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Class: Sample

Default Sample description

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

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

      Sample : anatomic_site

      Sample : biomaterial_provider

      Sample : collection_location





        Sample --> "0..1" CollectionLocationOntology : collection_location
        click CollectionLocationOntology href "../CollectionLocationOntology/"



      Sample : collection_time_point_relative





        Sample --> "0..1" TimePoint : collection_time_point_relative
        click TimePoint href "../TimePoint/"



      Sample : disease_state_sample

      Sample : sample_id

      Sample : sample_type

      Sample : tissue





        Sample --> "0..1" TissueOntology : tissue
        click TissueOntology href "../TissueOntology/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sample_id 0..1
String		 Sample ID assigned by submitter, unique within study direct
sample_type 0..1
String		 The way the sample was obtained, e direct
tissue 0..1
TissueOntology		 The actual tissue sampled, e direct
anatomic_site 0..1
String		 The anatomic location of the tissue, e direct
disease_state_sample 0..1
String		 Histopathologic evaluation of the sample direct
collection_time_point_relative 0..1
TimePoint		 Time point at which sample was taken, relative to label event direct
collection_location 0..1
CollectionLocationOntology		 Location where the sample was taken, preferred granularity is country-level direct
biomaterial_provider 0..1
String		 Name and address of the entity providing the sample direct

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: Sample
description: Default Sample description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- sample_id
- sample_type
- tissue
- anatomic_site
- disease_state_sample
- collection_time_point_relative
- collection_location
- biomaterial_provider

Induced

name: Sample
description: Default Sample description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  sample_id:
    name: sample_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Sample ID assigned by submitter, unique within study. If possible,
      a persistent sample ID linked to INSDC or similar repository study should be
      used.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  sample_type:
    name: sample_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The way the sample was obtained, e.g. fine-needle aspirate, organ
      harvest, peripheral venous puncture
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  tissue:
    name: tissue
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The actual tissue sampled, e.g. lymph node, liver, peripheral blood
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: TissueOntology
  anatomic_site:
    name: anatomic_site
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The anatomic location of the tissue, e.g. Inguinal, femur
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  disease_state_sample:
    name: disease_state_sample
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Histopathologic evaluation of the sample
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  collection_time_point_relative:
    name: collection_time_point_relative
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Time point at which sample was taken, relative to `label` event
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: TimePoint
  collection_location:
    name: collection_location
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Location where the sample was taken, preferred granularity is country-level
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: CollectionLocationOntology
  biomaterial_provider:
    name: biomaterial_provider
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Name and address of the entity providing the sample
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string