Skip to content

Class: Subject

Default Subject description

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

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

      Subject : age





        Subject --> "0..1" TimeInterval : age
        click TimeInterval href "../TimeInterval/"



      Subject : age_event

      Subject : ancestry_population





        Subject --> "0..1" AncestryPopulationOntology : ancestry_population
        click AncestryPopulationOntology href "../AncestryPopulationOntology/"



      Subject : diagnosis





        Subject --> "*" Diagnosis : diagnosis
        click Diagnosis href "../Diagnosis/"



      Subject : ethnicity

      Subject : genotype





        Subject --> "0..1" SubjectGenotype : genotype
        click SubjectGenotype href "../SubjectGenotype/"



      Subject : link_type

      Subject : linked_subjects

      Subject : location_birth





        Subject --> "0..1" LocationBirthOntology : location_birth
        click LocationBirthOntology href "../LocationBirthOntology/"



      Subject : race

      Subject : sex





        Subject --> "0..1" SexEnum : sex
        click SexEnum href "../SexEnum/"



      Subject : species





        Subject --> "0..1" SpeciesOntology : species
        click SpeciesOntology href "../SpeciesOntology/"



      Subject : strain_name

      Subject : subject_id

      Subject : synthetic

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subject_id 0..1
String		 Subject ID assigned by submitter, unique within study direct
synthetic 0..1
Boolean		 TRUE for libraries in which the diversity has been synthetically generated (e direct
species 0..1
SpeciesOntology		 Binomial designation of subject's species direct
sex 0..1
SexEnum		 Biological sex of subject direct
age 0..1
TimeInterval		 Age of subject expressed as a time interval direct
age_event 0..1
String		 Event in the study schedule to which Age refers direct
ancestry_population 0..1
AncestryPopulationOntology		 Broad geographic origin of ancestry (continent) direct
location_birth 0..1
LocationBirthOntology		 Self-reported location of birth of the subject, preferred granularity is coun... direct
ethnicity 0..1
String		 Ethnic group of subject (defined as cultural/language-based membership) direct
race 0..1
String		 Racial group of subject (as defined by NIH) direct
strain_name 0..1
String		 Non-human designation of the strain or breed of animal used direct
linked_subjects 0..1
String		 Subject ID to which Relation type refers direct
link_type 0..1
String		 Relation between subject and linked_subjects, can be genetic or environment... direct
diagnosis *
Diagnosis		 Diagnosis information for subject direct
genotype 0..1
SubjectGenotype		 Default genotype description direct

Usages

used by used in type used
Repertoire subject range Subject
SubjectMeta value range Subject

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: Subject
description: Default Subject description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- subject_id
- synthetic
- species
- sex
- age
- age_event
- ancestry_population
- location_birth
- ethnicity
- race
- strain_name
- linked_subjects
- link_type
- diagnosis
- genotype

Induced

name: Subject
description: Default Subject description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  subject_id:
    name: subject_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Subject ID assigned by submitter, unique within study. If possible,
      a persistent subject ID linked to an INSDC or similar repository study should
      be used.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  synthetic:
    name: synthetic
    annotations:
      nullable:
        tag: nullable
        value: false
    description: TRUE for libraries in which the diversity has been synthetically
      generated (e.g. phage display)
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: boolean
  species:
    name: species
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Binomial designation of subject's species
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - AlleleDescription
    - GermlineSet
    - Subject
    range: SpeciesOntology
  sex:
    name: sex
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Biological sex of subject
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: SexEnum
  age:
    name: age
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Age of subject expressed as a time interval. If singular time point
      then min == max in the time interval.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: TimeInterval
  age_event:
    name: age_event
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Event in the study schedule to which `Age` refers. For NCBI BioSample
      this MUST be `sampling`. For other implementations submitters need to be aware
      that there is currently no mechanism to encode to potential delta between `Age
      event` and `Sample collection time`, hence the chosen events should be in temporal
      proximity.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  ancestry_population:
    name: ancestry_population
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Broad geographic origin of ancestry (continent)
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: AncestryPopulationOntology
  location_birth:
    name: location_birth
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Self-reported location of birth of the subject, preferred granularity
      is country-level
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: LocationBirthOntology
  ethnicity:
    name: ethnicity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Ethnic group of subject (defined as cultural/language-based membership)
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  race:
    name: race
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Racial group of subject (as defined by NIH)
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  strain_name:
    name: strain_name
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Non-human designation of the strain or breed of animal used
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  linked_subjects:
    name: linked_subjects
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Subject ID to which `Relation type` refers
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: string
  link_type:
    name: link_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Relation between subject and `linked_subjects`, can be genetic or
      environmental (e.g.exposure)
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: Subject
    domain_of:
    - Subject
    range: string
  diagnosis:
    name: diagnosis
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Diagnosis information for subject
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: Diagnosis
    multivalued: true
  genotype:
    name: genotype
    description: Default genotype description
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Subject
    domain_of:
    - Subject
    range: SubjectGenotype