Skip to content

Class: Sequencing Experiment Assay (SequencingAssay)

A sequencing experiment performed on a Biospecimen.

URI: cam:SequencingAssay

 classDiagram
    class SequencingAssay
    click SequencingAssay href "../SequencingAssay/"
      Assay <|-- SequencingAssay
        click Assay href "../Assay/"


      SequencingAssay <|-- GenomicsAssay
        click GenomicsAssay href "../GenomicsAssay/"
      SequencingAssay <|-- TranscriptomicsAssay
        click TranscriptomicsAssay href "../TranscriptomicsAssay/"


      SequencingAssay : access_policy_id





        SequencingAssay --> "1" AccessPolicy : access_policy_id
        click AccessPolicy href "../AccessPolicy/"



      SequencingAssay : activity_definition_id





        SequencingAssay --> "0..1" ActivityDefinition : activity_definition_id
        click ActivityDefinition href "../ActivityDefinition/"



      SequencingAssay : adapter_sequencing

      SequencingAssay : assay_id

      SequencingAssay : assay_source

      SequencingAssay : assay_type





        SequencingAssay --> "1" EnumAssayType : assay_type
        click EnumAssayType href "../EnumAssayType/"



      SequencingAssay : experiment_date

      SequencingAssay : experiment_strategy





        SequencingAssay --> "0..1" EnumSequencingStrategy : experiment_strategy
        click EnumSequencingStrategy href "../EnumSequencingStrategy/"



      SequencingAssay : external_id

      SequencingAssay : file_id





        SequencingAssay --> "*" File : file_id
        click File href "../File/"



      SequencingAssay : flow_cell

      SequencingAssay : instrument_model





        SequencingAssay --> "0..1" EnumSequencingInstrument : instrument_model
        click EnumSequencingInstrument href "../EnumSequencingInstrument/"



      SequencingAssay : is_adapter_trimmed

      SequencingAssay : is_paired_end

      SequencingAssay : lane_number

      SequencingAssay : library_name

      SequencingAssay : platform





        SequencingAssay --> "0..1" EnumSequencingPlatform : platform
        click EnumSequencingPlatform href "../EnumSequencingPlatform/"



      SequencingAssay : quality_scale





        SequencingAssay --> "0..1" EnumReadGroupQualityScale : quality_scale
        click EnumReadGroupQualityScale href "../EnumReadGroupQualityScale/"



      SequencingAssay : reference_genome





        SequencingAssay --> "0..1" EnumReferenceGenome : reference_genome
        click EnumReferenceGenome href "../EnumReferenceGenome/"



      SequencingAssay : sample_id





        SequencingAssay --> "*" Sample : sample_id
        click Sample href "../Sample/"



      SequencingAssay : sequencing_center_id





        SequencingAssay --> "0..1" EnumSequencingCenter : sequencing_center_id
        click EnumSequencingCenter href "../EnumSequencingCenter/"



      SequencingAssay : study_id





        SequencingAssay --> "1" Study : study_id
        click Study href "../Study/"



      SequencingAssay : subject_id





        SequencingAssay --> "*" Subject : subject_id
        click Subject href "../Subject/"



      SequencingAssay : total_reads

      SequencingAssay : workflow_endpoint

      SequencingAssay : workflow_tool

      SequencingAssay : workflow_type

      SequencingAssay : workflow_version

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sequencing_center_id 0..1
EnumSequencingCenter		 The unique identifier for the sequencing center that performed the assay direct
library_name 0..1
String		 The name of the sequencing library direct
experiment_date 0..1
Date		 The date the sequencing experiment was performed direct
experiment_strategy 0..1
EnumSequencingStrategy		 The sequencing strategy used direct
is_paired_end 0..1
Boolean		 Whether the sequencing reads are paired-end direct
platform 0..1
EnumSequencingPlatform		 The sequencing platform used direct
instrument_model 0..1
EnumSequencingInstrument		 The sequencing instrument model used direct
total_reads 0..1
Integer		 The total number of reads generated direct
is_adapter_trimmed 0..1
Boolean		 Whether adapter sequences were trimmed direct
adapter_sequencing 0..1
String		 The adapter sequence used, if known direct
quality_scale 0..1
EnumReadGroupQualityScale		 The quality score scale used for this read group direct
reference_genome 0..1
EnumReferenceGenome		 The reference genome build this file is aligned to or was generated against direct
workflow_type 0..1
String		 The type of workflow that produced this file direct
workflow_tool 0..1
String		 The tool used by the workflow that produced this file direct
workflow_version 0..1
String		 The version of the workflow tool used to produce this file direct
workflow_endpoint 0..1
String		 The endpoint of the workflow that produced this file direct
flow_cell 0..1
String		 The flow cell identifier for this read group direct
lane_number 0..1
Integer		 The lane number for this read group direct
assay_id 1
DiGlobalID		 The unique identifier for the Assay Assay
subject_id *
Subject		 INCLUDE Global ID for the Subject Assay
sample_id *
Sample		 The unique identifier for this Sample Assay
file_id *
File		 Unique identifier for this File Assay
assay_type 1
EnumAssayType		 The type of assay performed Assay
assay_source 0..1
String		 The original description of the Assay performed Assay
activity_definition_id 0..1
ActivityDefinition		 Unique identifier for this Activity Definition Assay
external_id *
Uriorcurie		 Other identifiers for this entity, eg, from the submitting study or in system... Record
access_policy_id 1
AccessPolicy		 Global identifier for the access policy that applies to this row of data Record
study_id 1
Study		 INCLUDE Global ID for the study Record

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self cam:SequencingAssay
native cam:SequencingAssay

LinkML Source

Direct

name: SequencingAssay
description: A sequencing experiment performed on a Biospecimen.
title: Sequencing Experiment Assay
from_schema: https://includedcc.org/common-access-model
is_a: Assay
slots:
- sequencing_center_id
- library_name
- experiment_date
- experiment_strategy
- is_paired_end
- platform
- instrument_model
- total_reads
- is_adapter_trimmed
- adapter_sequencing
- quality_scale
- reference_genome
- workflow_type
- workflow_tool
- workflow_version
- workflow_endpoint
- flow_cell
- lane_number

Induced

name: SequencingAssay
description: A sequencing experiment performed on a Biospecimen.
title: Sequencing Experiment Assay
from_schema: https://includedcc.org/common-access-model
is_a: Assay
attributes:
  sequencing_center_id:
    name: sequencing_center_id
    description: The unique identifier for the sequencing center that performed the
      assay.
    title: Sequencing Center ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: EnumSequencingCenter
  library_name:
    name: library_name
    description: The name of the sequencing library.
    title: Library Name
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  experiment_date:
    name: experiment_date
    description: The date the sequencing experiment was performed.
    title: Experiment Date
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: date
  experiment_strategy:
    name: experiment_strategy
    description: The sequencing strategy used.
    title: Experiment Strategy
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: EnumSequencingStrategy
  is_paired_end:
    name: is_paired_end
    description: Whether the sequencing reads are paired-end.
    title: Is Paired End
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: boolean
  platform:
    name: platform
    description: The sequencing platform used.
    title: Platform
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: EnumSequencingPlatform
  instrument_model:
    name: instrument_model
    description: The sequencing instrument model used.
    title: Instrument Model
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: EnumSequencingInstrument
  total_reads:
    name: total_reads
    description: The total number of reads generated.
    title: Total Reads
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: integer
  is_adapter_trimmed:
    name: is_adapter_trimmed
    description: Whether adapter sequences were trimmed.
    title: Is Adapter Trimmed
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: boolean
  adapter_sequencing:
    name: adapter_sequencing
    description: The adapter sequence used, if known.
    title: Adapter Sequence
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  quality_scale:
    name: quality_scale
    description: The quality score scale used for this read group.
    title: Quality Scale
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: EnumReadGroupQualityScale
  reference_genome:
    name: reference_genome
    description: The reference genome build this file is aligned to or was generated
      against.
    title: Reference Genome
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: EnumReferenceGenome
  workflow_type:
    name: workflow_type
    description: 'The type of workflow that produced this file. (Kids First Dataservice
      field: worflow_type)'
    title: Workflow Type
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  workflow_tool:
    name: workflow_tool
    description: 'The tool used by the workflow that produced this file. (Kids First
      Dataservice field: worflow_tool)'
    title: Workflow Tool
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  workflow_version:
    name: workflow_version
    description: The version of the workflow tool used to produce this file.
    title: Workflow Version
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  workflow_endpoint:
    name: workflow_endpoint
    description: The endpoint of the workflow that produced this file. (Kids First
      Dataservice field - worflow_endpoint)
    title: Workflow Endpoint
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  flow_cell:
    name: flow_cell
    description: The flow cell identifier for this read group.
    title: Flow Cell
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: string
  lane_number:
    name: lane_number
    description: The lane number for this read group.
    title: Lane Number
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - SequencingAssay
    range: integer
  assay_id:
    name: assay_id
    description: The unique identifier for the Assay.
    title: Assay ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    identifier: true
    owner: SequencingAssay
    domain_of:
    - Assay
    range: diGlobalID
    required: true
  subject_id:
    name: subject_id
    description: INCLUDE Global ID for the Subject
    title: Study ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Subject
    - Demographics
    - Person
    - FamilyRelationship
    - FamilyMembership
    - SubjectAssertion
    - Sample
    - Encounter
    - File
    - Assay
    range: Subject
    multivalued: true
  sample_id:
    name: sample_id
    description: The unique identifier for this Sample.
    title: Sample ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Sample
    - Aliquot
    - File
    - Assay
    range: Sample
    multivalued: true
  file_id:
    name: file_id
    description: Unique identifier for this File.
    title: File ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - File
    - Assay
    - Dataset
    range: File
    multivalued: true
  assay_type:
    name: assay_type
    description: The type of assay performed.
    title: Assay Type
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Assay
    range: EnumAssayType
    required: true
  assay_source:
    name: assay_source
    description: The original description of the Assay performed.
    title: Assay Source Text
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Assay
    range: string
  activity_definition_id:
    name: activity_definition_id
    description: Unique identifier for this Activity Definition.
    title: Activity Definition ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - EncounterDefinition
    - ActivityDefinition
    - Assay
    range: ActivityDefinition
  external_id:
    name: external_id
    description: Other identifiers for this entity, eg, from the submitting study
      or in systems like dbGaP
    title: External Identifiers
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Record
    range: uriorcurie
    required: false
    multivalued: true
  access_policy_id:
    name: access_policy_id
    description: Global identifier for the access policy that applies to this row
      of data.
    title: Access Policy ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Record
    - AccessPolicy
    range: AccessPolicy
    required: true
  study_id:
    name: study_id
    description: INCLUDE Global ID for the study
    title: Study ID
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: SequencingAssay
    domain_of:
    - Record
    - StudyMetadata
    range: Study
    required: true
    multivalued: false