Class: Clone

Default Clone description

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

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

      Clone : clone_class





        Clone --> "0..1" CloneClassEnum : clone_class
        click CloneClassEnum href "../CloneClassEnum/"



      Clone : clone_count

      Clone : clone_id

      Clone : data_processing_id

      Clone : inferred_ancestor

      Clone : nodes





        Clone --> "*" Node : nodes
        click Node href "../Node/"



      Clone : repertoire_group_id

      Clone : repertoire_id

      Clone : seed_id

      Clone : tree

Inheritance

AIRRStandards
- Clone

Slots

Name	Cardinality and Range	Description	Inheritance
clone_id	0..1 String		direct
repertoire_group_id	0..1 String		direct
repertoire_id	0..1 String		direct
clone_class	0..1 CloneClassEnum	Is this a single-chain clone or a cell-based clone?	direct
data_processing_id	0..1 String		direct
nodes	* Node	List of Nodes that are members of this clone	direct
inferred_ancestor	0..1 String	Node_id string that acts as a key to the Node record for the inferred naive ...	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 or cell_id of the seed sequence/cell	direct
tree	0..1 String	Newick string describing the tree	direct

Identifier and Mapping Information

Schema Source

from schema: https://github.com/vdjserver/vdjserver-airr-schema

Mappings

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

LinkML Source

Direct

name: Clone
description: Default Clone description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- clone_id
- repertoire_group_id
- repertoire_id
- clone_class
- data_processing_id
- nodes
- inferred_ancestor
- clone_count
- seed_id
- tree

Induced

name: Clone
description: Default Clone description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  clone_id:
    name: clone_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Rearrangement
    - Clone
    range: string
  repertoire_group_id:
    name: repertoire_group_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - RepertoireGroup
    - Clone
    - VisualizationDocument
    range: string
  repertoire_id:
    name: repertoire_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Repertoire
    - RepertoireFilter
    - Rearrangement
    - Clone
    - Node
    - Cell
    - Expression
    - Reactivity
    - ADCRearrangementLoad
    - ADCDownloadCacheRepertoire
    - StatisticsCacheRepertoire
    - VisualizationDocument
    range: string
  clone_class:
    name: clone_class
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Is this a single-chain clone or a cell-based clone?
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Clone
    range: CloneClassEnum
  data_processing_id:
    name: data_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - DataProcessing
    - Rearrangement
    - Clone
    - Cell
    - Expression
    - Reactivity
    range: string
  nodes:
    name: nodes
    annotations:
      nullable:
        tag: nullable
        value: true
    description: List of Nodes that are members of this clone.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Clone
    range: Node
    multivalued: true
  inferred_ancestor:
    name: inferred_ancestor
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Node_id string that acts as a key to the Node record for the  inferred
      naive Rearrangement or Cell for this clone.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Clone
    range: string
  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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Clone
    range: integer
  seed_id:
    name: seed_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: sequence_id or cell_id of the seed sequence/cell. Empty string (or
      null) if there is no seed sequence.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Clone
    range: string
  tree:
    name: tree
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Newick string describing the tree.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Clone
    domain_of:
    - Clone
    range: string