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Class: Clone

URI: ak_schema:Clone

classDiagram class Clone click Clone href "../Clone" AIRRStandards <|-- Clone click AIRRStandards href "../AIRRStandards" Clone : clone_count Clone : clone_id Clone : d_alignment_end Clone : d_alignment_start Clone : d_call Clone : data_processing_id Clone : germline_alignment Clone : germline_alignment_aa Clone : j_alignment_end Clone : j_alignment_start Clone : j_call Clone : junction Clone : junction_aa Clone : junction_aa_length Clone : junction_end Clone : junction_length Clone : junction_start Clone : repertoire_id Clone : seed_id Clone : sequences Clone : umi_count Clone : v_alignment_end Clone : v_alignment_start Clone : v_call

Inheritance

Slots

Name Cardinality and Range Description Inheritance
clone_id 0..1
String		 direct
repertoire_id 0..1
String		 direct
data_processing_id 0..1
String		 direct
sequences *
String		 List sequence_id strings that act as keys to the Rearrangement records for me... direct
v_call 0..1
String		 direct
d_call 0..1
String		 direct
j_call 0..1
String		 direct
junction 0..1
String		 direct
junction_aa 0..1
String		 Amino acid translation of the junction direct
junction_length 0..1
Integer		 direct
junction_aa_length 0..1
Integer		 direct
germline_alignment 0..1
String		 direct
germline_alignment_aa 0..1
String		 direct
v_alignment_start 0..1
Integer		 direct
v_alignment_end 0..1
Integer		 direct
d_alignment_start 0..1
Integer		 direct
d_alignment_end 0..1
Integer		 direct
j_alignment_start 0..1
Integer		 Start position of the J gene alignment in both the sequence_alignment and ger... direct
j_alignment_end 0..1
Integer		 End position of the J gene alignment in both the sequence_alignment and germl... direct
junction_start 0..1
Integer		 Junction region start position in the alignment (1-based closed interval) direct
junction_end 0..1
Integer		 Junction region end position in the alignment (1-based closed interval) direct
umi_count 0..1
Integer		 direct
clone_count 0..1
Integer		 Absolute count of the size (number of members) of this clone in the repertoir... direct
seed_id 0..1
String		 sequence_id of the seed sequence direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Clone
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- clone_id
- repertoire_id
- data_processing_id
- sequences
- v_call
- d_call
- j_call
- junction
- junction_aa
- junction_length
- junction_aa_length
- germline_alignment
- germline_alignment_aa
- v_alignment_start
- v_alignment_end
- d_alignment_start
- d_alignment_end
- j_alignment_start
- j_alignment_end
- junction_start
- junction_end
- umi_count
- clone_count
- seed_id

Induced

name: Clone
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  clone_id:
    name: clone_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: clone_id
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    - Tree
    range: string
  repertoire_id:
    name: repertoire_id
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: repertoire_id
    owner: Clone
    domain_of:
    - AIRRSequencingAssay
    - Repertoire
    - RepertoireGroupDetail
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string
  data_processing_id:
    name: data_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: data_processing_id
    owner: Clone
    domain_of:
    - DataProcessing
    - Alignment
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string
  sequences:
    name: sequences
    annotations:
      nullable:
        tag: nullable
        value: true
    description: List sequence_id strings that act as keys to the Rearrangement records
      for members of the clone.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequences
    owner: Clone
    domain_of:
    - Clone
    range: string
    multivalued: true
  v_call:
    name: v_call
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_call
    owner: Clone
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  d_call:
    name: d_call
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_call
    owner: Clone
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  j_call:
    name: j_call
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_call
    owner: Clone
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  junction:
    name: junction
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    - Node
    range: string
  junction_aa:
    name: junction_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the junction.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_aa
    owner: Clone
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    - Node
    range: string
  junction_length:
    name: junction_length
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_length
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  junction_aa_length:
    name: junction_aa_length
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_aa_length
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  germline_alignment:
    name: germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_alignment
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: string
  germline_alignment_aa:
    name: germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_alignment_aa
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: string
  v_alignment_start:
    name: v_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_alignment_start
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  v_alignment_end:
    name: v_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_alignment_end
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  d_alignment_start:
    name: d_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_alignment_start
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  d_alignment_end:
    name: d_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_alignment_end
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  j_alignment_start:
    name: j_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the J gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_alignment_start
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  j_alignment_end:
    name: j_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the J gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_alignment_end
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  junction_start:
    name: junction_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Junction region start position in the alignment (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_start
    owner: Clone
    domain_of:
    - Clone
    range: integer
  junction_end:
    name: junction_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Junction region end position in the alignment (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_end
    owner: Clone
    domain_of:
    - Clone
    range: integer
  umi_count:
    name: umi_count
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: umi_count
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  clone_count:
    name: clone_count
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Absolute count of the size (number of members) of this clone in the
      repertoire. This could simply be the number of sequences (Rearrangement records)
      observed in this clone, the number of distinct cell barcodes (unique cell_id
      values), or a more sophisticated calculation appropriate to the experimental
      protocol. Absolute count is provided versus a frequency so that downstream analysis
      tools can perform their own normalization.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: clone_count
    owner: Clone
    domain_of:
    - Clone
    range: integer
  seed_id:
    name: seed_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: sequence_id of the seed sequence. Empty string (or null) if there
      is no seed sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: seed_id
    owner: Clone
    domain_of:
    - Clone
    range: string