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Class: Reactivity

Default Reactivity description

URI: https://github.com/vdjserver/vdjserver-airr-schema/Reactivity

 classDiagram
    class Reactivity
    click Reactivity href "../Reactivity/"
      AIRRStandards <|-- Reactivity
        click AIRRStandards href "../AIRRStandards/"

      Reactivity : antigen

      Reactivity : antigen_source_species





        Reactivity --> "0..1" AntigenSourceSpeciesOntology : antigen_source_species
        click AntigenSourceSpeciesOntology href "../AntigenSourceSpeciesOntology/"



      Reactivity : antigen_type





        Reactivity --> "0..1" AntigenTypeEnum : antigen_type
        click AntigenTypeEnum href "../AntigenTypeEnum/"



      Reactivity : cell_id

      Reactivity : data_processing_id

      Reactivity : ligand_type





        Reactivity --> "0..1" LigandTypeEnum : ligand_type
        click LigandTypeEnum href "../LigandTypeEnum/"



      Reactivity : mhc_allele_1

      Reactivity : mhc_allele_2

      Reactivity : mhc_class





        Reactivity --> "0..1" MhcClassEnum : mhc_class
        click MhcClassEnum href "../MhcClassEnum/"



      Reactivity : mhc_gene_1





        Reactivity --> "0..1" MhcGene1Ontology : mhc_gene_1
        click MhcGene1Ontology href "../MhcGene1Ontology/"



      Reactivity : mhc_gene_2





        Reactivity --> "0..1" MhcGene2Ontology : mhc_gene_2
        click MhcGene2Ontology href "../MhcGene2Ontology/"



      Reactivity : peptide_end

      Reactivity : peptide_sequence_aa

      Reactivity : peptide_start

      Reactivity : reactivity_id

      Reactivity : reactivity_method

      Reactivity : reactivity_readout

      Reactivity : reactivity_refs

      Reactivity : reactivity_unit

      Reactivity : reactivity_value

      Reactivity : repertoire_id

Inheritance

Slots

Name Cardinality and Range Description Inheritance
reactivity_id 0..1
String		 direct
cell_id 0..1
String		 direct
repertoire_id 0..1
String		 direct
data_processing_id 0..1
String		 direct
ligand_type 0..1
LigandTypeEnum		 Classification of ligand binding to the cell direct
antigen_type 0..1
AntigenTypeEnum		 The type of antigen before processing by the immune system direct
antigen 0..1
String		 The substance against which the receptor was tested direct
antigen_source_species 0..1
AntigenSourceSpeciesOntology		 The species from which the antigen was isolated direct
peptide_start 0..1
Integer		 Start position of the peptide within the reference protein sequence direct
peptide_end 0..1
Integer		 End position of the peptide within the reference protein sequence direct
peptide_sequence_aa 0..1
String		 The actual peptide sequence against which the receptor reactivity was measure... direct
mhc_class 0..1
MhcClassEnum		 direct
mhc_gene_1 0..1
MhcGene1Ontology		 The MHC gene to which the mhc_allele_1 belongs direct
mhc_allele_1 0..1
String		 Allele designation of the MHC alpha chain direct
mhc_gene_2 0..1
MhcGene2Ontology		 The MHC gene to which the mhc_allele_2 belongs direct
mhc_allele_2 0..1
String		 Allele designation of the MHC class II beta chain or the invariant beta2-micr... direct
reactivity_method 0..1
String		 The methodology used to assess/classify reactivity direct
reactivity_readout 0..1
String		 Reactivity measurement read-out direct
reactivity_value 0..1
Float		 The absolute (processed) value of the measurement direct
reactivity_unit 0..1
String		 The unit of the measurement direct
reactivity_refs *
String		 Array of cross references to external epitope reactivity records direct

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self https://github.com/vdjserver/vdjserver-airr-schema/Reactivity
native https://github.com/vdjserver/vdjserver-airr-schema/Reactivity

LinkML Source

Direct

name: Reactivity
description: Default Reactivity description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- reactivity_id
- cell_id
- repertoire_id
- data_processing_id
- ligand_type
- antigen_type
- antigen
- antigen_source_species
- peptide_start
- peptide_end
- peptide_sequence_aa
- mhc_class
- mhc_gene_1
- mhc_allele_1
- mhc_gene_2
- mhc_allele_2
- reactivity_method
- reactivity_readout
- reactivity_value
- reactivity_unit
- reactivity_refs

Induced

name: Reactivity
description: Default Reactivity description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  reactivity_id:
    name: reactivity_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Rearrangement
    - Reactivity
    range: string
  cell_id:
    name: cell_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Rearrangement
    - Node
    - Cell
    - Expression
    - Reactivity
    range: string
  repertoire_id:
    name: repertoire_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Repertoire
    - RepertoireFilter
    - Rearrangement
    - Clone
    - Node
    - Cell
    - Expression
    - Reactivity
    - ADCRearrangementLoad
    - ADCDownloadCacheRepertoire
    - StatisticsCacheRepertoire
    - VisualizationDocument
    range: string
  data_processing_id:
    name: data_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - DataProcessing
    - Rearrangement
    - Clone
    - Cell
    - Expression
    - Reactivity
    range: string
  ligand_type:
    name: ligand_type
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Classification of ligand binding to the cell
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: Reactivity
    domain_of:
    - Reactivity
    range: LigandTypeEnum
  antigen_type:
    name: antigen_type
    annotations:
      nullable:
        tag: nullable
        value: false
    description: The type of antigen before processing by the immune system.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: Reactivity
    domain_of:
    - Reactivity
    range: AntigenTypeEnum
  antigen:
    name: antigen
    annotations:
      nullable:
        tag: nullable
        value: false
    description: The substance against which the receptor was tested. This can be
      any substance that stimulates an adaptive immune response in the host, either
      through antibody production or by T cell activation after presentation via an
      MHC molecule.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  antigen_source_species:
    name: antigen_source_species
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The species from which the antigen was isolated
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: AntigenSourceSpeciesOntology
  peptide_start:
    name: peptide_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the peptide within the reference protein sequence
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: integer
  peptide_end:
    name: peptide_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the peptide within the reference protein sequence
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: integer
  peptide_sequence_aa:
    name: peptide_sequence_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The actual peptide sequence against which the receptor reactivity
      was measured. This field should be used as a convenience for antigens of antigen_type
      `protein` or `peptide`.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  mhc_class:
    name: mhc_class
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - MHCGenotype
    - Reactivity
    range: MhcClassEnum
  mhc_gene_1:
    name: mhc_gene_1
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The MHC gene to which the mhc_allele_1 belongs
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: MhcGene1Ontology
  mhc_allele_1:
    name: mhc_allele_1
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Allele designation of the MHC alpha chain
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  mhc_gene_2:
    name: mhc_gene_2
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The MHC gene to which the mhc_allele_2 belongs
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: MhcGene2Ontology
  mhc_allele_2:
    name: mhc_allele_2
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Allele designation of the MHC class II beta chain or the invariant
      beta2-microglobin chain
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  reactivity_method:
    name: reactivity_method
    annotations:
      nullable:
        tag: nullable
        value: false
    description: 'The methodology used to assess/classify reactivity. This should
      be either the assay utlizied in the experiment, delineated as "annotated" if
      annotated from an external source (e.g. IEDB), or inferred if imputed using
      a computational method. In future versions we anticipate this field being an
      enumerated type, and it is strongly recommended that users utilize one of the
      following keywords in this field if appropriate: native_protein, MHC_peptide_multimer,
      annotated, inferred.'
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  reactivity_readout:
    name: reactivity_readout
    annotations:
      nullable:
        tag: nullable
        value: false
    description: 'Reactivity measurement read-out. For physical assays, this should
      describe what was measured. For inferred and annotated methods this should indicate
      a confidence/quality level for the inference/annotation. In future versions
      we anticipate this field being an enumerated type, and it is strongly recommended
      that users utilize one of the following keywords in this field if appropriate:
      fluorescence_intensity, barcode_count, confidence.'
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  reactivity_value:
    name: reactivity_value
    annotations:
      nullable:
        tag: nullable
        value: false
    description: The absolute (processed) value of the measurement
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: float
  reactivity_unit:
    name: reactivity_unit
    annotations:
      nullable:
        tag: nullable
        value: false
    description: The unit of the measurement
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
  reactivity_refs:
    name: reactivity_refs
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Array of cross references to external epitope reactivity records
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Reactivity
    domain_of:
    - Reactivity
    range: string
    multivalued: true