Class: NucleicAcidProcessing

name: NucleicAcidProcessing
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- template_class
- template_quality
- template_amount
- template_amount_unit
- library_generation_method
- library_generation_protocol
- library_generation_kit_version
- pcr_target
- complete_sequences
- physical_linkage

name: NucleicAcidProcessing
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  template_class:
    name: template_class
    annotations:
      nullable:
        tag: nullable
        value: false
    description: The class of nucleic acid that was used as primary starting material
      for the following procedures
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: template_class
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: TemplateClassEnum
  template_quality:
    name: template_quality
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Description and results of the quality control performed on the template
      material
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: template_quality
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: string
  template_amount:
    name: template_amount
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amount of template that went into the process
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: template_amount
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: float
  template_amount_unit:
    name: template_amount_unit
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unit of template amount
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: template_amount_unit
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: TemplateAmountUnitOntology
  library_generation_method:
    name: library_generation_method
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Generic type of library generation
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: library_generation_method
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: LibraryGenerationMethodEnum
  library_generation_protocol:
    name: library_generation_protocol
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Description of processes applied to substrate to obtain a library
      that is ready for sequencing
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: library_generation_protocol
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: string
  library_generation_kit_version:
    name: library_generation_kit_version
    annotations:
      nullable:
        tag: nullable
        value: true
    description: When using a library generation protocol from a commercial provider,
      provide the protocol version number
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: library_generation_kit_version
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: string
  pcr_target:
    name: pcr_target
    annotations:
      nullable:
        tag: nullable
        value: false
    description: If a PCR step was performed that specifically targets the IG/TR loci,
      the target and primer locations need to be provided here. This field holds an
      array of PCRTarget objects, so that multiplex PCR setups amplifying multiple
      loci at the same time can be annotated using one record per locus. PCR setups
      not targeting any specific locus must not annotate this field but select the
      appropriate library_generation_method instead.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: pcr_target
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: PCRTarget
    multivalued: true
  complete_sequences:
    name: complete_sequences
    annotations:
      nullable:
        tag: nullable
        value: false
    description: To be considered `complete`, the procedure used for library construction
      MUST generate sequences that 1) include the first V gene codon that encodes
      the mature polypeptide chain (i.e. after the leader sequence) and 2) include
      the last complete codon of the J gene (i.e. 1 bp 5' of the J->C splice site)
      and 3) provide sequence information for all positions between 1) and 2). To
      be considered `complete & untemplated`, the sections of the sequences defined
      in points 1) to 3) of the previous sentence MUST be untemplated, i.e. MUST NOT
      overlap with the primers used in library preparation. `mixed` should only be
      used if the procedure used for library construction will likely produce multiple
      categories of sequences in the given experiment. It SHOULD NOT be used as a
      replacement of a NULL value.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: complete_sequences
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: CompleteSequencesEnum
  physical_linkage:
    name: physical_linkage
    annotations:
      nullable:
        tag: nullable
        value: false
    description: In case an experimental setup is used that physically links nucleic
      acids derived from distinct `Rearrangements` before library preparation, this
      field describes the mode of that linkage. All `hetero_*` terms indicate that
      in case of paired-read sequencing, the two reads should be expected to map to
      distinct IG/TR loci. `*_head-head` refers to techniques that link the 5' ends
      of transcripts in a single-cell context. `*_tail-head` refers to techniques
      that link the 3' end of one transcript to the 5' end of another one in a single-cell
      context. This term does not provide any information whether a continuous reading-frame
      between the two is generated. `*_prelinked` refers to constructs in which the
      linkage was already present on the DNA level (e.g. scFv).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: physical_linkage
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: PhysicalLinkageEnum