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Class: CellIsolationProcessing

URI: OBI:00000512

classDiagram class CellIsolationProcessing click CellIsolationProcessing href "../CellIsolationProcessing" SpecimenProcessing <|-- CellIsolationProcessing click SpecimenProcessing href "../SpecimenProcessing" CellIsolationProcessing : akc_id CellIsolationProcessing : cell_isolation CellIsolationProcessing : cell_number CellIsolationProcessing : cell_phenotype CellIsolationProcessing : cell_processing_protocol CellIsolationProcessing : cell_quality CellIsolationProcessing : cell_species CellIsolationProcessing --> "0..1" CellSpeciesOntology : cell_species click CellSpeciesOntology href "../CellSpeciesOntology" CellIsolationProcessing : cell_storage CellIsolationProcessing : cell_subset CellIsolationProcessing --> "0..1" CellSubsetOntology : cell_subset click CellSubsetOntology href "../CellSubsetOntology" CellIsolationProcessing : cells_per_reaction CellIsolationProcessing : description CellIsolationProcessing : name CellIsolationProcessing : single_cell CellIsolationProcessing : specimen CellIsolationProcessing --> "0..1" Specimen : specimen click Specimen href "../Specimen" CellIsolationProcessing : 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
specimen 0..1
Specimen		 The specimen that was input for an assay SpecimenProcessing
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:00000512
native ak_schema:CellIsolationProcessing

LinkML Source

Direct

name: CellIsolationProcessing
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: SpecimenProcessing
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
class_uri: OBI:00000512

Induced

name: CellIsolationProcessing
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: SpecimenProcessing
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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    domain_of:
    - CellIsolationProcessing
    - CellProcessing
    - SampleProcessing
    range: string
  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: CellIsolationProcessing
    domain_of:
    - SpecimenCollection
    - SpecimenProcessing
    - Assay
    range: Specimen
  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: CellIsolationProcessing
    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: CellIsolationProcessing
    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: CellIsolationProcessing
    domain_of:
    - AKObject
    range: uriorcurie
    required: true
class_uri: OBI:00000512