Skip to content

Class: AIRRSequencingAssay

URI: OBI:0600047

classDiagram class AIRRSequencingAssay click AIRRSequencingAssay href "../AIRRSequencingAssay" SequencingRun <|-- AIRRSequencingAssay click SequencingRun href "../SequencingRun" Assay <|-- AIRRSequencingAssay click Assay href "../Assay" AIRRSequencingAssay : akc_id AIRRSequencingAssay : assay_type AIRRSequencingAssay : description AIRRSequencingAssay : name AIRRSequencingAssay : repertoire_id AIRRSequencingAssay : sequencing_facility AIRRSequencingAssay : sequencing_files AIRRSequencingAssay --> "0..1" SequencingData : sequencing_files click SequencingData href "../SequencingData" AIRRSequencingAssay : sequencing_kit AIRRSequencingAssay : sequencing_platform AIRRSequencingAssay : sequencing_run_date AIRRSequencingAssay : sequencing_run_id AIRRSequencingAssay : specimen AIRRSequencingAssay --> "0..1" Specimen : specimen click Specimen href "../Specimen" AIRRSequencingAssay : specimen_processing AIRRSequencingAssay --> "*" SpecimenProcessing : specimen_processing click SpecimenProcessing href "../SpecimenProcessing" AIRRSequencingAssay : target_entity_type AIRRSequencingAssay : tcell_chains AIRRSequencingAssay --> "*" Chain : tcell_chains click Chain href "../Chain" AIRRSequencingAssay : tcell_receptors AIRRSequencingAssay --> "*" TCellReceptor : tcell_receptors click TCellReceptor href "../TCellReceptor" AIRRSequencingAssay : total_reads_passing_qc_filter AIRRSequencingAssay : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
repertoire_id 0..1
String		 direct
tcell_receptors *
TCellReceptor		 The T cell receptors being measured direct
tcell_chains *
Chain		 The T cell receptor chains being measured direct
sequencing_run_id 0..1
String		 ID of sequencing run assigned by the sequencing facility SequencingRun
total_reads_passing_qc_filter 0..1
Integer		 Number of usable reads for analysis SequencingRun
sequencing_platform 0..1
String		 Designation of sequencing instrument used SequencingRun
sequencing_facility 0..1
String		 Name and address of sequencing facility SequencingRun
sequencing_run_date 0..1
Datetime		 Date of sequencing run SequencingRun
sequencing_kit 0..1
String		 Name, manufacturer, order and lot numbers of sequencing kit SequencingRun
sequencing_files 0..1
SequencingData		 Set of sequencing files produced by the sequencing run SequencingRun
specimen 0..1
Specimen		 The specimen that was input for an assay Assay
specimen_processing *
SpecimenProcessing		 A series of zero or more specimen processing steps that precede an assay Assay
type 0..1
String		 Assay
assay_type 0..1
String		 The specific type of an assay Assay
target_entity_type 0..1
String		 The type of the entity being measured Assay
name 0..1
String		 A human-readable name for a thing NamedThing
description 0..1
String		 A human-readable description for a thing NamedThing
akc_id 1
Uriorcurie		 A unique identifier for a thing in the AKC AKObject

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/airr-knowledge/ak-schema

Mappings

Mapping Type Mapped Value
self OBI:0600047
native ak_schema:AIRRSequencingAssay

LinkML Source

Direct

name: AIRRSequencingAssay
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: Assay
mixins:
- SequencingRun
slots:
- repertoire_id
- tcell_receptors
- tcell_chains
class_uri: OBI:0600047

Induced

name: AIRRSequencingAssay
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: Assay
mixins:
- SequencingRun
attributes:
  repertoire_id:
    name: repertoire_id
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: repertoire_id
    owner: AIRRSequencingAssay
    domain_of:
    - AIRRSequencingAssay
    - Repertoire
    - RepertoireGroupDetail
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string
  tcell_receptors:
    name: tcell_receptors
    description: The T cell receptors being measured
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: tcell_receptors
    owner: AIRRSequencingAssay
    domain_of:
    - AIRRSequencingAssay
    - TCellReceptorEpitopeBindingAssay
    range: TCellReceptor
    multivalued: true
  tcell_chains:
    name: tcell_chains
    description: The T cell receptor chains being measured
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: tcell_chains
    owner: AIRRSequencingAssay
    domain_of:
    - AIRRSequencingAssay
    - TCellReceptorEpitopeBindingAssay
    range: Chain
    multivalued: true
  sequencing_run_id:
    name: sequencing_run_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ID of sequencing run assigned by the sequencing facility
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_run_id
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  total_reads_passing_qc_filter:
    name: total_reads_passing_qc_filter
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of usable reads for analysis
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: total_reads_passing_qc_filter
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: integer
  sequencing_platform:
    name: sequencing_platform
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Designation of sequencing instrument used
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_platform
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  sequencing_facility:
    name: sequencing_facility
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name and address of sequencing facility
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_facility
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  sequencing_run_date:
    name: sequencing_run_date
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Date of sequencing run
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_run_date
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: datetime
  sequencing_kit:
    name: sequencing_kit
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name, manufacturer, order and lot numbers of sequencing kit
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_kit
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  sequencing_files:
    name: sequencing_files
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Set of sequencing files produced by the sequencing run
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_files
    owner: AIRRSequencingAssay
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: SequencingData
  specimen:
    name: specimen
    description: The specimen that was input for an assay
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: OBI:0000293
    alias: specimen
    owner: AIRRSequencingAssay
    domain_of:
    - SpecimenCollection
    - SpecimenProcessing
    - Assay
    range: Specimen
  specimen_processing:
    name: specimen_processing
    description: A series of zero or more specimen processing steps that precede an
      assay
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: BFO:0000051
    alias: specimen_processing
    owner: AIRRSequencingAssay
    domain_of:
    - Assay
    range: SpecimenProcessing
    multivalued: true
  type:
    name: type
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    designates_type: true
    alias: type
    owner: AIRRSequencingAssay
    domain_of:
    - Assay
    - TCellReceptor
    - Epitope
    range: string
  assay_type:
    name: assay_type
    description: The specific type of an assay
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: assay_type
    owner: AIRRSequencingAssay
    domain_of:
    - Assay
    range: string
  target_entity_type:
    name: target_entity_type
    description: The type of the entity being measured
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: target_entity_type
    owner: AIRRSequencingAssay
    domain_of:
    - Assay
    - Assessment
    range: string
  name:
    name: name
    description: A human-readable name for a thing
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: AIRRSequencingAssay
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A human-readable description for a thing
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: AIRRSequencingAssay
    domain_of:
    - NamedThing
    range: string
  akc_id:
    name: akc_id
    description: A unique identifier for a thing in the AKC.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: akc_id
    owner: AIRRSequencingAssay
    domain_of:
    - AKObject
    range: uriorcurie
    required: true
class_uri: OBI:0600047