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Class: DataProcessing

URI: ak_schema:DataProcessing

classDiagram class DataProcessing click DataProcessing href "../DataProcessing" AIRRStandards <|-- DataProcessing click AIRRStandards href "../AIRRStandards" DataProcessing : analysis_provenance_id DataProcessing : collapsing_method DataProcessing : data_processing_files DataProcessing : data_processing_id DataProcessing : data_processing_protocols DataProcessing : germline_database DataProcessing : germline_set_ref DataProcessing : paired_reads_assembly DataProcessing : primary_annotation DataProcessing : primer_match_cutoffs DataProcessing : quality_thresholds DataProcessing : software_versions

Inheritance

Slots

Name Cardinality and Range Description Inheritance
data_processing_id 0..1
String		 direct
primary_annotation 0..1
Boolean		 If true, indicates this is the primary or default data processing for the rep... direct
software_versions 0..1
String		 Version number and / or date, include company pipelines direct
paired_reads_assembly 0..1
String		 How paired end reads were assembled into a single receptor sequence direct
quality_thresholds 0..1
String		 How/if sequences were removed from (4) based on base quality scores direct
primer_match_cutoffs 0..1
String		 How primers were identified in the sequences, were they removed/masked/etc? direct
collapsing_method 0..1
String		 The method used for combining multiple sequences from (4) into a single seque... direct
data_processing_protocols 0..1
String		 General description of how QC is performed direct
data_processing_files *
String		 Array of file names for data produced by this data processing direct
germline_database 0..1
String		 Source of germline V(D)J genes with version number or date accessed direct
germline_set_ref 0..1
String		 direct
analysis_provenance_id 0..1
String		 Identifier for machine-readable PROV model of analysis provenance direct

Usages

used by used in type used
Repertoire data_processing range DataProcessing

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/airr-knowledge/ak-schema

Mappings

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

LinkML Source

Direct

name: DataProcessing
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- data_processing_id
- primary_annotation
- software_versions
- paired_reads_assembly
- quality_thresholds
- primer_match_cutoffs
- collapsing_method
- data_processing_protocols
- data_processing_files
- germline_database
- germline_set_ref
- analysis_provenance_id

Induced

name: DataProcessing
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  data_processing_id:
    name: data_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: data_processing_id
    owner: DataProcessing
    domain_of:
    - DataProcessing
    - Alignment
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string
  primary_annotation:
    name: primary_annotation
    annotations:
      nullable:
        tag: nullable
        value: false
    description: If true, indicates this is the primary or default data processing
      for the repertoire and its rearrangements. If false, indicates this is a secondary
      or additional data processing.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: primary_annotation
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: boolean
  software_versions:
    name: software_versions
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Version number and / or date, include company pipelines
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: software_versions
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  paired_reads_assembly:
    name: paired_reads_assembly
    annotations:
      nullable:
        tag: nullable
        value: true
    description: How paired end reads were assembled into a single receptor sequence
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: paired_reads_assembly
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  quality_thresholds:
    name: quality_thresholds
    annotations:
      nullable:
        tag: nullable
        value: true
    description: How/if sequences were removed from (4) based on base quality scores
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: quality_thresholds
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  primer_match_cutoffs:
    name: primer_match_cutoffs
    annotations:
      nullable:
        tag: nullable
        value: true
    description: How primers were identified in the sequences, were they removed/masked/etc?
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: primer_match_cutoffs
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  collapsing_method:
    name: collapsing_method
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The method used for combining multiple sequences from (4) into a
      single sequence in (5)
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: collapsing_method
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  data_processing_protocols:
    name: data_processing_protocols
    annotations:
      nullable:
        tag: nullable
        value: true
    description: General description of how QC is performed
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: data_processing_protocols
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  data_processing_files:
    name: data_processing_files
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Array of file names for data produced by this data processing.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: data_processing_files
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
    multivalued: true
  germline_database:
    name: germline_database
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Source of germline V(D)J genes with version number or date accessed.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_database
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string
  germline_set_ref:
    name: germline_set_ref
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_set_ref
    owner: DataProcessing
    domain_of:
    - GermlineSet
    - DocumentedAllele
    - DeletedGene
    - DataProcessing
    range: string
  analysis_provenance_id:
    name: analysis_provenance_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Identifier for machine-readable PROV model of analysis provenance
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: analysis_provenance_id
    owner: DataProcessing
    domain_of:
    - DataProcessing
    range: string