Cqgc Implementation Guide
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Extension: Ferlab.bio StructureDefinition/sequencing-experiment

Official URL: http://fhir.cqgc.ferlab.bio/StructureDefinition/sequencing-experiment Version: 0.1.0
Active as of 2025-08-25 Computable Name: sequencing-experiment

Context of Use

This extension may be used on the following element(s):

  • Element ID Task

Usage info

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Extension Content

Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

This structure is derived from Extension

Summary

Complex Extension:

  • platform: string: Platform
  • sequencerId: string: Sequencer Id
  • runName: string: Run name
  • runDate: dateTime: Run date
  • runAlias: string: Run alias
  • flowCellId: integer: Flow cell id
  • isPairedEnd: boolean: isPairedEnd
  • fragmentSize: integer: Fragment Size
  • experimentalStrategy: Coding: Experimental Strategy
  • labAliquotId: string: labAliquotId
  • captureKit: string: Capture Kit
  • baitDefinition: string: Bait Definition
  • protocol: string: protocol

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Sequencing experiment Extension
... Slices for extension Content/Rules for all slices
.... extension:platform S 0..1 Extension Platform
..... url 1..1 uri "platform"
..... valueString 1..1 string Value of extension
.... extension:sequencerId S 0..1 Extension Sequencer Id
..... url 1..1 uri "sequencerId"
..... valueString 1..1 string Value of extension
.... extension:runName S 0..1 Extension Run name
..... url 1..1 uri "runName"
..... valueString 1..1 string Value of extension
.... extension:runDate S 0..1 Extension Run date
..... url 1..1 uri "runDate"
..... valueDateTime 1..1 dateTime Value of extension
.... extension:runAlias S 0..1 Extension Run alias
..... url 1..1 uri "runAlias"
..... valueString 1..1 string Value of extension
.... extension:flowCellId S 0..1 Extension Flow cell id
..... url 1..1 uri "flowCellId"
..... valueInteger 1..1 integer Value of extension
.... extension:isPairedEnd S 0..1 Extension isPairedEnd
..... url 1..1 uri "isPairedEnd"
..... valueBoolean 1..1 boolean Value of extension
.... extension:fragmentSize S 0..1 Extension Fragment Size
..... url 1..1 uri "fragmentSize"
..... valueInteger 1..1 integer Value of extension
.... extension:experimentalStrategy 0..1 Extension Experimental Strategy
..... url 1..1 uri "experimentalStrategy"
..... valueCoding 1..1 Coding Value of extension
Binding: Experimental strategies (required): Experimental strategy
.... extension:labAliquotId S 0..1 Extension labAliquotId
..... url 1..1 uri "labAliquotId"
..... valueString 1..1 string Value of extension
.... extension:captureKit S 0..1 Extension Capture Kit
..... url 1..1 uri "captureKit"
..... valueString 1..1 string Value of extension
.... extension:baitDefinition S 0..1 Extension Bait Definition
..... url 1..1 uri "baitDefinition"
..... valueString 1..1 string Value of extension
.... extension:protocol S 0..1 Extension protocol
..... url 1..1 uri "protocol"
..... valueString 1..1 string Value of extension
... url 1..1 uri "http://fhir.cqgc.ferlab.bio/StructureDefinition/sequencing-experiment"
... value[x] 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Sequencing experiment Extension
... id 0..1 string Unique id for inter-element referencing
... Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... extension:platform S 0..1 Extension Platform
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "platform"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:sequencerId S 0..1 Extension Sequencer Id
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "sequencerId"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:runName S 0..1 Extension Run name
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "runName"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:runDate S 0..1 Extension Run date
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "runDate"
..... Slices for value[x] 1..1 dateTime Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueDateTime 1..1 dateTime Value of extension
.... extension:runAlias S 0..1 Extension Run alias
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "runAlias"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:flowCellId S 0..1 Extension Flow cell id
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "flowCellId"
..... Slices for value[x] 1..1 integer Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger 1..1 integer Value of extension
.... extension:isPairedEnd S 0..1 Extension isPairedEnd
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "isPairedEnd"
..... Slices for value[x] 1..1 boolean Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean 1..1 boolean Value of extension
.... extension:fragmentSize S 0..1 Extension Fragment Size
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "fragmentSize"
..... Slices for value[x] 1..1 integer Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger 1..1 integer Value of extension
.... extension:experimentalStrategy 0..1 Extension Experimental Strategy
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "experimentalStrategy"
..... Slices for value[x] 1..1 Coding Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueCoding 1..1 Coding Value of extension
Binding: Experimental strategies (required): Experimental strategy
.... extension:labAliquotId S 0..1 Extension labAliquotId
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "labAliquotId"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:captureKit S 0..1 Extension Capture Kit
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "captureKit"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:baitDefinition S 0..1 Extension Bait Definition
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "baitDefinition"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:protocol S 0..1 Extension protocol
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "protocol"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
... url 1..1 uri "http://fhir.cqgc.ferlab.bio/StructureDefinition/sequencing-experiment"

doco Documentation for this format

This structure is derived from Extension

Summary

Complex Extension:

  • platform: string: Platform
  • sequencerId: string: Sequencer Id
  • runName: string: Run name
  • runDate: dateTime: Run date
  • runAlias: string: Run alias
  • flowCellId: integer: Flow cell id
  • isPairedEnd: boolean: isPairedEnd
  • fragmentSize: integer: Fragment Size
  • experimentalStrategy: Coding: Experimental Strategy
  • labAliquotId: string: labAliquotId
  • captureKit: string: Capture Kit
  • baitDefinition: string: Bait Definition
  • protocol: string: protocol

Differential View

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Sequencing experiment Extension
... Slices for extension Content/Rules for all slices
.... extension:platform S 0..1 Extension Platform
..... url 1..1 uri "platform"
..... valueString 1..1 string Value of extension
.... extension:sequencerId S 0..1 Extension Sequencer Id
..... url 1..1 uri "sequencerId"
..... valueString 1..1 string Value of extension
.... extension:runName S 0..1 Extension Run name
..... url 1..1 uri "runName"
..... valueString 1..1 string Value of extension
.... extension:runDate S 0..1 Extension Run date
..... url 1..1 uri "runDate"
..... valueDateTime 1..1 dateTime Value of extension
.... extension:runAlias S 0..1 Extension Run alias
..... url 1..1 uri "runAlias"
..... valueString 1..1 string Value of extension
.... extension:flowCellId S 0..1 Extension Flow cell id
..... url 1..1 uri "flowCellId"
..... valueInteger 1..1 integer Value of extension
.... extension:isPairedEnd S 0..1 Extension isPairedEnd
..... url 1..1 uri "isPairedEnd"
..... valueBoolean 1..1 boolean Value of extension
.... extension:fragmentSize S 0..1 Extension Fragment Size
..... url 1..1 uri "fragmentSize"
..... valueInteger 1..1 integer Value of extension
.... extension:experimentalStrategy 0..1 Extension Experimental Strategy
..... url 1..1 uri "experimentalStrategy"
..... valueCoding 1..1 Coding Value of extension
Binding: Experimental strategies (required): Experimental strategy
.... extension:labAliquotId S 0..1 Extension labAliquotId
..... url 1..1 uri "labAliquotId"
..... valueString 1..1 string Value of extension
.... extension:captureKit S 0..1 Extension Capture Kit
..... url 1..1 uri "captureKit"
..... valueString 1..1 string Value of extension
.... extension:baitDefinition S 0..1 Extension Bait Definition
..... url 1..1 uri "baitDefinition"
..... valueString 1..1 string Value of extension
.... extension:protocol S 0..1 Extension protocol
..... url 1..1 uri "protocol"
..... valueString 1..1 string Value of extension
... url 1..1 uri "http://fhir.cqgc.ferlab.bio/StructureDefinition/sequencing-experiment"
... value[x] 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Sequencing experiment Extension
... id 0..1 string Unique id for inter-element referencing
... Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... extension:platform S 0..1 Extension Platform
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "platform"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:sequencerId S 0..1 Extension Sequencer Id
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "sequencerId"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:runName S 0..1 Extension Run name
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "runName"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:runDate S 0..1 Extension Run date
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "runDate"
..... Slices for value[x] 1..1 dateTime Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueDateTime 1..1 dateTime Value of extension
.... extension:runAlias S 0..1 Extension Run alias
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "runAlias"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:flowCellId S 0..1 Extension Flow cell id
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "flowCellId"
..... Slices for value[x] 1..1 integer Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger 1..1 integer Value of extension
.... extension:isPairedEnd S 0..1 Extension isPairedEnd
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "isPairedEnd"
..... Slices for value[x] 1..1 boolean Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueBoolean 1..1 boolean Value of extension
.... extension:fragmentSize S 0..1 Extension Fragment Size
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "fragmentSize"
..... Slices for value[x] 1..1 integer Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueInteger 1..1 integer Value of extension
.... extension:experimentalStrategy 0..1 Extension Experimental Strategy
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "experimentalStrategy"
..... Slices for value[x] 1..1 Coding Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueCoding 1..1 Coding Value of extension
Binding: Experimental strategies (required): Experimental strategy
.... extension:labAliquotId S 0..1 Extension labAliquotId
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "labAliquotId"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:captureKit S 0..1 Extension Capture Kit
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "captureKit"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:baitDefinition S 0..1 Extension Bait Definition
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "baitDefinition"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
.... extension:protocol S 0..1 Extension protocol
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... url 1..1 uri "protocol"
..... Slices for value[x] 1..1 string Value of extension
Slice: Unordered, Closed by type:$this
...... value[x]:valueString 1..1 string Value of extension
... url 1..1 uri "http://fhir.cqgc.ferlab.bio/StructureDefinition/sequencing-experiment"

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSetURI
Extension.extension:experimentalStrategy.value[x]:valueCodingrequiredexperimental-strategy(a valid code from Experimental strategies)
http://fhir.cqgc.ferlab.bio/ValueSet/experimental-strategy
From this IG

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()