Class: Nucleic Acid Processing (NucleicAcidProcessing)

A record of the procedures used to prepare nucleic acid libraries for sequencing, including template handling and library generation.

__

URI: nfdi4immuno:NucleicAcidProcessing

 classDiagram
    class NucleicAcidProcessing
    click NucleicAcidProcessing href "../NucleicAcidProcessing/"
      NucleicAcidProcessing : complete_sequences





        NucleicAcidProcessing --> "1" CompleteSequences : complete_sequences
        click CompleteSequences href "../CompleteSequences/"



      NucleicAcidProcessing : library_generation_kit_version

      NucleicAcidProcessing : library_generation_method





        NucleicAcidProcessing --> "1" LibraryGenerationMethod : library_generation_method
        click LibraryGenerationMethod href "../LibraryGenerationMethod/"



      NucleicAcidProcessing : library_generation_protocol

      NucleicAcidProcessing : pcr_targets





        NucleicAcidProcessing --> "1..*" PCRTarget : pcr_targets
        click PCRTarget href "../PCRTarget/"



      NucleicAcidProcessing : physical_linkage





        NucleicAcidProcessing --> "1" PhysicalLinkage : physical_linkage
        click PhysicalLinkage href "../PhysicalLinkage/"



      NucleicAcidProcessing : template_amount_unit





        NucleicAcidProcessing --> "0..1 _recommended_" WeightUnits : template_amount_unit
        click WeightUnits href "../WeightUnits/"



      NucleicAcidProcessing : template_amount_value

      NucleicAcidProcessing : template_class





        NucleicAcidProcessing --> "1" TemplateClass : template_class
        click TemplateClass href "../TemplateClass/"



      NucleicAcidProcessing : template_quality

Slots

Name	Cardinality and Range	Description	Inheritance
template_class	1 TemplateClass	The class of nucleic acid that was used as primary starting material for the ...	direct
template_quality	0..1 recommended String	Description and results of the quality control performed on the template mate...	direct
template_amount_value	0..1 recommended Integer	Amount of template that went into the process	direct
template_amount_unit	0..1 recommended WeightUnits	The unit of the template amount that went into the process	direct
library_generation_method	1 LibraryGenerationMethod	Generic type of library generation	direct
library_generation_protocol	0..1 recommended String	Description of processes applied to substrate to obtain a library that is rea...	direct
library_generation_kit_version	0..1 recommended String	When using a library generation protocol from a commercial provider, provide ...	direct
pcr_targets	1..* PCRTarget	The IG/TR locus or loci under investigation	direct
complete_sequences	1 CompleteSequences	To be considered complete, the procedure used for library construction MUST...	direct
physical_linkage	1 PhysicalLinkage	In case an experimental setup is used that physically links nucleic acids der...	direct

Usages

used by	used in	type	used
AIRRRun	nucleic_acid_processing	range	NucleicAcidProcessing

Identifier and Mapping Information

Schema Source

• from schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema

Mappings

Mapping Type	Mapped Value
self	nfdi4immuno:NucleicAcidProcessing
native	nfdi4immuno:NucleicAcidProcessing

LinkML Source

Direct

name: NucleicAcidProcessing
description: 'A record of the procedures used to prepare nucleic acid libraries for
  sequencing, including template handling and library generation.

  '
title: Nucleic Acid Processing
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
slots:
- template_class
- template_quality
- template_amount_value
- template_amount_unit
- library_generation_method
- library_generation_protocol
- library_generation_kit_version
- pcr_targets
- complete_sequences
- physical_linkage

Induced

name: NucleicAcidProcessing
description: 'A record of the procedures used to prepare nucleic acid libraries for
  sequencing, including template handling and library generation.

  '
title: Nucleic Acid Processing
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
attributes:
  template_class:
    name: template_class
    description: 'The class of nucleic acid that was used as primary starting material
      for the following procedures.

      '
    title: Target substrate
    examples:
    - value: rna
      description: RNA.
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: template_class
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: TemplateClass
    required: true
    pattern: ^.+$
  template_quality:
    name: template_quality
    description: 'Description and results of the quality control performed on the
      template material.

      '
    title: Target substrate quality
    examples:
    - value: RIN 9.2
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: template_quality
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: string
    recommended: true
  template_amount_value:
    name: template_amount_value
    description: Amount of template that went into the process.
    title: Template amount value
    examples:
    - value: '1000'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: template_amount_value
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: integer
    recommended: true
  template_amount_unit:
    name: template_amount_unit
    description: The unit of the template amount that went into the process.
    title: Template amount unit
    examples:
    - value: nanogram
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: template_amount_unit
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: WeightUnits
    recommended: true
  library_generation_method:
    name: library_generation_method
    description: Generic type of library generation.
    title: Library generation method
    examples:
    - value: rt_oligo_d_t_ts_umi_pcr
      description: RT(oligo-dT)+TS(UMI)+PCR.
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: library_generation_method
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: LibraryGenerationMethod
    required: true
    pattern: ^.+$
  library_generation_protocol:
    name: library_generation_protocol
    description: 'Description of processes applied to substrate to obtain a library
      that is ready for sequencing.

      '
    title: Library generation protocol
    examples:
    - value: cDNA was generated using
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: library_generation_protocol
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: string
    recommended: true
  library_generation_kit_version:
    name: library_generation_kit_version
    description: 'When using a library generation protocol from a commercial provider,
      provide the protocol version number.

      '
    title: Protocol IDs
    examples:
    - value: v2.1 (2016-09-15)
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: library_generation_kit_version
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: string
    recommended: true
  pcr_targets:
    name: pcr_targets
    description: 'The IG/TR locus or loci under investigation. This field holds an
      array of PCRTarget objects, with one record per locus for multiplex PCR setups.
      Required to register which receptor loci are being deposited, including for
      bulk-amplified repertoires.

      '
    title: PCR targets
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: pcr_targets
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: PCRTarget
    required: true
    multivalued: true
    minimum_cardinality: 1
  complete_sequences:
    name: complete_sequences
    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.

      '
    title: Complete sequences
    examples:
    - value: partial
      description: Sequences are partial and do not meet the criteria for complete
        sequences.
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: complete_sequences
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: CompleteSequences
    required: true
    pattern: ^.+$
  physical_linkage:
    name: physical_linkage
    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.

      '
    title: Physical linkage of different rearrangements
    examples:
    - value: hetero_head-head
      description: The 5' ends of transcripts are linked in a single-cell context.
    - value: no_physical_linkage
      description: No physical linkage between rearrangements.
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: physical_linkage
    owner: NucleicAcidProcessing
    domain_of:
    - NucleicAcidProcessing
    range: PhysicalLinkage
    required: true
    pattern: ^.+$