Class: SampleProcessing

name: SampleProcessing
description: Default SampleProcessing description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- sample_processing_id
- sample_id
- sample_type
- tissue
- anatomic_site
- disease_state_sample
- collection_time_point_relative
- collection_location
- biomaterial_provider
- tissue_processing
- cell_subset
- cell_phenotype
- cell_label
- cell_species
- single_cell
- cell_number
- cells_per_reaction
- cell_storage
- cell_quality
- cell_isolation
- cell_processing_protocol
- template_class
- template_quality
- template_amount
- library_generation_method
- library_generation_protocol
- library_generation_kit_version
- pcr_target
- complete_sequences
- physical_linkage
- sequencing_run_id
- total_reads_passing_qc_filter
- sequencing_platform
- sequencing_facility
- sequencing_run_date
- sequencing_kit
- sequencing_files

name: SampleProcessing
description: Default SampleProcessing description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  sample_processing_id:
    name: sample_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Rearrangement
    - SampleProcessing
    range: string
  sample_id:
    name: sample_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Sample ID assigned by submitter, unique within study. If possible,
      a persistent sample ID linked to INSDC or similar repository study should be
      used.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  sample_type:
    name: sample_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The way the sample was obtained, e.g. fine-needle aspirate, organ
      harvest, peripheral venous puncture
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  tissue:
    name: tissue
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The actual tissue sampled, e.g. lymph node, liver, peripheral blood
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: TissueOntology
  anatomic_site:
    name: anatomic_site
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The anatomic location of the tissue, e.g. Inguinal, femur
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  disease_state_sample:
    name: disease_state_sample
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Histopathologic evaluation of the sample
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  collection_time_point_relative:
    name: collection_time_point_relative
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Time point at which sample was taken, relative to `label` event
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: TimePoint
  collection_location:
    name: collection_location
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Location where the sample was taken, preferred granularity is country-level
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: CollectionLocationOntology
  biomaterial_provider:
    name: biomaterial_provider
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name and address of the entity providing the sample
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  tissue_processing:
    name: tissue_processing
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Enzymatic digestion and/or physical methods used to isolate cells
      from sample
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  cell_subset:
    name: cell_subset
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: CellSubsetOntology
  cell_phenotype:
    name: cell_phenotype
    annotations:
      nullable:
        tag: nullable
        value: true
    description: List of cellular markers and their expression levels used to isolate
      the cell population.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: string
  cell_label:
    name: cell_label
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Free text cell type annotation. Primarily used for annotating cell
      types that are not  provided in the Cell Ontology.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - Cell
    - SampleProcessing
    range: string
  cell_species:
    name: cell_species
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Binomial designation of the species from which the analyzed cells
      originate. Typically, this value should be identical to `species`, in which
      case it SHOULD NOT be set explicitly. However, there are valid experimental
      setups in which the two might differ, e.g., chimeric animal models. If set,
      this key will overwrite the `species` information for all lower layers of the
      schema.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: CellSpeciesOntology
  single_cell:
    name: single_cell
    annotations:
      nullable:
        tag: nullable
        value: true
    description: TRUE if single cells were isolated into separate compartments
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: boolean
  cell_number:
    name: cell_number
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Total number of cells that went into the experiment
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: integer
  cells_per_reaction:
    name: cells_per_reaction
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of cells for each biological replicate
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: integer
  cell_storage:
    name: cell_storage
    annotations:
      nullable:
        tag: nullable
        value: true
    description: TRUE if cells were cryo-preserved between isolation and further processing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: boolean
  cell_quality:
    name: cell_quality
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Relative amount of viable cells after preparation and (if applicable)
      thawing
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  cell_isolation:
    name: cell_isolation
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Description of the procedure used for marker-based isolation or enrich
      cells
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  cell_processing_protocol:
    name: cell_processing_protocol
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Description of the methods applied to the sample including cell preparation/
      isolation/enrichment and nucleic acid extraction. This should closely mirror
      the Materials and methods section in the manuscript.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - CellProcessing
    - SampleProcessing
    range: string
  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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: PhysicalQuantity
  library_generation_method:
    name: library_generation_method
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Generic type of library generation
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - NucleicAcidProcessing
    - SampleProcessing
    range: PhysicalLinkageEnum
  sequencing_run_id:
    name: sequencing_run_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ID of sequencing run assigned by the sequencing facility
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  total_reads_passing_qc_filter:
    name: total_reads_passing_qc_filter
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of usable reads for analysis
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: integer
  sequencing_platform:
    name: sequencing_platform
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Designation of sequencing instrument used
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  sequencing_facility:
    name: sequencing_facility
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name and address of sequencing facility
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  sequencing_run_date:
    name: sequencing_run_date
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Date of sequencing run
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: date
  sequencing_kit:
    name: sequencing_kit
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name, manufacturer, order and lot numbers of sequencing kit
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: string
  sequencing_files:
    name: sequencing_files
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Set of sequencing files produced by the sequencing run
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: SampleProcessing
    domain_of:
    - SequencingRun
    - SampleProcessing
    range: SequencingData