Class: Sample

URI: ak_schema:Sample

classDiagram class Sample click Sample href "../Sample" AIRRStandards <|-- Sample click AIRRStandards href "../AIRRStandards" Sample : anatomic_site Sample : biomaterial_provider Sample : collection_time_point_reference Sample : collection_time_point_relative Sample : collection_time_point_relative_unit Sample --> "0..1" CollectionTimePointRelativeUnitOntology : collection_time_point_relative_unit click CollectionTimePointRelativeUnitOntology href "../CollectionTimePointRelativeUnitOntology" Sample : disease_state_sample Sample : sample_id Sample : sample_type Sample : tissue Sample --> "0..1" TissueOntology : tissue click TissueOntology href "../TissueOntology"

Inheritance

AIRRStandards
- Sample

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 Float	Time point at which sample was taken, relative to `Collection time event`	direct
collection_time_point_relative_unit	0..1 CollectionTimePointRelativeUnitOntology	Unit of Sample collection time	direct
collection_time_point_reference	0..1 String	Event in the study schedule to which `Sample collection time` relates to	direct
biomaterial_provider	0..1 String	Name and address of the entity providing the sample	direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Sample
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- sample_id
- sample_type
- tissue
- anatomic_site
- disease_state_sample
- collection_time_point_relative
- collection_time_point_relative_unit
- collection_time_point_reference
- biomaterial_provider

Induced

name: Sample
from_schema: https://github.com/airr-knowledge/ak-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/airr-knowledge/ak-schema
    rank: 1000
    alias: sample_id
    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/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: sample_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/airr-knowledge/ak-schema
    rank: 1000
    alias: tissue
    owner: Sample
    domain_of:
    - Specimen
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: anatomic_site
    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/airr-knowledge/ak-schema
    rank: 1000
    alias: disease_state_sample
    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 `Collection time
      event`
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: collection_time_point_relative
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: float
  collection_time_point_relative_unit:
    name: collection_time_point_relative_unit
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unit of Sample collection time
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: collection_time_point_relative_unit
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: CollectionTimePointRelativeUnitOntology
  collection_time_point_reference:
    name: collection_time_point_reference
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Event in the study schedule to which `Sample collection time` relates
      to
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: collection_time_point_reference
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string
  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/airr-knowledge/ak-schema
    rank: 1000
    alias: biomaterial_provider
    owner: Sample
    domain_of:
    - Sample
    - SampleProcessing
    range: string