Class: UploadedFileSource

Represents the source of a sequence that is uploaded as a file

URI: opencloning_linkml:UploadedFileSource

classDiagram class UploadedFileSource click UploadedFileSource href "../UploadedFileSource" Source <|-- UploadedFileSource click Source href "../Source" UploadedFileSource : circularize UploadedFileSource : coordinates UploadedFileSource : database_id UploadedFileSource : file_name UploadedFileSource : id UploadedFileSource : index_in_file UploadedFileSource : input UploadedFileSource --> "*" Sequence : input click Sequence href "../Sequence" UploadedFileSource : output UploadedFileSource --> "0..1" Sequence : output click Sequence href "../Sequence" UploadedFileSource : output_name UploadedFileSource : sequence_file_format UploadedFileSource --> "1" SequenceFileFormat : sequence_file_format click SequenceFileFormat href "../SequenceFileFormat" UploadedFileSource : type

Inheritance

NamedThing
- Source
  - UploadedFileSource

Slots

Name	Cardinality and Range	Description	Inheritance
sequence_file_format	1 SequenceFileFormat	The format of a sequence file	direct
file_name	0..1 String	The name of the file	direct
index_in_file	0..1 Integer	The index of the sequence in the file	direct
circularize	0..1 Boolean	Whether the sequence should be circularized (FASTA only)	direct
coordinates	0..1 SequenceRange	If provided, coordinates within the sequence of the file to extract a subsequ...	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:UploadedFileSource
native	opencloning_linkml:UploadedFileSource

LinkML Source

Direct

name: UploadedFileSource
description: Represents the source of a sequence that is uploaded as a file
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Source
slots:
- sequence_file_format
slot_usage:
  sequence_file_format:
    name: sequence_file_format
    required: true
attributes:
  file_name:
    name: file_name
    description: The name of the file
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - UploadedFileSource
    - AssociatedFile
    range: string
  index_in_file:
    name: index_in_file
    description: The index of the sequence in the file
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - UploadedFileSource
    range: integer
  circularize:
    name: circularize
    description: Whether the sequence should be circularized (FASTA only)
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - UploadedFileSource
    range: boolean
  coordinates:
    name: coordinates
    description: If provided, coordinates within the sequence of the file to extract
      a subsequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    domain_of:
    - UploadedFileSource
    range: sequence_range
    required: false

Induced

name: UploadedFileSource
description: Represents the source of a sequence that is uploaded as a file
from_schema: https://opencloning.github.io/OpenCloning_LinkML
is_a: Source
slot_usage:
  sequence_file_format:
    name: sequence_file_format
    required: true
attributes:
  file_name:
    name: file_name
    description: The name of the file
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: file_name
    owner: UploadedFileSource
    domain_of:
    - UploadedFileSource
    - AssociatedFile
    range: string
  index_in_file:
    name: index_in_file
    description: The index of the sequence in the file
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: index_in_file
    owner: UploadedFileSource
    domain_of:
    - UploadedFileSource
    range: integer
  circularize:
    name: circularize
    description: Whether the sequence should be circularized (FASTA only)
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: circularize
    owner: UploadedFileSource
    domain_of:
    - UploadedFileSource
    range: boolean
  coordinates:
    name: coordinates
    description: If provided, coordinates within the sequence of the file to extract
      a subsequence
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: coordinates
    owner: UploadedFileSource
    domain_of:
    - UploadedFileSource
    range: sequence_range
    required: false
  sequence_file_format:
    name: sequence_file_format
    description: The format of a sequence file
    from_schema: https://opencloning.github.io/OpenCloning_LinkML
    rank: 1000
    alias: sequence_file_format
    owner: UploadedFileSource
    domain_of:
    - TextFileSequence
    - UploadedFileSource
    range: SequenceFileFormat
    required: true
  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: UploadedFileSource
    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: UploadedFileSource
    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: UploadedFileSource
    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: UploadedFileSource
    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: UploadedFileSource
    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: UploadedFileSource
    domain_of:
    - NamedThing
    - Sequence
    range: integer
    required: true