Class: TarAmpBioinformaticsInfo

the targeted amplicon bioinformatics pipeline

URI: portable_microhaplotype_object:TarAmpBioinformaticsInfo

classDiagram class TarAmpBioinformaticsInfo click TarAmpBioinformaticsInfo href "../TarAmpBioinformaticsInfo" TarAmpBioinformaticsInfo : additional_methods TarAmpBioinformaticsInfo --> "*" BioMethod : additional_methods click BioMethod href "../BioMethod" TarAmpBioinformaticsInfo : demultiplexing_method TarAmpBioinformaticsInfo --> "1" BioMethod : demultiplexing_method click BioMethod href "../BioMethod" TarAmpBioinformaticsInfo : denoising_method TarAmpBioinformaticsInfo --> "1" BioMethod : denoising_method click BioMethod href "../BioMethod" TarAmpBioinformaticsInfo : population_clustering_method TarAmpBioinformaticsInfo --> "1" BioMethod : population_clustering_method click BioMethod href "../BioMethod" TarAmpBioinformaticsInfo : tar_amp_bioinformatics_info_id

Slots

Name	Cardinality and Range	Description	Inheritance
tar_amp_bioinformatics_info_id	1 String	a unique identifier for this targeted amplicon bioinformatics pipeline run	direct
demultiplexing_method	1 BioMethod	the demultiplexing method used to separate raw reads from barcodes and primer...	direct
denoising_method	1 BioMethod	the method used to de-noise and/or cluster the raw reads	direct
population_clustering_method	1 BioMethod	the method used to compare clustered/de-noised reads across samples for a tar...	direct
additional_methods	* BioMethod	any additional methods used to analyze the data	direct

Usages

used by	used in	type	used
PortableMicrohaplotypeObject	taramp_bioinformatics_infos	range	TarAmpBioinformaticsInfo

Identifier and Mapping Information

Schema Source

from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type	Mapped Value
self	portable_microhaplotype_object:TarAmpBioinformaticsInfo
native	portable_microhaplotype_object:TarAmpBioinformaticsInfo

LinkML Source

Direct

name: TarAmpBioinformaticsInfo
description: the targeted amplicon bioinformatics pipeline
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- tar_amp_bioinformatics_info_id
slot_usage:
  tar_amp_bioinformatics_info_id:
    name: tar_amp_bioinformatics_info_id
    identifier: true
    domain_of:
    - MicrohaplotypesDetected
    - DemultiplexedExperimentSamples
    - TarAmpBioinformaticsInfo
attributes:
  demultiplexing_method:
    name: demultiplexing_method
    description: the demultiplexing method used to separate raw reads from barcodes
      and primer targets
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: true
  denoising_method:
    name: denoising_method
    description: the method used to de-noise and/or cluster the raw reads
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: true
  population_clustering_method:
    name: population_clustering_method
    description: the method used to compare clustered/de-noised reads across samples
      for a target
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: true
  additional_methods:
    name: additional_methods
    description: any additional methods used to analyze the data
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: TarAmpBioinformaticsInfo
description: the targeted amplicon bioinformatics pipeline
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slot_usage:
  tar_amp_bioinformatics_info_id:
    name: tar_amp_bioinformatics_info_id
    identifier: true
    domain_of:
    - MicrohaplotypesDetected
    - DemultiplexedExperimentSamples
    - TarAmpBioinformaticsInfo
attributes:
  demultiplexing_method:
    name: demultiplexing_method
    description: the demultiplexing method used to separate raw reads from barcodes
      and primer targets
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: demultiplexing_method
    owner: TarAmpBioinformaticsInfo
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: true
  denoising_method:
    name: denoising_method
    description: the method used to de-noise and/or cluster the raw reads
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: denoising_method
    owner: TarAmpBioinformaticsInfo
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: true
  population_clustering_method:
    name: population_clustering_method
    description: the method used to compare clustered/de-noised reads across samples
      for a target
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: population_clustering_method
    owner: TarAmpBioinformaticsInfo
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: true
  additional_methods:
    name: additional_methods
    description: any additional methods used to analyze the data
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: additional_methods
    owner: TarAmpBioinformaticsInfo
    domain_of:
    - TarAmpBioinformaticsInfo
    range: BioMethod
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  tar_amp_bioinformatics_info_id:
    name: tar_amp_bioinformatics_info_id
    description: a unique identifier for this targeted amplicon bioinformatics pipeline
      run
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    alias: tar_amp_bioinformatics_info_id
    owner: TarAmpBioinformaticsInfo
    domain_of:
    - MicrohaplotypesDetected
    - DemultiplexedExperimentSamples
    - TarAmpBioinformaticsInfo
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]$