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Class: SequenceDelineationV

Delineation of a V-gene in a particular system

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

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

Mappings

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

LinkML Source

Direct

name: SequenceDelineationV
description: Delineation of a V-gene in a particular system
from_schema: https://github.com/vdjserver/vdjserver-airr-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
description: Delineation of a V-gene in a particular system
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  sequence_delineation_id:
    name: sequence_delineation_id
    description: Unique identifier of this SequenceDelineationV within the file. Typically,
      generated by the  repository hosting the record.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  delineation_scheme:
    name: delineation_scheme
    description: Name of the delineation scheme
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  unaligned_sequence:
    name: unaligned_sequence
    description: entire V-sequence covered by this delineation
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  aligned_sequence:
    name: aligned_sequence
    description: Aligned sequence if this delineation provides an alignment. An aligned
      sequence should always be  provided for IMGT delineations.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
  fwr1_start:
    name: fwr1_start
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr1_end:
    name: fwr1_end
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr1_start:
    name: cdr1_start
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr1_end:
    name: cdr1_end
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr2_start:
    name: fwr2_start
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr2_end:
    name: fwr2_end
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr2_start:
    name: cdr2_start
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr2_end:
    name: cdr2_end
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr3_start:
    name: fwr3_start
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr3_end:
    name: fwr3_end
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr3_start:
    name: cdr3_start
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  alignment_labels:
    name: alignment_labels
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SequenceDelineationV
    domain_of:
    - SequenceDelineationV
    range: string
    multivalued: true