Class: CellProcessing

Default CellProcessing description

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

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

      CellProcessing : cell_isolation

      CellProcessing : cell_label

      CellProcessing : cell_number

      CellProcessing : cell_phenotype

      CellProcessing : cell_processing_protocol

      CellProcessing : cell_quality

      CellProcessing : cell_species





        CellProcessing --> "0..1" CellSpeciesOntology : cell_species
        click CellSpeciesOntology href "../CellSpeciesOntology/"



      CellProcessing : cell_storage

      CellProcessing : cell_subset





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



      CellProcessing : cells_per_reaction

      CellProcessing : single_cell

      CellProcessing : tissue_processing

Inheritance

AIRRStandards
- CellProcessing

Slots

Name	Cardinality and Range	Description	Inheritance
tissue_processing	0..1 String	Enzymatic digestion and/or physical methods used to isolate cells from sample	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
cell_species	0..1 CellSpeciesOntology	Binomial designation of the species from which the analyzed cells originate	direct
single_cell	0..1 Boolean	TRUE if single cells were isolated into separate compartments	direct
cell_number	0..1 Integer	Total number of cells that went into the experiment	direct
cells_per_reaction	0..1 Integer	Number of cells for each biological replicate	direct
cell_storage	0..1 Boolean	TRUE if cells were cryo-preserved between isolation and further processing	direct
cell_quality	0..1 String	Relative amount of viable cells after preparation and (if applicable) thawing	direct
cell_isolation	0..1 String	Description of the procedure used for marker-based isolation or enrich cells	direct
cell_processing_protocol	0..1 String	Description of the methods applied to the sample including cell preparation/ ...	direct

Identifier and Mapping Information

Schema Source

from schema: https://github.com/vdjserver/vdjserver-airr-schema

Mappings

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

LinkML Source

Direct

name: CellProcessing
description: Default CellProcessing description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- tissue_processing
- cell_subset
- cell_phenotype
- cell_label
- cell_species
- single_cell
- cell_number
- cells_per_reaction
- cell_storage
- cell_quality
- cell_isolation
- cell_processing_protocol

Induced

name: CellProcessing
description: Default CellProcessing description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  tissue_processing:
    name: tissue_processing
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Enzymatic digestion and/or physical methods used to isolate cells
      from sample
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  cell_subset:
    name: cell_subset
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    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: CellProcessing
    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: CellProcessing
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: string
  cell_species:
    name: cell_species
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Binomial designation of the species from which the analyzed cells
      originate. Typically, this value should be identical to `species`, in which
      case it SHOULD NOT be set explicitly. However, there are valid experimental
      setups in which the two might differ, e.g., chimeric animal models. If set,
      this key will overwrite the `species` information for all lower layers of the
      schema.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: CellSpeciesOntology
  single_cell:
    name: single_cell
    annotations:
      nullable:
        tag: nullable
        value: true
    description: TRUE if single cells were isolated into separate compartments
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: boolean
  cell_number:
    name: cell_number
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Total number of cells that went into the experiment
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: integer
  cells_per_reaction:
    name: cells_per_reaction
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of cells for each biological replicate
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: integer
  cell_storage:
    name: cell_storage
    annotations:
      nullable:
        tag: nullable
        value: true
    description: TRUE if cells were cryo-preserved between isolation and further processing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: boolean
  cell_quality:
    name: cell_quality
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Relative amount of viable cells after preparation and (if applicable)
      thawing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  cell_isolation:
    name: cell_isolation
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Description of the procedure used for marker-based isolation or enrich
      cells
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  cell_processing_protocol:
    name: cell_processing_protocol
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Description of the methods applied to the sample including cell preparation/
      isolation/enrichment and nucleic acid extraction. This should closely mirror
      the Materials and methods section in the manuscript.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: CellProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string