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Class: Chain

URI: ak_schema:Chain

classDiagram class Chain click Chain href "../Chain" AKObject <|-- Chain click AKObject href "../AKObject" Chain : aa_hash Chain : akc_id Chain : c_call Chain : cdr1_aa Chain : cdr1_end Chain : cdr1_start Chain : cdr2_aa Chain : cdr2_end Chain : cdr2_start Chain : cdr3_aa Chain : cdr3_end Chain : cdr3_start Chain : chain_type Chain --> "0..1" ChainTypeEnum : chain_type click ChainTypeEnum href "../ChainTypeEnum" Chain : complete_vdj Chain : d_call Chain : j_call Chain : junction_aa Chain : junction_aa_vj_allele_hash Chain : junction_aa_vj_gene_hash Chain : sequence Chain : sequence_aa Chain : v_call

Inheritance

Slots

Name Cardinality and Range Description Inheritance
aa_hash 0..1
String		 direct
junction_aa_vj_allele_hash 0..1
String		 direct
junction_aa_vj_gene_hash 0..1
String		 direct
complete_vdj 0..1
Boolean		 Complete VDJ flag direct
sequence 0..1
String		 Nucleotide sequence direct
sequence_aa 0..1
String		 Amino acid translation of the query nucleotide sequence direct
chain_type 0..1
ChainTypeEnum		 Gene locus (chain type) direct
v_call 0..1
String		 direct
d_call 0..1
String		 direct
j_call 0..1
String		 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
cdr1_start 0..1
Integer		 direct
cdr1_end 0..1
Integer		 direct
cdr2_start 0..1
Integer		 direct
cdr2_end 0..1
Integer		 direct
cdr3_start 0..1
Integer		 direct
cdr3_end 0..1
Integer		 CDR3 end position in the query sequence (1-based closed interval) direct
akc_id 1
Uriorcurie		 A unique identifier for a thing in the AKC AKObject

Usages

used by used in type used
AIRRKnowledgeCommons chains range Chain
AIRRSequencingAssay tcell_chains range Chain
TCellReceptorEpitopeBindingAssay tcell_chains range Chain
AlphaBetaTCR tra_chain range Chain
AlphaBetaTCR trb_chain range Chain
GammaDeltaTCR trg_chain range Chain
GammaDeltaTCR trd_chain range Chain
BCellReceptor igh_chain range Chain
BCellReceptor igk_chain range Chain
BCellReceptor igl_chain range Chain
SimilarityCalculation chain_domain range Chain
SimilarityCalculation chain_codomain range Chain
ChainSimilarity chain_domain range Chain
ChainSimilarity chain_codomain 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
slots:
- aa_hash
- junction_aa_vj_allele_hash
- junction_aa_vj_gene_hash
- complete_vdj
- sequence
- sequence_aa
- chain_type
- v_call
- d_call
- j_call
- c_call
- junction_aa
- cdr1_aa
- cdr2_aa
- cdr3_aa
- cdr1_start
- cdr1_end
- cdr2_start
- cdr2_end
- cdr3_start
- cdr3_end

Induced

name: Chain
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AKObject
attributes:
  aa_hash:
    name: aa_hash
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: aa_hash
    owner: Chain
    domain_of:
    - Chain
    range: string
  junction_aa_vj_allele_hash:
    name: junction_aa_vj_allele_hash
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_aa_vj_allele_hash
    owner: Chain
    domain_of:
    - Chain
    range: string
  junction_aa_vj_gene_hash:
    name: junction_aa_vj_gene_hash
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_aa_vj_gene_hash
    owner: Chain
    domain_of:
    - Chain
    range: string
  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
  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
  chain_type:
    name: chain_type
    description: Gene locus (chain type).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: chain_type
    owner: Chain
    domain_of:
    - Chain
    range: ChainTypeEnum
  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
  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
  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
  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
  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: Chain
    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: Chain
    domain_of:
    - Chain
    - 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: Chain
    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: Chain
    domain_of:
    - Chain
    - 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: Chain
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr3_end:
    name: cdr3_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CDR3 end position in the query sequence (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3_end
    owner: Chain
    domain_of:
    - Chain
    - Rearrangement
    range: integer
  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