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Class: AIRRSequencingData

URI: ak_schema:AIRRSequencingData

classDiagram class AIRRSequencingData click AIRRSequencingData href "../AIRRSequencingData" SequencingData <|-- AIRRSequencingData click SequencingData href "../SequencingData" SequenceData <|-- AIRRSequencingData click SequenceData href "../SequenceData" AIRRSequencingData : akc_id AIRRSequencingData : data_item_types AIRRSequencingData --> "*" DataItemTypeEnum : data_item_types click DataItemTypeEnum href "../DataItemTypeEnum" AIRRSequencingData : file_type AIRRSequencingData --> "0..1" FileTypeEnum : file_type click FileTypeEnum href "../FileTypeEnum" AIRRSequencingData : filename AIRRSequencingData : index_filename AIRRSequencingData : index_length AIRRSequencingData : paired_filename AIRRSequencingData : paired_read_direction AIRRSequencingData --> "0..1" PairedReadDirectionEnum : paired_read_direction click PairedReadDirectionEnum href "../PairedReadDirectionEnum" AIRRSequencingData : paired_read_length AIRRSequencingData : read_direction AIRRSequencingData --> "0..1" ReadDirectionEnum : read_direction click ReadDirectionEnum href "../ReadDirectionEnum" AIRRSequencingData : read_length AIRRSequencingData : sequencing_data_id AIRRSequencingData : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sequencing_data_id 0..1
String		 Persistent identifier of raw data stored in an archive (e SequencingData
file_type 0..1
FileTypeEnum		 File format for the raw reads or sequences SequencingData
filename 0..1
String		 File name for the raw reads or sequences SequencingData
read_direction 0..1
ReadDirectionEnum		 Read direction for the raw reads or sequences SequencingData
read_length 0..1
Integer		 Read length in bases for the first file in paired-read sequencing SequencingData
paired_filename 0..1
String		 File name for the second file in paired-read sequencing SequencingData
paired_read_direction 0..1
PairedReadDirectionEnum		 Read direction for the second file in paired-read sequencing SequencingData
paired_read_length 0..1
Integer		 Read length in bases for the second file in paired-read sequencing SequencingData
index_filename 0..1
String		 File name for the index file SequencingData
index_length 0..1
Integer		 Read length in bases for the index file SequencingData
type 0..1
String		 AKDataItem
data_item_types *
DataItemTypeEnum		 semantic types of the data AKDataItem
akc_id 1
Uriorcurie		 A unique identifier for a thing in the AKC AKObject

Usages

used by used in type used
AIRRSequencingAssay sequencing_files range AIRRSequencingData

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/airr-knowledge/ak-schema

Mappings

Mapping Type Mapped Value
self ak_schema:AIRRSequencingData
native ak_schema:AIRRSequencingData

LinkML Source

Direct

name: AIRRSequencingData
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: SequenceData
mixins:
- SequencingData

Induced

name: AIRRSequencingData
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: SequenceData
mixins:
- SequencingData
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/airr-knowledge/ak-schema
    rank: 1000
    alias: sequencing_data_id
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: file_type
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: filename
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: read_direction
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: read_length
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: paired_filename
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: paired_read_direction
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: paired_read_length
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: index_filename
    owner: AIRRSequencingData
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: index_length
    owner: AIRRSequencingData
    domain_of:
    - SequencingData
    range: integer
  type:
    name: type
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    designates_type: true
    alias: type
    owner: AIRRSequencingData
    domain_of:
    - LifeEvent
    - Assay
    - AKDataItem
    - TCellReceptor
    - Epitope
    range: string
  data_item_types:
    name: data_item_types
    description: semantic types of the data
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: data_item_types
    owner: AIRRSequencingData
    domain_of:
    - AKDataItem
    range: DataItemTypeEnum
    multivalued: true
  akc_id:
    name: akc_id
    description: A unique identifier for a thing in the AKC.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: akc_id
    owner: AIRRSequencingData
    domain_of:
    - AKObject
    range: uriorcurie
    required: true