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Class: WGS/WXS Assay (GenomicsAssay)

A whole genome or whole exome sequencing experiment performed on a Biospecimen.

URI: cam:GenomicsAssay

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

      GenomicsAssay : access_policy_id





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



      GenomicsAssay : activity_definition_id





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



      GenomicsAssay : adapter_sequencing

      GenomicsAssay : assay_id

      GenomicsAssay : assay_source

      GenomicsAssay : assay_type





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



      GenomicsAssay : experiment_date

      GenomicsAssay : experiment_strategy





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



      GenomicsAssay : external_id

      GenomicsAssay : file_id





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



      GenomicsAssay : flow_cell

      GenomicsAssay : instrument_model





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



      GenomicsAssay : is_adapter_trimmed

      GenomicsAssay : is_paired_end

      GenomicsAssay : lane_number

      GenomicsAssay : library_name

      GenomicsAssay : max_insert_size

      GenomicsAssay : mean_depth

      GenomicsAssay : mean_insert_size

      GenomicsAssay : mean_read_length

      GenomicsAssay : platform





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



      GenomicsAssay : quality_scale





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



      GenomicsAssay : reference_genome





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



      GenomicsAssay : sample_id





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



      GenomicsAssay : sequencing_center_id





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



      GenomicsAssay : study_id





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



      GenomicsAssay : subject_id





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



      GenomicsAssay : target_capture_kit

      GenomicsAssay : total_reads

      GenomicsAssay : workflow_endpoint

      GenomicsAssay : workflow_tool

      GenomicsAssay : workflow_type

      GenomicsAssay : workflow_version

Inheritance

Slots

Name Cardinality and Range Description Inheritance
max_insert_size 0..1
Integer		 The maximum insert size, in base pairs direct
mean_insert_size 0..1
Float		 The mean insert size, in base pairs direct
mean_depth 0..1
Float		 The mean sequencing depth of coverage direct
mean_read_length 0..1
Integer		 The mean read length, in base pairs direct
target_capture_kit 0..1
String		 The target capture kit used, if any direct
sequencing_center_id 0..1
EnumSequencingCenter		 The unique identifier for the sequencing center that performed the assay SequencingAssay
library_name 0..1
String		 The name of the sequencing library SequencingAssay
experiment_date 0..1
Date		 The date the sequencing experiment was performed SequencingAssay
experiment_strategy 0..1
EnumSequencingStrategy		 The sequencing strategy used SequencingAssay
is_paired_end 0..1
Boolean		 Whether the sequencing reads are paired-end SequencingAssay
platform 0..1
EnumSequencingPlatform		 The sequencing platform used SequencingAssay
instrument_model 0..1
EnumSequencingInstrument		 The sequencing instrument model used SequencingAssay
total_reads 0..1
Integer		 The total number of reads generated SequencingAssay
is_adapter_trimmed 0..1
Boolean		 Whether adapter sequences were trimmed SequencingAssay
adapter_sequencing 0..1
String		 The adapter sequence used, if known SequencingAssay
quality_scale 0..1
EnumReadGroupQualityScale		 The quality score scale used for this read group SequencingAssay
reference_genome 0..1
EnumReferenceGenome		 The reference genome build this file is aligned to or was generated against SequencingAssay
workflow_type 0..1
String		 The type of workflow that produced this file SequencingAssay
workflow_tool 0..1
String		 The tool used by the workflow that produced this file SequencingAssay
workflow_version 0..1
String		 The version of the workflow tool used to produce this file SequencingAssay
workflow_endpoint 0..1
String		 The endpoint of the workflow that produced this file SequencingAssay
flow_cell 0..1
String		 The flow cell identifier for this read group SequencingAssay
lane_number 0..1
Integer		 The lane number for this read group SequencingAssay
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:GenomicsAssay
native cam:GenomicsAssay

LinkML Source

Direct

name: GenomicsAssay
description: A whole genome or whole exome sequencing experiment performed on a Biospecimen.
title: WGS/WXS Assay
from_schema: https://includedcc.org/common-access-model
is_a: SequencingAssay
slots:
- max_insert_size
- mean_insert_size
- mean_depth
- mean_read_length
- target_capture_kit

Induced

name: GenomicsAssay
description: A whole genome or whole exome sequencing experiment performed on a Biospecimen.
title: WGS/WXS Assay
from_schema: https://includedcc.org/common-access-model
is_a: SequencingAssay
attributes:
  max_insert_size:
    name: max_insert_size
    description: The maximum insert size, in base pairs.
    title: Max Insert Size
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: GenomicsAssay
    domain_of:
    - GenomicsAssay
    range: integer
  mean_insert_size:
    name: mean_insert_size
    description: The mean insert size, in base pairs.
    title: Mean Insert Size
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: GenomicsAssay
    domain_of:
    - GenomicsAssay
    range: float
  mean_depth:
    name: mean_depth
    description: The mean sequencing depth of coverage.
    title: Mean Depth
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: GenomicsAssay
    domain_of:
    - GenomicsAssay
    range: float
  mean_read_length:
    name: mean_read_length
    description: The mean read length, in base pairs.
    title: Mean Read Length
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: GenomicsAssay
    domain_of:
    - GenomicsAssay
    range: integer
  target_capture_kit:
    name: target_capture_kit
    description: The target capture kit used, if any.
    title: Target Capture Kit
    from_schema: https://includedcc.org/common-access-model
    rank: 1000
    owner: GenomicsAssay
    domain_of:
    - GenomicsAssay
    range: string
  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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    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: GenomicsAssay
    domain_of:
    - Record
    - StudyMetadata
    range: Study
    required: true
    multivalued: false