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Class: ManuallyTypedSequence

Represents a sequence that is manually typed by the user

URI: opencloning_linkml:ManuallyTypedSequence

classDiagram class ManuallyTypedSequence click ManuallyTypedSequence href "../ManuallyTypedSequence" Sequence <|-- ManuallyTypedSequence click Sequence href "../Sequence" ManuallyTypedSequence : circular ManuallyTypedSequence : id ManuallyTypedSequence : overhang_crick_3prime ManuallyTypedSequence : overhang_watson_3prime ManuallyTypedSequence : sequence ManuallyTypedSequence : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
overhang_crick_3prime 0..1
Integer		 Taken from pydna's dseq::ovhgAn integer describing the length of the crick ... direct
overhang_watson_3prime 0..1
Integer		 The equivalent of overhang_crick_3prime but for the watson strand direct
sequence 1
String		 The sequence of the manually typed sequence direct
circular 0..1
Boolean		 Whether the sequence is circular or linear direct
id 1
Integer		 A unique identifier for a thing Sequence, NamedThing
type 0..1
String		 Designates the class Sequence

Identifier and Mapping Information

Schema Source

  • from schema: https://opencloning.github.io/OpenCloning_LinkML

Mappings

Mapping Type Mapped Value
self opencloning_linkml:ManuallyTypedSequence
native opencloning_linkml:ManuallyTypedSequence

LinkML Source

Direct

name: ManuallyTypedSequence
description: Represents a sequence that is manually typed by the user
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Sequence
slots:
- overhang_crick_3prime
- overhang_watson_3prime
slot_usage:
  overhang_crick_3prime:
    name: overhang_crick_3prime
    ifabsent: int(0)
  overhang_watson_3prime:
    name: overhang_watson_3prime
    ifabsent: int(0)
attributes:
  sequence:
    name: sequence
    description: The sequence of the manually typed sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - ManuallyTypedSequence
    - Primer
    - SourceInput
    - PlannotateAnnotationReport
    range: string
    required: true
    pattern: ^[acgtACGT]+$
  circular:
    name: circular
    description: Whether the sequence is circular or linear
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    ifabsent: boolean(false)
    domain_of:
    - TemplateSequence
    - ManuallyTypedSequence
    - AssemblySource
    range: boolean
    required: false

Induced

name: ManuallyTypedSequence
description: Represents a sequence that is manually typed by the user
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Sequence
slot_usage:
  overhang_crick_3prime:
    name: overhang_crick_3prime
    ifabsent: int(0)
  overhang_watson_3prime:
    name: overhang_watson_3prime
    ifabsent: int(0)
attributes:
  sequence:
    name: sequence
    description: The sequence of the manually typed sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: sequence
    owner: ManuallyTypedSequence
    domain_of:
    - ManuallyTypedSequence
    - Primer
    - SourceInput
    - PlannotateAnnotationReport
    range: string
    required: true
    pattern: ^[acgtACGT]+$
  circular:
    name: circular
    description: Whether the sequence is circular or linear
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    ifabsent: boolean(false)
    alias: circular
    owner: ManuallyTypedSequence
    domain_of:
    - TemplateSequence
    - ManuallyTypedSequence
    - AssemblySource
    range: boolean
    required: false
  overhang_crick_3prime:
    name: overhang_crick_3prime
    description: Taken from pydna's `dseq::ovhg`An integer describing the length of
      the crick strand overhang in the 5' of the molecule, or 3' of the crick strand
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    ifabsent: int(0)
    alias: overhang_crick_3prime
    owner: ManuallyTypedSequence
    domain_of:
    - TextFileSequence
    - ManuallyTypedSequence
    - OligoHybridizationSource
    range: integer
  overhang_watson_3prime:
    name: overhang_watson_3prime
    description: The equivalent of `overhang_crick_3prime` but for the watson strand
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    ifabsent: int(0)
    alias: overhang_watson_3prime
    owner: ManuallyTypedSequence
    domain_of:
    - TextFileSequence
    - ManuallyTypedSequence
    range: integer
  id:
    name: id
    description: A unique identifier for a thing
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: ManuallyTypedSequence
    domain_of:
    - NamedThing
    - Sequence
    range: integer
    required: true
  type:
    name: type
    description: Designates the class
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    designates_type: true
    alias: type
    owner: ManuallyTypedSequence
    domain_of:
    - Sequence
    - SourceInput
    - Source
    - CollectionOptionInfo
    - AnnotationReport
    - AssociatedFile
    range: string