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Class: Cell

Default Cell description

URI: https://github.com/vdjserver/vdjserver-airr-schema/Cell

 classDiagram
    class Cell
    click Cell href "../Cell/"
      AIRRStandards <|-- Cell
        click AIRRStandards href "../AIRRStandards/"

      Cell : cell_id

      Cell : cell_label

      Cell : cell_phenotype

      Cell : cell_subset





        Cell --> "0..1" CellSubsetOntology : cell_subset
        click CellSubsetOntology href "../CellSubsetOntology/"



      Cell : cell_type





        Cell --> "0..1" CellTypeEnum : cell_type
        click CellTypeEnum href "../CellTypeEnum/"



      Cell : data_processing_id

      Cell : receptors

      Cell : repertoire_id

      Cell : virtual_pairing

Inheritance

Slots

Name Cardinality and Range Description Inheritance
cell_id 0..1
String		 direct
repertoire_id 0..1
String		 direct
data_processing_id 0..1
String		 direct
receptors *
String		 Array of receptor identifiers defined for the Receptor objects associated wit... direct
cell_subset 0..1
CellSubsetOntology		 direct
cell_phenotype 0..1
String		 List of cellular markers and their expression levels used to isolate the cell... direct
cell_label 0..1
String		 Free text cell type annotation direct
virtual_pairing 0..1
Boolean		 boolean to indicate if pairing was inferred direct
cell_type 0..1
CellTypeEnum		 Cell type (source) direct

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self https://github.com/vdjserver/vdjserver-airr-schema/Cell
native https://github.com/vdjserver/vdjserver-airr-schema/Cell

LinkML Source

Direct

name: Cell
description: Default Cell description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- cell_id
- repertoire_id
- data_processing_id
- receptors
- cell_subset
- cell_phenotype
- cell_label
- virtual_pairing
- cell_type

Induced

name: Cell
description: Default Cell description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  cell_id:
    name: cell_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - Rearrangement
    - Node
    - Cell
    - Expression
    - Reactivity
    range: string
  repertoire_id:
    name: repertoire_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - Repertoire
    - RepertoireFilter
    - Rearrangement
    - Clone
    - Node
    - Cell
    - Expression
    - Reactivity
    - ADCRearrangementLoad
    - ADCDownloadCacheRepertoire
    - StatisticsCacheRepertoire
    - VisualizationDocument
    range: string
  data_processing_id:
    name: data_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - DataProcessing
    - Rearrangement
    - Clone
    - Cell
    - Expression
    - Reactivity
    range: string
  receptors:
    name: receptors
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Array of receptor identifiers defined for the Receptor objects associated
      with this cell
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - Cell
    range: string
    multivalued: true
  cell_subset:
    name: cell_subset
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: CellSubsetOntology
  cell_phenotype:
    name: cell_phenotype
    annotations:
      nullable:
        tag: nullable
        value: true
    description: List of cellular markers and their expression levels used to isolate
      the cell population.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: string
  cell_label:
    name: cell_label
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Free text cell type annotation. Primarily used for annotating cell
      types that are not  provided in the Cell Ontology.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: string
  virtual_pairing:
    name: virtual_pairing
    annotations:
      nullable:
        tag: nullable
        value: true
    description: boolean to indicate if pairing was inferred.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Cell
    domain_of:
    - Cell
    range: boolean
  cell_type:
    name: cell_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Cell type (source). Most often the type should be "observed," meaning
      it corresponds to an actual physical sample that was sequenced. Other allowed
      values are "simulated," i.e. the Cells were generated in silico and there is
      no linked Subject/Sample metadata, and "inferred" for Cells that are phylogenetically
      reconstructed from observed sequences. Inferred Cells should be assigned to
      a Repertoire with repertoire_type=inferred.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: Cell
    domain_of:
    - Cell
    range: CellTypeEnum