Skip to content

Class: InVivoSubject

A living human or animal subject from whom measurements are taken. Used for clinical assays (lung function, BALF/sputum) and any assay performed on living subjects.

URI: soma:InVivoSubject

 classDiagram
    class InVivoSubject
    click InVivoSubject href "../InVivoSubject/"
      StudySubject <|-- InVivoSubject
        click StudySubject href "../StudySubject/"

      InVivoSubject : age





        InVivoSubject --> "0..1" QuantityValue : age
        click QuantityValue href "../QuantityValue/"



      InVivoSubject : clinical_context

      InVivoSubject : collection_date

      InVivoSubject : collection_site

      InVivoSubject : description

      InVivoSubject : disease_state

      InVivoSubject : id

      InVivoSubject : model_species





        InVivoSubject --> "0..1" SpeciesReference : model_species
        click SpeciesReference href "../SpeciesReference/"



      InVivoSubject : name

      InVivoSubject : sample_collection_method

      InVivoSubject : sample_type





        InVivoSubject --> "0..1" SampleTypeEnum : sample_type
        click SampleTypeEnum href "../SampleTypeEnum/"



      InVivoSubject : sex

      InVivoSubject : subject_characteristics

      InVivoSubject : subject_type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
age 0..1
QuantityValue		 Age of the subject direct
sex 0..1
String		 Biological sex of the subject direct
subject_characteristics 0..1
String		 Relevant subject characteristics (disease state, medications, etc direct
disease_state 0..1
String		 direct
sample_type 0..1
SampleTypeEnum		 Type of biological sample (e direct
collection_site 0..1
String		 Anatomical site of sample collection direct
collection_date 0..1
Date		 Date when the sample was collected direct
sample_collection_method 0..1
String		 Method used for sample collection in vivo (e direct
clinical_context 0..1
String		 Clinical context for in vivo measurements (e direct
subject_type 0..1
String		 The specific type of study subject StudySubject
model_species 0..1
SpeciesReference		 The species of origin for the cells or organism being studied StudySubject
id 1
Uriorcurie		 A unique identifier for the entity NamedThing
name 0..1
String		 A human-readable name for the entity NamedThing
description 0..1
String		 A detailed description of the entity NamedThing

Usages

used by used in type used
PopulationSubject subjects range InVivoSubject
BALFSputumAssay study_subject range InVivoSubject
LungFunctionAssay study_subject range InVivoSubject

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/EHS-Data-Standards/soma

Mappings

Mapping Type Mapped Value
self soma:InVivoSubject
native soma:InVivoSubject

LinkML Source

Direct

name: InVivoSubject
description: A living human or animal subject from whom measurements are taken. Used
  for clinical assays (lung function, BALF/sputum) and any assay performed on living
  subjects.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: StudySubject
slots:
- age
- sex
- subject_characteristics
- disease_state
- sample_type
- collection_site
- collection_date
- sample_collection_method
- clinical_context

Induced

name: InVivoSubject
description: A living human or animal subject from whom measurements are taken. Used
  for clinical assays (lung function, BALF/sputum) and any assay performed on living
  subjects.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: StudySubject
attributes:
  age:
    name: age
    description: Age of the subject.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: age
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: QuantityValue
    inlined: true
  sex:
    name: sex
    description: Biological sex of the subject.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: sex
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: string
  subject_characteristics:
    name: subject_characteristics
    description: Relevant subject characteristics (disease state, medications, etc.).
      TIER 1 for LungFunctionAssay per user feedback.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: subject_characteristics
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: string
  disease_state:
    name: disease_state
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: disease_state
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    - CellLine
    range: string
  sample_type:
    name: sample_type
    description: Type of biological sample (e.g., sputum, BALF, blood).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: sample_type
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: SampleTypeEnum
  collection_site:
    name: collection_site
    description: Anatomical site of sample collection.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: collection_site
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: string
  collection_date:
    name: collection_date
    description: Date when the sample was collected.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: collection_date
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: date
  sample_collection_method:
    name: sample_collection_method
    description: Method used for sample collection in vivo (e.g., bronchoscopy, induced
      sputum, spirometry).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: sample_collection_method
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: string
  clinical_context:
    name: clinical_context
    description: Clinical context for in vivo measurements (e.g., routine screening,
      post-exposure assessment, disease monitoring, baseline spirometry).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: clinical_context
    owner: InVivoSubject
    domain_of:
    - InVivoSubject
    range: string
  subject_type:
    name: subject_type
    description: The specific type of study subject. Used to designate which concrete
      class (e.g., CellularSystem, InVivoSubject) is instantiated for polymorphic
      study_subject slots.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    designates_type: true
    alias: subject_type
    owner: InVivoSubject
    domain_of:
    - StudySubject
    range: string
  model_species:
    name: model_species
    description: The species of origin for the cells or organism being studied. Reference
      to NCBITaxon term.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: model_species
    owner: InVivoSubject
    domain_of:
    - StudySubject
    - CellLine
    range: SpeciesReference
    inlined: true
  id:
    name: id
    description: A unique identifier for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    identifier: true
    alias: id
    owner: InVivoSubject
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: InVivoSubject
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: string
  description:
    name: description
    description: A detailed description of the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: InVivoSubject
    domain_of:
    - NamedThing
    range: string