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Class: Data & Processing (CytometryDataProcessing)

The data processing steps used in a cytometry experiment.

URI: nfdi4immuno:CytometryDataProcessing

 classDiagram
    class CytometryDataProcessing
    click CytometryDataProcessing href "../CytometryDataProcessing/"
      CytometryDataProcessing : batch_normalization_method

      CytometryDataProcessing : compensation_method

      CytometryDataProcessing : data_transformation_method

      CytometryDataProcessing : debarcoding_method

      CytometryDataProcessing : gating_description

      CytometryDataProcessing : normalization_method

      CytometryDataProcessing : randomization_method

      CytometryDataProcessing : unmixing_method

Slots

Name Cardinality and Range Description Inheritance
compensation_method 1
String		 Which compensation methods were used? If none were used, please write: no me... direct
unmixing_method 0..1
String		 Which unmixing method was used? If none was used, please write: no method wa... direct
gating_description 0..1
String		 The gating strategy or a reference to where it is described in detail (e direct
batch_normalization_method 0..1
String		 Which batch normalization method was used? If none was used, please write: n... direct
normalization_method 0..1
String		 Which other normalization methods, besides the compensation methods and batch... direct
randomization_method 0..1
String		 Which randomization methods were used? If none were used, please write: no m... direct
debarcoding_method 0..1
String		 Which debarcoding method was used? If none was used, please write: no method... direct
data_transformation_method 0..1
String		 Which data transformation methods were used? If none were used, please write... direct

Usages

used by used in type used
StainingPanel data_processing range CytometryDataProcessing

Identifier and Mapping Information

Schema Source

  • from schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema

Mappings

Mapping Type Mapped Value
self nfdi4immuno:CytometryDataProcessing
native nfdi4immuno:CytometryDataProcessing

LinkML Source

Direct

name: CytometryDataProcessing
description: The data processing steps used in a cytometry experiment.
title: Data & Processing
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
slots:
- compensation_method
- unmixing_method
- gating_description
- batch_normalization_method
- normalization_method
- randomization_method
- debarcoding_method
- data_transformation_method

Induced

name: CytometryDataProcessing
description: The data processing steps used in a cytometry experiment.
title: Data & Processing
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
attributes:
  compensation_method:
    name: compensation_method
    description: 'Which compensation methods were used?  If none were used, please
      write: no method was applied.

      '
    title: Compensation methods
    examples:
    - value: compensation beads
    - value: spillover compensation
    - value: no method was applied
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: compensation_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
    required: true
    pattern: ^.+$
  unmixing_method:
    name: unmixing_method
    description: 'Which unmixing method was used?  If none was used, please write:
      no method was applied.

      '
    title: Unmixing method
    examples:
    - value: least square
    - value: no method was applied
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: unmixing_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
  gating_description:
    name: gating_description
    description: The gating strategy or a reference to where it is described in detail
      (e.g., a manuscript) should be provided.
    title: Gating description
    examples:
    - value: CD34 negative, dim, high (between 3rd and 4th log) or Gating-ML 2.0 file
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: gating_description
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
  batch_normalization_method:
    name: batch_normalization_method
    description: 'Which batch normalization method was used?  If none was used, please
      write: no method was applied.

      '
    title: Batch normalization method
    examples:
    - value: CytoNorm,
      description: CytoNorm is an R package.
    - value: No method was applied
      description: No batches were created. Each sample was measured individually.
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: batch_normalization_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
  normalization_method:
    name: normalization_method
    description: 'Which other normalization methods, besides the compensation methods
      and batch normalization methods, were used?  If none were used, please write:
      no method was applied.

      '
    title: Batch normalization method
    examples:
    - value: FlowAI, FlowCut, MESF (Molecules of Equivalent Soluble Fluorochrome),
        no method was applied
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: normalization_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
  randomization_method:
    name: randomization_method
    description: 'Which randomization methods were used?  If none were used, please
      write: no method was applied.

      '
    title: Randomization method
    examples:
    - value: Uniform negative distribution, no method was applied
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: randomization_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
  debarcoding_method:
    name: debarcoding_method
    description: 'Which debarcoding method was used?  If none was used, please write:
      no method was applied.

      '
    title: Debarcoding methods
    examples:
    - value: Fluorescent Cell Barcoding, no method was applied
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: debarcoding_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string
  data_transformation_method:
    name: data_transformation_method
    description: 'Which data transformation methods were used?  If none were used,
      please write: no method was applied.

      '
    title: Data transformation methods
    examples:
    - value: hyperlog, no method was applied
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: data_transformation_method
    owner: CytometryDataProcessing
    domain_of:
    - CytometryDataProcessing
    range: string