Class: SequenceDelineationV

URI: ak_schema:SequenceDelineationV

classDiagram class SequenceDelineationV click SequenceDelineationV href "../SequenceDelineationV" AIRRStandards <|-- SequenceDelineationV click AIRRStandards href "../AIRRStandards" SequenceDelineationV : aligned_sequence SequenceDelineationV : alignment_labels SequenceDelineationV : cdr1_end SequenceDelineationV : cdr1_start SequenceDelineationV : cdr2_end SequenceDelineationV : cdr2_start SequenceDelineationV : cdr3_start SequenceDelineationV : delineation_scheme SequenceDelineationV : fwr1_end SequenceDelineationV : fwr1_start SequenceDelineationV : fwr2_end SequenceDelineationV : fwr2_start SequenceDelineationV : fwr3_end SequenceDelineationV : fwr3_start SequenceDelineationV : sequence_delineation_id SequenceDelineationV : unaligned_sequence

Inheritance

AIRRStandards
- SequenceDelineationV

Slots

Name	Cardinality and Range	Description	Inheritance
sequence_delineation_id	0..1 String	Unique identifier of this SequenceDelineationV within the file	direct
delineation_scheme	0..1 String	Name of the delineation scheme	direct
unaligned_sequence	0..1 String	entire V-sequence covered by this delineation	direct
aligned_sequence	0..1 String	Aligned sequence if this delineation provides an alignment	direct
fwr1_start	0..1 Integer		direct
fwr1_end	0..1 Integer		direct
cdr1_start	0..1 Integer		direct
cdr1_end	0..1 Integer		direct
fwr2_start	0..1 Integer		direct
fwr2_end	0..1 Integer		direct
cdr2_start	0..1 Integer		direct
cdr2_end	0..1 Integer		direct
fwr3_start	0..1 Integer		direct
fwr3_end	0..1 Integer		direct
cdr3_start	0..1 Integer		direct
alignment_labels	* String	One string for each codon in the aligned_sequence indicating the label of tha...	direct

Usages

used by	used in	type	used
AlleleDescription	v_gene_delineations	range	SequenceDelineationV

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: SequenceDelineationV
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- sequence_delineation_id
- delineation_scheme
- unaligned_sequence
- aligned_sequence
- fwr1_start
- fwr1_end
- cdr1_start
- cdr1_end
- fwr2_start
- fwr2_end
- cdr2_start
- cdr2_end
- fwr3_start
- fwr3_end
- cdr3_start
- alignment_labels

Induced

name: SequenceDelineationV
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  sequence_delineation_id:
    name: sequence_delineation_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unique identifier of this SequenceDelineationV within the file. Typically,
      generated by the  repository hosting the record.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_delineation_id
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  delineation_scheme:
    name: delineation_scheme
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name of the delineation scheme
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: delineation_scheme
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  unaligned_sequence:
    name: unaligned_sequence
    annotations:
      nullable:
        tag: nullable
        value: true
    description: entire V-sequence covered by this delineation
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: unaligned_sequence
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  aligned_sequence:
    name: aligned_sequence
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Aligned sequence if this delineation provides an alignment. An aligned
      sequence should always be  provided for IMGT delineations.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: aligned_sequence
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  fwr1_start:
    name: fwr1_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr1_start
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr1_end:
    name: fwr1_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr1_end
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr1_start:
    name: cdr1_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1_start
    owner: SequenceDelineationV
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr1_end:
    name: cdr1_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1_end
    owner: SequenceDelineationV
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr2_start:
    name: fwr2_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr2_start
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr2_end:
    name: fwr2_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr2_end
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr2_start:
    name: cdr2_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2_start
    owner: SequenceDelineationV
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr2_end:
    name: cdr2_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2_end
    owner: SequenceDelineationV
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr3_start:
    name: fwr3_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr3_start
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr3_end:
    name: fwr3_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr3_end
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr3_start:
    name: cdr3_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3_start
    owner: SequenceDelineationV
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  alignment_labels:
    name: alignment_labels
    annotations:
      nullable:
        tag: nullable
        value: true
    description: One string for each codon in the aligned_sequence indicating the
      label of that codon according to  the numbering of the delineation scheme if
      it provides one.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: alignment_labels
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
    multivalued: true