R5.GenomicStudy for use in FHIR R4
This cross-version extension represents GenomicStudy from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
A GenomicStudy is a set of analyses performed to analyze and generate genomic data.
All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])
Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])
registered | available | cancelled | entered-in-error | unknown
Additional content defined by implementations
May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
Source of the definition for the extension code - a logical name or a URL.
The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.
The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)
The type of the study, e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling.
The healthcare event with which this genomics study is associated
This cross-version extension represents GenomicStudy.encounter from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.startDate from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Event resources that the genomic study is based on
This cross-version extension represents GenomicStudy.basedOn from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Healthcare professional who requested or referred the genomic study
This cross-version extension represents GenomicStudy.referrer from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Healthcare professionals who interpreted the genomic study
This cross-version extension represents GenomicStudy.interpreter from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.reason from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
A reference to a concept - e.g. the information is identified by its general class to the degree of precision found in the terminology.
A reference to a resource the provides exact details about the information being referenced.
Data type name for GenomicStudy.reason from FHIR R5
Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R5/extensibility.html) for a list).
Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list).
The defined protocol that describes the study
This cross-version extension represents GenomicStudy.instantiatesCanonical from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
The URL pointing to an externally maintained protocol that describes the study
This cross-version extension represents GenomicStudy.instantiatesUri from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.note from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.description from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
The details about a specific analysis that was performed in this GenomicStudy.
This cross-version extension represents GenomicStudy.analysis.identifier from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)
Type of the methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI).
The method type of the GenomicStudy analysis.
Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)
Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid change.
The change type relevant to GenomicStudy analysis.
Genome build that is used in this analysis
The reference genome build that is used in this analysis.
The defined protocol that describes the analysis
This cross-version extension represents GenomicStudy.analysis.instantiatesCanonical from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
The URL pointing to an externally maintained protocol that describes the analysis
This cross-version extension represents GenomicStudy.analysis.instantiatesUri from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Name of the analysis event (human friendly)
This cross-version extension represents GenomicStudy.analysis.title from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
What the genomic analysis is about, when it is not about the subject of record
The focus of a genomic analysis when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, child, or sibling. For example, in trio testing, the GenomicStudy.subject would be the child (proband) and the GenomicStudy.analysis.focus of a specific analysis would be the parent.
This cross-version extension represents GenomicStudy.analysis.specimen from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.date from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Any notes capture with the analysis event
This cross-version extension represents GenomicStudy.analysis.note from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
The protocol that was performed for the analysis event
This cross-version extension represents GenomicStudy.analysis.protocolPerformed from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
The genomic regions to be studied in the analysis (BED file)
This cross-version extension represents GenomicStudy.analysis.regionsStudied from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Genomic regions actually called in the analysis event (BED file)
This cross-version extension represents GenomicStudy.analysis.regionsCalled from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.input from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.input.file from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Type of input data (e.g., BAM, CRAM, or FASTA)
Type of input data, e.g., BAM, CRAM, or FASTA.
The analysis event or other GenomicStudy that generated this input file
This cross-version extension represents GenomicStudy.analysis.input.generatedBy[x] from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.output from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.output.file from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Type of output data (e.g., VCF, MAF, or BAM)
Type of output data, e.g., VCF, MAF, or BAM.
This cross-version extension represents GenomicStudy.analysis.performer from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
The organization, healthcare professional, or others who participated in performing this analysis
This cross-version extension represents GenomicStudy.analysis.performer.actor from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.performer.role from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Devices used for the analysis (e.g., instruments, software), with settings and parameters
This cross-version extension represents GenomicStudy.analysis.device from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
This cross-version extension represents GenomicStudy.analysis.device.device from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.
Specific function for the device used for the analysis
This cross-version extension represents GenomicStudy.analysis.device.function from http://hl7.org/fhir/StructureDefinition/GenomicStudy|5.0.0 for use in FHIR R4.