Skip to content

Class: CellProcessing

URI: ak_schema:CellProcessing

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

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		 Commonly-used designation of isolated cell population direct
cell_phenotype 0..1
String		 List of cellular markers and their expression levels used to isolate the cell... 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/airr-knowledge/ak-schema

Mappings

Mapping Type Mapped Value
self ak_schema:CellProcessing
native ak_schema:CellProcessing

LinkML Source

Direct

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

Induced

name: CellProcessing
from_schema: https://github.com/airr-knowledge/ak-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/airr-knowledge/ak-schema
    rank: 1000
    alias: tissue_processing
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - CellProcessing
    - SampleProcessing
    range: string
  cell_subset:
    name: cell_subset
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Commonly-used designation of isolated cell population
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_subset
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - CellProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_phenotype
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - CellProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_species
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: single_cell
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_number
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cells_per_reaction
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_storage
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_quality
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_isolation
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_processing_protocol
    owner: CellProcessing
    domain_of:
    - CellIsolationProcessing
    - CellProcessing
    - SampleProcessing
    range: string