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Class: ManuallyTypedSource

Represents the source of a sequence that is manually typed by the user

URI: opencloning_linkml:ManuallyTypedSource

classDiagram class ManuallyTypedSource click ManuallyTypedSource href "../ManuallyTypedSource" Source <|-- ManuallyTypedSource click Source href "../Source" ManuallyTypedSource : circular ManuallyTypedSource : database_id ManuallyTypedSource : id ManuallyTypedSource : input ManuallyTypedSource --> "*" Sequence : input click Sequence href "../Sequence" ManuallyTypedSource : output ManuallyTypedSource --> "0..1" Sequence : output click Sequence href "../Sequence" ManuallyTypedSource : output_name ManuallyTypedSource : overhang_crick_3prime ManuallyTypedSource : overhang_watson_3prime ManuallyTypedSource : type ManuallyTypedSource : user_input

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
user_input 1
String		 direct
circular 0..1
Boolean		 Whether the sequence is circular or not direct
input *
Sequence		 The sequences that are an input to this source Source
output 0..1
Sequence		 Identifier of the sequence that is the output of this source Source
type 0..1
String		 Designates the class Source
output_name 0..1
String		 Used to specify the name of the output sequence Source
database_id 0..1
Integer		 The id of an entity in a database Source
id 1
Integer		 A unique identifier for a thing NamedThing

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ManuallyTypedSource
description: Represents the source of a sequence that is manually typed by the user
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Source
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:
  user_input:
    name: user_input
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - ManuallyTypedSource
    range: string
    required: true
    pattern: ^[acgtACGT]+$
  circular:
    name: circular
    description: Whether the sequence is circular or not
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    domain_of:
    - TemplateSequence
    - ManuallyTypedSource
    - AssemblySource
    range: boolean

Induced

name: ManuallyTypedSource
description: Represents the source of a sequence that is manually typed by the user
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Source
slot_usage:
  overhang_crick_3prime:
    name: overhang_crick_3prime
    ifabsent: int(0)
  overhang_watson_3prime:
    name: overhang_watson_3prime
    ifabsent: int(0)
attributes:
  user_input:
    name: user_input
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: user_input
    owner: ManuallyTypedSource
    domain_of:
    - ManuallyTypedSource
    range: string
    required: true
    pattern: ^[acgtACGT]+$
  circular:
    name: circular
    description: Whether the sequence is circular or not
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    alias: circular
    owner: ManuallyTypedSource
    domain_of:
    - TemplateSequence
    - ManuallyTypedSource
    - AssemblySource
    range: boolean
  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: ManuallyTypedSource
    domain_of:
    - TextFileSequence
    - ManuallyTypedSource
    - 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: ManuallyTypedSource
    domain_of:
    - TextFileSequence
    - ManuallyTypedSource
    range: integer
  input:
    name: input
    description: The sequences that are an input to this source. If the source represents
      external import of a sequence, it's empty.
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:object
    alias: input
    owner: ManuallyTypedSource
    domain_of:
    - Source
    range: Sequence
    required: false
    multivalued: true
    inlined_as_list: false
  output:
    name: output
    description: Identifier of the sequence that is the output of this source.
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:result
    alias: output
    owner: ManuallyTypedSource
    domain_of:
    - Source
    range: Sequence
    required: false
    inlined: false
  type:
    name: type
    description: Designates the class
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    designates_type: true
    alias: type
    owner: ManuallyTypedSource
    domain_of:
    - Sequence
    - Source
    - CollectionOptionInfo
    - AnnotationReport
    - AssociatedFile
    range: string
  output_name:
    name: output_name
    description: Used to specify the name of the output sequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: output_name
    owner: ManuallyTypedSource
    domain_of:
    - Source
    range: string
    required: false
  database_id:
    name: database_id
    description: The id of an entity in a database
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    slot_uri: schema:identifier
    alias: database_id
    owner: ManuallyTypedSource
    domain_of:
    - Primer
    - Source
    - DatabaseSource
    range: integer
    required: false
  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: ManuallyTypedSource
    domain_of:
    - NamedThing
    - Sequence
    range: integer
    required: true