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Class: Alignment

URI: ak_schema:Alignment

classDiagram class Alignment click Alignment href "../Alignment" AIRRStandards <|-- Alignment click AIRRStandards href "../AIRRStandards" Alignment : call Alignment : cigar Alignment : data_processing_id Alignment : germline_end Alignment : germline_start Alignment : identity Alignment : rank Alignment : rev_comp Alignment : score Alignment : segment Alignment : sequence_end Alignment : sequence_id Alignment : sequence_start Alignment : support

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sequence_id 0..1
String		 direct
segment 0..1
String		 The segment for this alignment direct
rev_comp 0..1
Boolean		 direct
call 0..1
String		 Gene assignment with allele direct
score 0..1
Float		 Alignment score direct
identity 0..1
Float		 Alignment fractional identity direct
support 0..1
Float		 Alignment E-value, p-value, likelihood, probability or other similar measure ... direct
cigar 0..1
String		 Alignment CIGAR string direct
sequence_start 0..1
Integer		 direct
sequence_end 0..1
Integer		 direct
germline_start 0..1
Integer		 Alignment start position in the reference sequence (1-based closed interval) direct
germline_end 0..1
Integer		 Alignment end position in the reference sequence (1-based closed interval) direct
rank 0..1
Integer		 Alignment rank direct
data_processing_id 0..1
String		 direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Alignment
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- sequence_id
- segment
- rev_comp
- call
- score
- identity
- support
- cigar
- sequence_start
- sequence_end
- germline_start
- germline_end
- rank
- data_processing_id

Induced

name: Alignment
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  sequence_id:
    name: sequence_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_id
    owner: Alignment
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - Alignment
    - Rearrangement
    - Node
    range: string
  segment:
    name: segment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The segment for this alignment. One of V, D, J or C.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: segment
    owner: Alignment
    domain_of:
    - Alignment
    range: string
  rev_comp:
    name: rev_comp
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: rev_comp
    owner: Alignment
    domain_of:
    - Alignment
    - Rearrangement
    range: boolean
  call:
    name: call
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Gene assignment with allele.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: call
    owner: Alignment
    domain_of:
    - Alignment
    range: string
  score:
    name: score
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment score.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: score
    owner: Alignment
    domain_of:
    - Alignment
    range: float
  identity:
    name: identity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment fractional identity.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: identity
    owner: Alignment
    domain_of:
    - Alignment
    range: float
  support:
    name: support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment E-value, p-value, likelihood, probability or other similar
      measure of support for the gene assignment as defined by the alignment tool.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: support
    owner: Alignment
    domain_of:
    - Alignment
    range: float
  cigar:
    name: cigar
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment CIGAR string.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cigar
    owner: Alignment
    domain_of:
    - Alignment
    range: string
  sequence_start:
    name: sequence_start
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_start
    owner: Alignment
    domain_of:
    - RearrangedSequence
    - Alignment
    range: integer
  sequence_end:
    name: sequence_end
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_end
    owner: Alignment
    domain_of:
    - RearrangedSequence
    - Alignment
    range: integer
  germline_start:
    name: germline_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment start position in the reference sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_start
    owner: Alignment
    domain_of:
    - Alignment
    range: integer
  germline_end:
    name: germline_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment end position in the reference sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_end
    owner: Alignment
    domain_of:
    - Alignment
    range: integer
  rank:
    name: rank
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment rank.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: rank
    owner: Alignment
    domain_of:
    - Alignment
    range: integer
  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: Alignment
    domain_of:
    - DataProcessing
    - Alignment
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string