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Class: Chain

  • NOTE: this is an abstract class and should not be instantiated directly

URI: ak_schema:Chain

classDiagram class Chain click Chain href "../Chain" AKObject <|-- Chain click AKObject href "../AKObject" Chain <|-- AlphaChain click AlphaChain href "../AlphaChain" Chain <|-- BetaChain click BetaChain href "../BetaChain" Chain <|-- DeltaChain click DeltaChain href "../DeltaChain" Chain <|-- GammaChain click GammaChain href "../GammaChain" Chain <|-- HeavyChain click HeavyChain href "../HeavyChain" Chain <|-- KappaChain click KappaChain href "../KappaChain" Chain <|-- LambdaChain click LambdaChain href "../LambdaChain" Chain : akc_id Chain : c_call Chain : cdr1_aa Chain : cdr2_aa Chain : cdr3_aa Chain : complete_vdj Chain : d_call Chain : hash_infer_vdj_sequence Chain : hash_infer_vdj_sequence_aa Chain : infer_vdj_sequence Chain : infer_vdj_sequence_aa Chain : j_call Chain : j_gene Chain : j_subgroup Chain : junction_aa Chain : locus Chain --> "0..1" LocusEnum : locus click LocusEnum href "../LocusEnum" Chain : sequence Chain : sequence_aa Chain : species Chain --> "0..1" SpeciesOntology : species click SpeciesOntology href "../SpeciesOntology" Chain : v_call Chain : v_gene Chain : v_subgroup

Inheritance

Slots

Name Cardinality and Range Description Inheritance
species 0..1
SpeciesOntology		 Binomial designation of subject's species direct
complete_vdj 0..1
Boolean		 Complete VDJ flag direct
sequence 0..1
String		 Nucleotide sequence direct
infer_vdj_sequence 0..1
String		 Inferred complete VDJ nucleotide sequence direct
hash_infer_vdj_sequence 0..1
Uriorcurie		 Hash of the inferred complete VDJ nucleotide sequence direct
sequence_aa 0..1
String		 Amino acid translation of the query nucleotide sequence direct
infer_vdj_sequence_aa 0..1
String		 Translation of inferred complete VDJ nucleotide sequence direct
hash_infer_vdj_sequence_aa 0..1
Uriorcurie		 Hash of the translation of inferred complete VDJ nucleotide sequence direct
locus 0..1
LocusEnum		 direct
v_call 0..1
String		 direct
v_gene 0..1
String		 V gene designation for the chain direct
v_subgroup 0..1
String		 V gene subgroup/family designation for the chain direct
d_call 0..1
String		 direct
j_call 0..1
String		 direct
j_gene 0..1
String		 J gene designation for the chain direct
j_subgroup 0..1
String		 J gene subgroup/family designation for the chain direct
c_call 0..1
String		 Constant region gene with allele direct
junction_aa 0..1
String		 Amino acid translation of the junction direct
cdr1_aa 0..1
String		 Amino acid translation of the cdr1 field direct
cdr2_aa 0..1
String		 Amino acid translation of the cdr2 field direct
cdr3_aa 0..1
String		 Amino acid translation of the cdr3 field direct
akc_id 1
Uriorcurie		 A unique identifier for a thing in the AKC AKObject

Usages

used by used in type used
SimilarityCalculation chain_domain range Chain
SimilarityCalculation chain_codomain range Chain
ChainSimilarity chain_domain range Chain
ChainSimilarity chain_codomain range Chain
QueryAlphaBetaTCR tra_chain range Chain
QueryAlphaBetaTCR trb_chain range Chain

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Chain
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AKObject
abstract: true
slots:
- species
- complete_vdj
- sequence
- infer_vdj_sequence
- hash_infer_vdj_sequence
- sequence_aa
- infer_vdj_sequence_aa
- hash_infer_vdj_sequence_aa
- locus
- v_call
- v_gene
- v_subgroup
- d_call
- j_call
- j_gene
- j_subgroup
- c_call
- junction_aa
- cdr1_aa
- cdr2_aa
- cdr3_aa
slot_usage:
  sequence_aa:
    name: sequence_aa
    pattern: ^[ACDEFGHIKLMNPQRSTVWY]+$
  junction_aa:
    name: junction_aa
    pattern: ^C[ACDEFGHIKLMNPQRSTVWY]+$

Induced

name: Chain
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AKObject
abstract: true
slot_usage:
  sequence_aa:
    name: sequence_aa
    pattern: ^[ACDEFGHIKLMNPQRSTVWY]+$
  junction_aa:
    name: junction_aa
    pattern: ^C[ACDEFGHIKLMNPQRSTVWY]+$
attributes:
  species:
    name: species
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Binomial designation of subject's species
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: species
    owner: Chain
    domain_of:
    - Participant
    - Chain
    - ImmuneReceptor
    - AntibodyAntigenComplex
    - TCRpMHCComplex
    - ReceptorComposite
    - AlphaBetaReceptorComposite
    - GammaDeltaReceptorComposite
    - BCellReceptorComposite
    - AlleleDescription
    - GermlineSet
    - Subject
    range: SpeciesOntology
  complete_vdj:
    name: complete_vdj
    description: Complete VDJ flag.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: complete_vdj
    owner: Chain
    domain_of:
    - Chain
    - Rearrangement
    range: boolean
  sequence:
    name: sequence
    description: Nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence
    owner: Chain
    domain_of:
    - Chain
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - UndocumentedAllele
    - Rearrangement
    range: string
  infer_vdj_sequence:
    name: infer_vdj_sequence
    description: Inferred complete VDJ nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: infer_vdj_sequence
    owner: Chain
    domain_of:
    - Chain
    range: string
  hash_infer_vdj_sequence:
    name: hash_infer_vdj_sequence
    description: Hash of the inferred complete VDJ nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: hash_infer_vdj_sequence
    owner: Chain
    domain_of:
    - Chain
    range: uriorcurie
  sequence_aa:
    name: sequence_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the query nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_aa
    owner: Chain
    domain_of:
    - Chain
    - PeptidicEpitope
    - Rearrangement
    range: string
    pattern: ^[ACDEFGHIKLMNPQRSTVWY]+$
  infer_vdj_sequence_aa:
    name: infer_vdj_sequence_aa
    description: Translation of inferred complete VDJ nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: infer_vdj_sequence_aa
    owner: Chain
    domain_of:
    - Chain
    range: string
  hash_infer_vdj_sequence_aa:
    name: hash_infer_vdj_sequence_aa
    description: Hash of the translation of inferred complete VDJ nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: hash_infer_vdj_sequence_aa
    owner: Chain
    domain_of:
    - Chain
    range: uriorcurie
  locus:
    name: locus
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: locus
    owner: Chain
    domain_of:
    - Chain
    - AlleleDescription
    - GermlineSet
    - Genotype
    - Rearrangement
    range: LocusEnum
  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: Chain
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  v_gene:
    name: v_gene
    description: V gene designation for the chain
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_gene
    owner: Chain
    domain_of:
    - Chain
    range: string
  v_subgroup:
    name: v_subgroup
    description: V gene subgroup/family designation for the chain
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_subgroup
    owner: Chain
    domain_of:
    - Chain
    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: Chain
    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: Chain
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  j_gene:
    name: j_gene
    description: J gene designation for the chain
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_gene
    owner: Chain
    domain_of:
    - Chain
    range: string
  j_subgroup:
    name: j_subgroup
    description: J gene subgroup/family designation for the chain
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_subgroup
    owner: Chain
    domain_of:
    - Chain
    range: string
  c_call:
    name: c_call
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Constant region gene with allele. If referring to a known reference
      sequence in a database the relevant gene/allele nomenclature should be followed
      (e.g., IGHG1*01 if using IMGT/GENE-DB).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_call
    owner: Chain
    domain_of:
    - Chain
    - Rearrangement
    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: Chain
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    - Node
    range: string
    pattern: ^C[ACDEFGHIKLMNPQRSTVWY]+$
  cdr1_aa:
    name: cdr1_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the cdr1 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1_aa
    owner: Chain
    domain_of:
    - Chain
    - Rearrangement
    range: string
  cdr2_aa:
    name: cdr2_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the cdr2 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2_aa
    owner: Chain
    domain_of:
    - Chain
    - Rearrangement
    range: string
  cdr3_aa:
    name: cdr3_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the cdr3 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3_aa
    owner: Chain
    domain_of:
    - Chain
    - Rearrangement
    range: string
  akc_id:
    name: akc_id
    description: A unique identifier for a thing in the AKC.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: akc_id
    owner: Chain
    domain_of:
    - AKObject
    range: uriorcurie
    required: true