Class: Sample (Sample)

A biological sample collected from a subject.

URI: nfdi4immuno:Sample

 classDiagram
    class Sample
    click Sample href "../Sample/"
      Sample : additional_information

      Sample : disease_or_healthy





        Sample --> "1" DiseaseOrHealthy : disease_or_healthy
        click DiseaseOrHealthy href "../DiseaseOrHealthy/"



      Sample : disease_states

      Sample : diseases





        Sample --> "* _recommended_" Disease : diseases
        click Disease href "../Disease/"



      Sample : medications

      Sample : sample_event_id

      Sample : sample_id

      Sample : subject_id

      Sample : tissue





        Sample --> "1" Tissue : tissue
        click Tissue href "../Tissue/"

Slots

Name	Cardinality and Range	Description	Inheritance
sample_id	1 String	The user defined sample ID used to associate samples with the sample event	direct
subject_id	1 String	The user defined subject ID used to associate subject with samples	direct
sample_event_id	1 String	A sample ID to associate the subjects with a sample event	direct
disease_or_healthy	1 DiseaseOrHealthy	Indicate if subject had a disease or if healthy	direct
diseases	* recommended Disease	Relevant diseases at the time of sampling	direct
disease_states	* recommended String	The current state of the diseases of the subject at the time of sampling	direct
tissue	1 Tissue	The tissue from which the sample was taken	direct
medications	* recommended String	Medications given to the subject	direct
additional_information	0..1 String	Additional information related to this object	direct

Usages

used by	used in	type	used
Container	samples	range	Sample

Identifier and Mapping Information

Schema Source

• from schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema

Mappings

Mapping Type	Mapped Value
self	nfdi4immuno:Sample
native	nfdi4immuno:Sample

LinkML Source

Direct

name: Sample
description: A biological sample collected from a subject.
title: Sample
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
slots:
- sample_id
- subject_id
- sample_event_id
- disease_or_healthy
- diseases
- disease_states
- tissue
- medications
- additional_information

Induced

name: Sample
description: A biological sample collected from a subject.
title: Sample
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
attributes:
  sample_id:
    name: sample_id
    description: 'The user defined sample ID used to associate samples with the sample
      event. Must be unique within the study.

      '
    title: Sample ID
    examples:
    - value: MH031_v01
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    is_a: abstract_id
    identifier: true
    alias: sample_id
    owner: Sample
    domain_of:
    - AIRRAssay
    - CytometryExperiment
    - DataFile
    - Sample
    range: string
    required: true
    pattern: ^.+$
  subject_id:
    name: subject_id
    description: 'The user defined subject ID used to associate subject with samples.
      Must be unique within the study.

      '
    title: Subject ID
    examples:
    - value: MH031
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    is_a: abstract_id
    identifier: true
    alias: subject_id
    owner: Sample
    domain_of:
    - Sample
    - AbstractSubject
    range: string
    required: true
    pattern: ^.+$
  sample_event_id:
    name: sample_event_id
    description: 'A sample ID to associate the subjects with a sample event.

      '
    title: SampleEvent ID
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    is_a: abstract_id
    identifier: true
    alias: sample_event_id
    owner: Sample
    domain_of:
    - SampleEventCollection
    - SampleEvent
    - Sample
    range: string
    required: true
    pattern: ^.+$
  disease_or_healthy:
    name: disease_or_healthy
    description: Indicate if subject had a disease or if healthy.
    title: Disease or healthy
    examples:
    - value: healthy
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: disease_or_healthy
    owner: Sample
    domain_of:
    - Sample
    range: DiseaseOrHealthy
    required: true
    pattern: ^.+$
  diseases:
    name: diseases
    description: Relevant diseases at the time of sampling.
    title: Diseases
    examples:
    - value: '[{"key": "icd10:C34", "term": "Malignant neoplasm of bronchus and lung"}]'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: diseases
    owner: Sample
    domain_of:
    - Sample
    range: Disease
    recommended: true
    multivalued: true
  disease_states:
    name: disease_states
    description: The current state of the diseases of the subject at the time of sampling.
    title: Disease states
    examples:
    - value: Remission
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: disease_states
    owner: Sample
    domain_of:
    - Sample
    range: string
    recommended: true
    multivalued: true
  tissue:
    name: tissue
    description: The tissue from which the sample was taken.
    title: Tissue
    examples:
    - value: '{"key": "UBERON:0003920", "term": "Venous blood vessel"}'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: tissue
    owner: Sample
    domain_of:
    - Sample
    - CellCultureSubject
    range: Tissue
    required: true
    pattern: ^.+$
  medications:
    name: medications
    description: Medications given to the subject.
    title: Medications
    examples:
    - value: Rituximab 1000mg, 3 months ago
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: medications
    owner: Sample
    domain_of:
    - Sample
    range: string
    recommended: true
    multivalued: true
  additional_information:
    name: additional_information
    annotations:
      preferred_format:
        tag: preferred_format
        value: json
    description: 'Additional information related to this object. Can be in any format,
      but JSON key-value pairs are preferred.

      '
    title: Additional information
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: additional_information
    owner: Sample
    domain_of:
    - SampleEvent
    - Sample
    - Study
    - AbstractSubject
    range: string