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Class: BioMethod

methodology description of a portion of a bioinformatics pipeline

URI: portable_microhaplotype_object:BioMethod

classDiagram class BioMethod click BioMethod href "../BioMethod" BioMethod : additional_argument BioMethod : program BioMethod : program_description BioMethod : program_version

Slots

Name Cardinality and Range Description Inheritance
program_version 1
String		 the version of generation method, should be in the format of v[MAJOR] direct
program 1
String		 name of the program used for this portion of the pipeline direct
program_description 0..1
String		 a short description of what this method does direct
additional_argument *
String		 any additional arguments that differ from the default direct

Usages

used by used in type used
BioinformaticsMethodInfo demultiplexing_method range BioMethod
BioinformaticsMethodInfo denoising_method range BioMethod
BioinformaticsMethodInfo additional_methods range BioMethod

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: BioMethod
description: methodology description of a portion of a bioinformatics pipeline
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- program_version
attributes:
  program:
    name: program
    description: name of the program used for this portion of the pipeline
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - BioMethod
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  program_description:
    name: program_description
    description: a short description of what this method does
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - BioMethod
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  additional_argument:
    name: additional_argument
    description: any additional arguments that differ from the default
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - BioMethod
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
    pattern: ^[A-z-._0-9{}\(\),\/\ ]+$

Induced

name: BioMethod
description: methodology description of a portion of a bioinformatics pipeline
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  program:
    name: program
    description: name of the program used for this portion of the pipeline
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: program
    owner: BioMethod
    domain_of:
    - BioMethod
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$
  program_description:
    name: program_description
    description: a short description of what this method does
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: program_description
    owner: BioMethod
    domain_of:
    - BioMethod
    range: string
    required: false
    pattern: ^[A-z-._0-9\(\),\/\ ]+$
  additional_argument:
    name: additional_argument
    description: any additional arguments that differ from the default
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: additional_argument
    owner: BioMethod
    domain_of:
    - BioMethod
    range: string
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
    pattern: ^[A-z-._0-9{}\(\),\/\ ]+$
  program_version:
    name: program_version
    description: the version of generation method, should be in the format of v[MAJOR].[MINOR].[PATCH]
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: program_version
    owner: BioMethod
    domain_of:
    - BioMethod
    - PmoGenerationMethod
    range: string
    required: true
    pattern: ^[A-z-._0-9 ]+$