Class: AlleleDescription

name: AlleleDescription
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- allele_description_id
- allele_description_ref
- maintainer
- acknowledgements
- lab_address
- release_version
- release_date
- release_description
- label
- sequence
- coding_sequence
- aliases
- locus
- chromosome
- sequence_type
- functional
- inference_type
- species
- species_subgroup
- species_subgroup_type
- status
- subgroup_designation
- gene_designation
- allele_designation
- allele_similarity_cluster_designation
- allele_similarity_cluster_member_id
- j_codon_frame
- gene_start
- gene_end
- utr_5_prime_start
- utr_5_prime_end
- leader_1_start
- leader_1_end
- leader_2_start
- leader_2_end
- v_rs_start
- v_rs_end
- d_rs_3_prime_start
- d_rs_3_prime_end
- d_rs_5_prime_start
- d_rs_5_prime_end
- j_cdr3_end
- j_rs_start
- j_rs_end
- j_donor_splice
- v_gene_delineations
- unrearranged_support
- rearranged_support
- paralogs
- curation
- curational_tags

name: AlleleDescription
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  allele_description_id:
    name: allele_description_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unique identifier of this AlleleDescription within the file. Typically,
      generated by the  repository hosting the record.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: allele_description_id
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  allele_description_ref:
    name: allele_description_ref
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unique reference to the allele description, in standardized form
      (Repo:Label:Version)
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: allele_description_ref
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  maintainer:
    name: maintainer
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Maintainer of this sequence record
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: maintainer
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  acknowledgements:
    name: acknowledgements
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: acknowledgements
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: Acknowledgement
    multivalued: true
  lab_address:
    name: lab_address
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: lab_address
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    - Study
    range: string
  release_version:
    name: release_version
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: release_version
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: integer
  release_date:
    name: release_date
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Date of this release
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: release_date
    owner: AlleleDescription
    domain_of:
    - Investigation
    - AlleleDescription
    - GermlineSet
    range: datetime
  release_description:
    name: release_description
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Brief descriptive notes of the reason for this release and the changes
      embodied
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: release_description
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: string
  label:
    name: label
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: label
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - DocumentedAllele
    - DeletedGene
    range: string
  sequence:
    name: sequence
    description: Nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence
    owner: AlleleDescription
    domain_of:
    - Chain
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - UndocumentedAllele
    - Rearrangement
    range: string
  coding_sequence:
    name: coding_sequence
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the core coding region, such as the coding
      region of a D-, J- or C- gene  or the coding region of a V-gene excluding the
      leader.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: coding_sequence
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  aliases:
    name: aliases
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alternative names for this sequence
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: aliases
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
    multivalued: true
  locus:
    name: locus
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: locus
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    - Genotype
    - Rearrangement
    range: LocusEnum
  chromosome:
    name: chromosome
    annotations:
      nullable:
        tag: nullable
        value: true
    description: chromosome on which the gene is located
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: chromosome
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  sequence_type:
    name: sequence_type
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Sequence type (V, D, J, C)
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: sequence_type
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: SequenceTypeEnum
  functional:
    name: functional
    annotations:
      nullable:
        tag: nullable
        value: true
    description: True if the gene is functional, false if it is a pseudogene
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: functional
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: boolean
  inference_type:
    name: inference_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Type of inference(s) from which this gene sequence was inferred
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: inference_type
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: InferenceTypeEnum
  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: AlleleDescription
    domain_of:
    - Participant
    - AlleleDescription
    - GermlineSet
    - Subject
    range: SpeciesOntology
  species_subgroup:
    name: species_subgroup
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Race, strain or other species subgroup to which this subject belongs
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: species_subgroup
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: string
  species_subgroup_type:
    name: species_subgroup_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ''
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: species_subgroup_type
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: SpeciesSubgroupTypeEnum
  status:
    name: status
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Status of record, assumed active if the field is not present
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: status
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: StatusEnum
  subgroup_designation:
    name: subgroup_designation
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Identifier of the gene subgroup or clade, as (and if) defined
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: subgroup_designation
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  gene_designation:
    name: gene_designation
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Gene number or other identifier, as (and if) defined
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: gene_designation
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  allele_designation:
    name: allele_designation
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: allele_designation
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    - MHCAllele
    range: string
  allele_similarity_cluster_designation:
    name: allele_similarity_cluster_designation
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ID of the similarity cluster used in this germline set, if designated
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: allele_similarity_cluster_designation
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  allele_similarity_cluster_member_id:
    name: allele_similarity_cluster_member_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Membership ID of the allele within the similarity cluster, if a cluster
      is designated
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: allele_similarity_cluster_member_id
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
  j_codon_frame:
    name: j_codon_frame
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Codon position of the first nucleotide in the 'coding_sequence' field.
      Mandatory for J genes.  Not used for V or D genes. '1' means the sequence is
      in-frame, '2' means that the first bp is  missing from the first codon, and
      '3' means that the first 2 bp are missing.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_codon_frame
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: JCodonFrameEnum
  gene_start:
    name: gene_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Co-ordinate in the sequence field of the first nucleotide in the
      coding_sequence field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: gene_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  gene_end:
    name: gene_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Co-ordinate in the sequence field of the last gene-coding nucleotide
      in the coding_sequence field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: gene_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  utr_5_prime_start:
    name: utr_5_prime_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of the 5 prime UTR (V-genes
      only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: utr_5_prime_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  utr_5_prime_end:
    name: utr_5_prime_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of the 5 prime UTR (V-genes
      only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: utr_5_prime_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  leader_1_start:
    name: leader_1_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of L-PART1 (V-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: leader_1_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  leader_1_end:
    name: leader_1_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of L-PART1 (V-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: leader_1_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  leader_2_start:
    name: leader_2_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of L-PART2 (V-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: leader_2_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  leader_2_end:
    name: leader_2_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of L-PART2 (V-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: leader_2_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  v_rs_start:
    name: v_rs_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of the V recombination site
      (V-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_rs_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  v_rs_end:
    name: v_rs_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of the V recombination site
      (V-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_rs_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  d_rs_3_prime_start:
    name: d_rs_3_prime_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of the 3 prime D recombination
      site (D-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_rs_3_prime_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  d_rs_3_prime_end:
    name: d_rs_3_prime_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of the 3 prime D recombination
      site (D-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_rs_3_prime_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  d_rs_5_prime_start:
    name: d_rs_5_prime_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of the 5 prime D recombination
      site (D-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_rs_5_prime_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  d_rs_5_prime_end:
    name: d_rs_5_prime_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of 5 the prime D recombination
      site (D-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_rs_5_prime_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  j_cdr3_end:
    name: j_cdr3_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: In the case of a J-gene, the co-ordinate in the sequence field of
      the first nucelotide of the  conserved PHE or TRP (IMGT codon position 118).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_cdr3_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  j_rs_start:
    name: j_rs_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start co-ordinate in the sequence field of J recombination site (J-genes
      only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_rs_start
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  j_rs_end:
    name: j_rs_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End co-ordinate in the sequence field of J recombination site (J-genes
      only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_rs_end
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  j_donor_splice:
    name: j_donor_splice
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Co-ordinate in the sequence field of the final 3' nucleotide of the
      J-REGION (J-genes only).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_donor_splice
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: integer
  v_gene_delineations:
    name: v_gene_delineations
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ''
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_gene_delineations
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: SequenceDelineationV
    multivalued: true
  unrearranged_support:
    name: unrearranged_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ''
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: unrearranged_support
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: UnrearrangedSequence
    multivalued: true
  rearranged_support:
    name: rearranged_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ''
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: rearranged_support
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: RearrangedSequence
    multivalued: true
  paralogs:
    name: paralogs
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Gene symbols of any paralogs
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: paralogs
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: string
    multivalued: true
  curation:
    name: curation
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: curation
    owner: AlleleDescription
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - GermlineSet
    range: string
  curational_tags:
    name: curational_tags
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Controlled-vocabulary tags applied to this description
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: curational_tags
    owner: AlleleDescription
    domain_of:
    - AlleleDescription
    range: CurationalTagsEnum
    multivalued: true