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Example MolecularDefinition/example-starting-sequence-2b-relative (Narrative)

10.4.7 Resource GenomicStudy - Detailed Descriptions

Clinical Genomics icon Work Group Maturity Level : N/A 0   Trial Use Standards Status : Informative Security Category : Patient Compartments : No defined compartments Patient

Detailed Descriptions for the elements in the GenomicStudy resource.

XML JSON Literals - *
Narrative GenomicStudy
Element Id GenomicStudy
Definition

A Genomic Study is a set of analysis performed to analyze and generate genomic data.

Short Display Genomic Study
Cardinality 0..*
Type TTL DomainResource
Summary false
GenomicStudy.identifier
Element Id GenomicStudy.identifier
Definition

Identifiers for this genomic study.

Short Display Identifiers for this genomic study
Note This is a business identifier, not a resource identifier (see discussion )
Cardinality 0..*
Type Identifier
Summary false
GenomicStudy.status
Element Id GenomicStudy.status
Definition

The status of the narrative for genomic study.

Short Display The status of the resource. See also genomic study
Cardinality 1..1
Terminology Binding GenomicStudyStatus ( Required )
Type CodeableConcept
Is Modifier true (Reason: This element is labeled as a modifier because it is a status element that contains status entered-in-error which means that the XML , JSON resource should not be treated as valid)
Summary true
GenomicStudy.type
Element Id GenomicStudy.type
Definition

The type of the study, e.g., Familial variant segregation, Functional variation detection, or Turtle Gene expression profiling.

Short Display The type of the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)
Cardinality format. This example conforms to 0..*
Terminology Binding GenomicStudyType ( Example )
Type CodeableConcept
Summary false
GenomicStudy.subject
Element Id GenomicStudy.subject
Definition

The primary subject of the profile MolecularDefinition . genomic study.

Short Display The primary subject of the genomic study
Cardinality 1..1
Type Reference ( Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct )
Summary true
Generated Narrative: MolecularDefinition example-starting-sequence-2b-relative GenomicStudy.encounter
Element Id GenomicStudy.encounter
Definition

The healthcare event with which this genomics study is associated.

Short Display The healthcare event with which this genomics study is associated
Cardinality 0..1
Type Reference ( Encounter )
Summary false
GenomicStudy.startDate
Element Id GenomicStudy.startDate
Definition

When the genomic study was started.

Short Display When the genomic study was started
Cardinality 0..1
Type dateTime
Summary false
moleculeType : DNA Sequence GenomicStudy.basedOn
Element Id GenomicStudy.basedOn
Definition

Event resources that the genomic study is based on.

Short Display Event resources that the genomic study is based on
Cardinality 0..*
Type Reference ( ServiceRequest | Task )
Summary false
GenomicStudy.referrer
Element Id GenomicStudy.referrer
Definition

Healthcare professional who requested or referred the genomic study.

Short Display Healthcare professional who requested or referred the genomic study
Cardinality 0..1
Type Reference ( Practitioner | PractitionerRole )
Summary false
representation GenomicStudy.interpreter
Element Id GenomicStudy.interpreter
Definition

Healthcare professionals who interpreted the genomic study.

Short Display Healthcare professionals who interpreted the genomic study
Cardinality 0..*
Type Reference ( Practitioner | PractitionerRole )
Summary false
Value GenomicStudy.reason
Element Id CCCCCCAGACAAGTAAAAGACATGACAGYGATACTTTCCCAGAGCTGAAGTTAACAAATGCACCTGGTTC TTTTACTAAGTGTTCAAATACCAGTGAACTTAAAGAATTTGTCAATCCTAGCCTTCCAAGAGAAGAAAAA GAAGAGAAACTAGAAACAGTTAAAGTGTCTAATAATGCTGAAGACCCCAAAGATCTCATGTTAAGTGGAG AAAGGGTTTTGCAAACTGAAAGATCTGTAGAGAGTAGCAGTATTTCAYTGGTACCTGGTACTGATTATGG CACTCAGGAAAGTATCTCGTTACTGGAAGTTAGCACTCTAGGGAAGGCAAAAACAGAACCAAATAAATGT GTGAGTCAGTGTGCAGCATTTGAAAACCCCAAGGGACTAATTCATGGTTGTTCCAAAGATAATAGAAATG ACACAGAAGGCTTTAAGTATCCATTGGGACATGAAGTTAACCACAGTCGGGAAACAAGCATAGAAATGGA AGAAAGTGAACTTGATGCTCAGTATTTGCAGAATACATTCAAGGTTTCAAAGCGCCAGTCATTTGCTCYG TTTTCAAATCCAGGAAATGCAGAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAAC AAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAA GCCTGTACAGACAGTTAATATCACTGCAGGCTTTCCTGTGGTTGGTCAGAAAGA GenomicStudy.reason
Definition

  Why the genomic study was performed.

Short Display Why the genomic study was performed
Cardinality 0..*
Type CodeableReference ( Condition | Observation )
Summary false
GenomicStudy.instantiatesCanonical
Element Id GenomicStudy.instantiatesCanonical
Definition

  The defined protocol that describes the study.

Short Display The defined protocol that describes the study
Cardinality 0..1
Type canonical ( PlanDefinition )
Summary false
GenomicStudy.instantiatesUri
Element Id GenomicStudy.instantiatesUri
Definition

Usage note: every effort has been made The URL pointing to ensure an externally maintained protocol that describes the examples are correct and useful, but they are study.

Short Display The URL pointing to an externally maintained protocol that describes the study
Cardinality 0..1
Type uri
Summary false
GenomicStudy.note
Element Id GenomicStudy.note
Definition

Comments related to the genomic study.

Short Display Comments related to the genomic study
Cardinality 0..*
Type Annotation
Summary false
GenomicStudy.description
Element Id GenomicStudy.description
Definition

Description of the genomic study.

Short Display Description of the genomic study
Cardinality 0..1
Type string
Summary false
GenomicStudy.analysis
Element Id GenomicStudy.analysis
Definition

The details about a specific analysis that was performed in this GenomicStudy.

Short Display Genomic Analysis Event
Cardinality 0..*
Summary false
GenomicStudy.analysis.identifier
Element Id GenomicStudy.analysis.identifier
Definition

Identifiers for the analysis event.

Short Display Identifiers for the analysis event
Note This is a business identifier, not a normative part resource identifier (see discussion )
Cardinality 0..*
Type Identifier
Summary false
GenomicStudy.analysis.methodType
Element Id GenomicStudy.analysis.methodType
Definition

Type of the specification. methods used in the analysis, e.g., Fluorescence in situ hybridization (FISH), Karyotyping, or Microsatellite instability testing (MSI).

Short Display Type of the methods used in the analysis (e.g., FISH, Karyotyping, MSI)
Cardinality 0..*
Terminology Binding GenomicStudyMethodType ( Example )
Type CodeableConcept
Summary false
GenomicStudy.analysis.changeType
Element Id GenomicStudy.analysis.changeType
Definition

Type of the genomic changes studied in the analysis, e.g., DNA, RNA, or amino acid change.

Short Display Type of the genomic changes studied in the analysis (e.g., DNA, RNA, or AA change)
Cardinality 0..*
Terminology Binding GenomicStudyChangeType ( Example )
Type CodeableConcept
Summary false
GenomicStudy.analysis.genomeBuild
Element Id GenomicStudy.analysis.genomeBuild
Definition

The reference genome build that is used in this analysis.

Short Display Genome build that is used in this analysis
Cardinality 0..1
Terminology Binding HumanRefSeqNCBIBuildId icon:
Type CodeableConcept
Summary false
GenomicStudy.analysis.instantiatesCanonical
Element Id GenomicStudy.analysis.instantiatesCanonical
Definition

The defined protocol that describes the analysis.

Short Display The defined protocol that describes the analysis
Cardinality 0..1
Type canonical ( PlanDefinition | ActivityDefinition )
Summary false
GenomicStudy.analysis.instantiatesUri
Element Id GenomicStudy.analysis.instantiatesUri
Definition

The URL pointing to an externally maintained protocol that describes the analysis.

Short Display The URL pointing to an externally maintained protocol that describes the analysis
Cardinality 0..1
Type uri
Summary false
GenomicStudy.analysis.title
Element Id GenomicStudy.analysis.title
Definition

Name of the analysis event (human friendly).

Short Display Name of the analysis event (human friendly)
Cardinality 0..1
Type string
Summary false
GenomicStudy.analysis.subject
Element Id GenomicStudy.analysis.subject
Definition

The subject of the analysis event.

Short Display The subject of the analysis event
Cardinality 0..1
Type Reference ( Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct )
Summary false
GenomicStudy.analysis.specimen
Element Id GenomicStudy.analysis.specimen
Definition

The specimen used in the analysis event.

Short Display The specimen used in the analysis event
Cardinality 0..*
Type Reference ( Specimen )
Summary false
GenomicStudy.analysis.date
Element Id GenomicStudy.analysis.date
Definition

The date of the analysis event.

Short Display The date of the analysis event
Cardinality 0..1
Type dateTime
Summary false
GenomicStudy.analysis.note
Element Id GenomicStudy.analysis.note
Definition

Any notes capture with the analysis event.

Short Display Any notes capture with the analysis event
Cardinality 0..*
Type Annotation
Summary false
GenomicStudy.analysis.protocolPerformed
Element Id GenomicStudy.analysis.protocolPerformed
Definition

The protocol that was performed for the analysis event.

Short Display The protocol that was performed for the analysis event
Cardinality 0..1
Type Reference ( Procedure | Task )
Summary false
GenomicStudy.analysis.regionsStudied
Element Id GenomicStudy.analysis.regionsStudied
Definition

The genomic regions to be studied in the analysis (BED file).

Short Display The genomic regions to be studied in the analysis (BED file)
Cardinality 0..*
Type Reference ( DocumentReference | Observation )
Summary false
GenomicStudy.analysis.regionsCalled
Element Id GenomicStudy.analysis.regionsCalled
Definition

Genomic regions actually called in the analysis event (BED file).

Short Display Genomic regions actually called in the analysis event (BED file)
Cardinality 0..*
Type Reference ( DocumentReference | Observation )
Summary false
GenomicStudy.analysis.input
Element Id GenomicStudy.analysis.input
Definition

Inputs for the analysis event.

Short Display Inputs for the analysis event
Cardinality 0..*
Summary false
GenomicStudy.analysis.input.file
Element Id GenomicStudy.analysis.input.file
Definition

File containing input data.

Short Display File containing input data
Cardinality 0..1
Type Reference ( DocumentReference )
Summary false
GenomicStudy.analysis.input.type
Element Id GenomicStudy.analysis.input.type
Definition

Type of input data, e.g., BAM, CRAM, or FASTA.

Short Display Type of input data (e.g., BAM, CRAM, or FASTA)
Cardinality 0..1
Terminology Binding GenomicStudyDataFormat ( Example )
Type CodeableConcept
Summary false
GenomicStudy.analysis.input.generatedBy[x]
Element Id GenomicStudy.analysis.input.generatedBy[x]
Definition

The analysis event or other GenomicStudy that generated this input file.

Short Display The analysis event or other GenomicStudy that generated this input file
Cardinality 0..1
Type Identifier | Reference ( GenomicStudy )
[x] Note See Choice of Datatypes for further information about how to use [x]
Summary false
GenomicStudy.analysis.output
Element Id GenomicStudy.analysis.output
Definition

Outputs for the analysis event.

Short Display Outputs for the analysis event
Cardinality 0..*
Summary false
GenomicStudy.analysis.output.file
Element Id GenomicStudy.analysis.output.file
Definition

File containing output data.

Short Display File containing output data
Cardinality 0..1
Type Reference ( DocumentReference )
Summary false
GenomicStudy.analysis.output.type
Element Id GenomicStudy.analysis.output.type
Definition

Type of output data, e.g., VCF, MAF, or BAM.

Short Display Type of output data (e.g., VCF, MAF, or BAM)
Cardinality 0..1
Terminology Binding GenomicStudyDataFormat ( Example )
Type CodeableConcept
Summary false
GenomicStudy.analysis.performer
Element Id GenomicStudy.analysis.performer
Definition

Performer for the analysis event.

Short Display Performer for the analysis event
Cardinality 0..*
Summary false
GenomicStudy.analysis.performer.actor
Element Id GenomicStudy.analysis.performer.actor
Definition

The organization, healthcare professional, or others who participated in performing this analysis.

Short Display The organization, healthcare professional, or others who participated in performing this analysis
Cardinality 0..1
Type Reference ( Practitioner | PractitionerRole | Organization | Device )
Summary false
GenomicStudy.analysis.performer.role
Element Id GenomicStudy.analysis.performer.role
Definition

Role of the actor for this analysis.

Short Display Role of the actor for this analysis
Cardinality 0..1
Type CodeableConcept
Summary false
GenomicStudy.analysis.device
Element Id GenomicStudy.analysis.device
Definition

Devices used for the analysis (e.g., instruments, software), with settings and parameters.

Short Display Devices used for the analysis (e.g., instruments, software), with settings and parameters
Cardinality 0..*
Summary false
GenomicStudy.analysis.device.device
Element Id GenomicStudy.analysis.device.device
Definition

Device used for the analysis.

Short Display Device used for the analysis
Cardinality 0..1
Type Reference ( Device )
Summary false
GenomicStudy.analysis.device.function
Element Id GenomicStudy.analysis.device.function
Definition

Specific function for the device used for the analysis.

Short Display Specific function for the device used for the analysis
Cardinality 0..1
Type CodeableConcept
Summary false