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Class: Subject

URI: ak_schema:Subject

classDiagram class Subject click Subject href "../Subject" AIRRStandards <|-- Subject click AIRRStandards href "../AIRRStandards" Subject : age_event Subject : age_max Subject : age_min Subject : age_unit Subject --> "0..1" AgeUnitOntology : age_unit click AgeUnitOntology href "../AgeUnitOntology" Subject : ancestry_population 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 : 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_min 0..1
Float		 Specific age or lower boundary of age range direct
age_max 0..1
Float		 Upper boundary of age range or equal to age_min for specific age direct
age_unit 0..1
AgeUnitOntology		 Unit of age range direct
age_event 0..1
String		 Event in the study schedule to which Age refers direct
ancestry_population 0..1
String		 Broad geographic origin of ancestry (continent) 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		 direct

Usages

used by used in type used
Repertoire subject range Subject

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/airr-knowledge/ak-schema

Mappings

Mapping Type Mapped Value
self ak_schema:Subject
native ak_schema:Subject

LinkML Source

Direct

name: Subject
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- subject_id
- synthetic
- species
- sex
- age_min
- age_max
- age_unit
- age_event
- ancestry_population
- ethnicity
- race
- strain_name
- linked_subjects
- link_type
- diagnosis
- genotype

Induced

name: Subject
from_schema: https://github.com/airr-knowledge/ak-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/airr-knowledge/ak-schema
    rank: 1000
    alias: subject_id
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: synthetic
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: species
    owner: Subject
    domain_of:
    - Participant
    - AlleleDescription
    - GermlineSet
    - Subject
    range: SpeciesOntology
  sex:
    name: sex
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Biological sex of subject
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sex
    owner: Subject
    domain_of:
    - Subject
    range: SexEnum
  age_min:
    name: age_min
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Specific age or lower boundary of age range.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: age_min
    owner: Subject
    domain_of:
    - Subject
    range: float
  age_max:
    name: age_max
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Upper boundary of age range or equal to age_min for specific age.
      This field should only be null if age_min is null.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: age_max
    owner: Subject
    domain_of:
    - Subject
    range: float
  age_unit:
    name: age_unit
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unit of age range
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: age_unit
    owner: Subject
    domain_of:
    - Participant
    - Subject
    range: AgeUnitOntology
  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/airr-knowledge/ak-schema
    rank: 1000
    alias: age_event
    owner: Subject
    domain_of:
    - Participant
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: ancestry_population
    owner: Subject
    domain_of:
    - Subject
    range: string
  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/airr-knowledge/ak-schema
    rank: 1000
    alias: ethnicity
    owner: Subject
    domain_of:
    - Participant
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: race
    owner: Subject
    domain_of:
    - Participant
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: strain_name
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: linked_subjects
    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/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: link_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/airr-knowledge/ak-schema
    rank: 1000
    alias: diagnosis
    owner: Subject
    domain_of:
    - Subject
    range: Diagnosis
    multivalued: true
  genotype:
    name: genotype
    annotations:
      nullable:
        tag: nullable
        value: true
    description: ''
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: genotype
    owner: Subject
    domain_of:
    - Subject
    range: SubjectGenotype