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Class: SequencingData

Default SequencingData description

URI: https://github.com/vdjserver/vdjserver-airr-schema/SequencingData

 classDiagram
    class SequencingData
    click SequencingData href "../SequencingData/"
      AIRRStandards <|-- SequencingData
        click AIRRStandards href "../AIRRStandards/"

      SequencingData : file_type





        SequencingData --> "0..1" FileTypeEnum : file_type
        click FileTypeEnum href "../FileTypeEnum/"



      SequencingData : filename

      SequencingData : index_filename

      SequencingData : index_length

      SequencingData : paired_filename

      SequencingData : paired_read_direction





        SequencingData --> "0..1" PairedReadDirectionEnum : paired_read_direction
        click PairedReadDirectionEnum href "../PairedReadDirectionEnum/"



      SequencingData : paired_read_length

      SequencingData : read_direction





        SequencingData --> "0..1" ReadDirectionEnum : read_direction
        click ReadDirectionEnum href "../ReadDirectionEnum/"



      SequencingData : read_length

      SequencingData : sequencing_data_id

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sequencing_data_id 0..1
String		 Persistent identifier of raw data stored in an archive (e direct
file_type 0..1
FileTypeEnum		 File format for the raw reads or sequences direct
filename 0..1
String		 File name for the raw reads or sequences direct
read_direction 0..1
ReadDirectionEnum		 Read direction for the raw reads or sequences direct
read_length 0..1
Integer		 Read length in bases for the first file in paired-read sequencing direct
paired_filename 0..1
String		 File name for the second file in paired-read sequencing direct
paired_read_direction 0..1
PairedReadDirectionEnum		 Read direction for the second file in paired-read sequencing direct
paired_read_length 0..1
Integer		 Read length in bases for the second file in paired-read sequencing direct
index_filename 0..1
String		 File name for the index file direct
index_length 0..1
Integer		 Read length in bases for the index file direct

Usages

used by used in type used
SequencingRun sequencing_files range SequencingData
SampleProcessing sequencing_files range SequencingData

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self https://github.com/vdjserver/vdjserver-airr-schema/SequencingData
native https://github.com/vdjserver/vdjserver-airr-schema/SequencingData

LinkML Source

Direct

name: SequencingData
description: Default SequencingData description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- sequencing_data_id
- file_type
- filename
- read_direction
- read_length
- paired_filename
- paired_read_direction
- paired_read_length
- index_filename
- index_length

Induced

name: SequencingData
description: Default SequencingData description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  sequencing_data_id:
    name: sequencing_data_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Persistent identifier of raw data stored in an archive (e.g. INSDC
      run ID). Data archive should  be identified in the CURIE prefix.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: string
  file_type:
    name: file_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: File format for the raw reads or sequences
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: SequencingData
    domain_of:
    - SequencingData
    range: FileTypeEnum
  filename:
    name: filename
    annotations:
      nullable:
        tag: nullable
        value: true
    description: File name for the raw reads or sequences. The first file in paired-read
      sequencing.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: string
  read_direction:
    name: read_direction
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Read direction for the raw reads or sequences. The first file in
      paired-read sequencing.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: ReadDirectionEnum
  read_length:
    name: read_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Read length in bases for the first file in paired-read sequencing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: integer
  paired_filename:
    name: paired_filename
    annotations:
      nullable:
        tag: nullable
        value: true
    description: File name for the second file in paired-read sequencing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: string
  paired_read_direction:
    name: paired_read_direction
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Read direction for the second file in paired-read sequencing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: PairedReadDirectionEnum
  paired_read_length:
    name: paired_read_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Read length in bases for the second file in paired-read sequencing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: integer
  index_filename:
    name: index_filename
    annotations:
      nullable:
        tag: nullable
        value: true
    description: File name for the index file
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: string
  index_length:
    name: index_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Read length in bases for the index file
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequencingData
    domain_of:
    - SequencingData
    range: integer