FHIR Release 3 (STU) 5 Ballot

This page is part of the FHIR Specification (v3.0.2: STU (v5.0.0-ballot: R5 Ballot - see ballot notes 3). ). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions

Vocabulary Clinical Genomics icon Work Group   Maturity Level : 0 Informative   Trial Use Use Context Security Category : Any Patient Compartments : Patient

This is a code system defined by Detailed Descriptions for the FHIR project. elements in the GenomicStudy resource.

Orders and Observations Implant Status Implant Status
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 DomainResource
Summary false
GenomicStudy.identifier
Element Id GenomicStudy.identifier
Definition

Identifiers for this genomic study.

Defining URL: Short Display http://hl7.org/fhir/implant-status Identifiers for this genomic study
Name: Note Implant Status This is a business identifier, not a resource identifier (see discussion )
Definition: Cardinality A set codes that define the functional 0..*
Type Identifier
Summary false
GenomicStudy.status
Element Id GenomicStudy.status
Definition

The status of an implanted device. the genomic study.

Committee: Short Display The status of the genomic study
Cardinality Work Group 1..1
OID: Terminology Binding 2.16.840.1.113883.4.642.1.866 (for OID based terminology systems) GenomicStudyStatus ( Required )
Source Resource Type XML / JSON CodeableConcept
Is Modifier true (Reason: This Code system element is used in labeled as a modifier because it is a status element that contains status entered-in-error which means that the following value sets: resource should not be treated as valid)
Summary (A set codes that define true
GenomicStudy.type
Element Id GenomicStudy.type
Definition

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

Short Display The type of an implanted device.) the study (e.g., Familial variant segregation, Functional variation detection, or Gene expression profiling)
Cardinality 4.2.12.866.1 Content 0..*
Terminology Binding 4.2.12.866.2 GenomicStudyType ( Example )
Type CodeableConcept
Summary false
GenomicStudy.subject
Element Id GenomicStudy.subject
Definition

A set codes that define The primary subject of the functional status genomic study.

Short Display The primary subject of an implanted device. the genomic study
Cardinality 1..1
Type Reference ( Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct )
Summary true
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

This code system http://hl7.org/fhir/implant-status defines When the following codes: genomic study was started.

Short Display When the genomic study was started
Cardinality 0..1
Type dateTime
Summary false
Code 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
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
GenomicStudy.reason
Element Id GenomicStudy.reason
functional Definition

Why the genomic study was performed.

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

The implanted device is working normally defined protocol that describes the study.

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

The implanted device is not working URL pointing to an externally maintained protocol that describes the study.

Short Display The URL pointing to an externally maintained protocol that describes the study
Cardinality 0..1
disabled Type Disabled uri
Summary The implanted device has been turned off false
GenomicStudy.note
Element Id GenomicStudy.note
unknown Definition

Comments related to the genomic study.

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

Description of the functional status genomic study.

Short Display Description of the implant has not been determined 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

See Identifiers for the full registry of value sets analysis event.

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

Type of FHIR. the 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

Explanation Type of the columns 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 may appear on is used in this page: analysis.

Level Short Display A few code lists Genome build that FHIR defines are hierarchical - each code is assigned a level. In used in this scheme, some codes are under other codes, and imply 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 code they are under also applies analysis.

Source Short Display The source 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 definition analysis event (human friendly).

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

The subject of the value set draws in codes defined elsewhere) analysis event.

Code Short Display The code (used as subject of the code 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 resource instance). If the code is analysis event.

Short Display The specimen used in italics, this indicates 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 code is not selectable ('Abstract') analysis event.

Short Display The display (used 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 display element of a Coding analysis (BED file).

Short Display The genomic regions to be studied in the analysis (BED file)
Cardinality ). If there is no display, implementers should not simply display 0..*
Type Reference ( DocumentReference | Observation )
Summary false
GenomicStudy.analysis.regionsCalled
Element Id GenomicStudy.analysis.regionsCalled
Definition

Genomic regions actually called in the code, but map analysis event (BED file).

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

Inputs for the meaning of analysis event.

Short Display Inputs for the concept analysis event
Comments Cardinality Additional notes 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 code 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