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Class: Sample

A biological sample used in assays. Examples include a whole organism, tissue or cell line.

URI: modos:Sample

classDiagram class Sample click Sample href "../Sample" NamedThing <|-- Sample click NamedThing href "../NamedThing" Sample : cell_type Sample : collector Sample : description Sample : id Sample : name Sample : sex Sample --> "0..1" Sex : sex click Sex href "../Sex" Sample : source_material Sample : taxon_id

Inheritance

Slots

Name Cardinality and Range Description Inheritance
cell_type 0..1
Uriorcurie		 The cell type of the sample, if applicable direct
source_material 0..1
Uriorcurie		 The biological source from which the sample was isolated (tissue, organ) direct
sex 0..1
Sex		 The biological sex of a sample direct
taxon_id *
Uriorcurie		 The NCBI taxon code from [ncbitaxon](https://obofoundry direct
collector *
String		 The organization responsible for collecting a given sample direct
id 1
Uriorcurie		 A unique identifier for a thing NamedThing
name 0..1
String		 A human-readable name for a thing NamedThing
description 0..1
String		 A human-readable description for a thing NamedThing

Usages

used by used in type used
Assay has_sample range Sample
DataEntity has_sample range Sample
AlignmentSet has_sample range Sample
VariantSet has_sample range Sample
MassSpectrometryResults has_sample range Sample
Array has_sample range Sample

See Also

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/sdsc-ordes/modos-schema

Mappings

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

LinkML Source

Direct

name: Sample
description: A biological sample used in assays. Examples include a whole organism,
  tissue or cell line.
from_schema: https://w3id.org/sdsc-ordes/modos-schema
see_also:
- bioschemas:Sample
is_a: NamedThing
slots:
- cell_type
- source_material
- sex
- taxon_id
- collector

Induced

name: Sample
description: A biological sample used in assays. Examples include a whole organism,
  tissue or cell line.
from_schema: https://w3id.org/sdsc-ordes/modos-schema
see_also:
- bioschemas:Sample
is_a: NamedThing
attributes:
  cell_type:
    name: cell_type
    description: 'The cell type of the sample, if applicable.

      Should be a cell type code URI from the cell ontology.

      See: [https://bioregistry.io/registry/cl](https://bioregistry.io/registry/cl)

      '
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: cell_type
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
  source_material:
    name: source_material
    description: 'The biological source from which the sample was isolated (tissue,
      organ).

      Should be a code URI from the [UBERON](https://bioregistry.io/registry/uberon)
      ontology or [fairgenomes biospecimen types](https://raw.githubusercontent.com/fairgenomes/fairgenomes-semantic-model/refs/tags/v1.2/generated/ontology/fair-genomes-biospecimentypes.ttl).

      '
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: source_material
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
  sex:
    name: sex
    description: The biological sex of a sample.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: sex
    owner: Sample
    domain_of:
    - Sample
    range: Sex
  taxon_id:
    name: taxon_id
    description: 'The NCBI taxon code from [ncbitaxon](https://obofoundry.org/ontology/ncbitaxon.html)
      describing the taxonomic range of a sample.

      '
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: taxon_id
    owner: Sample
    domain_of:
    - Sample
    - ReferenceGenome
    range: uriorcurie
    multivalued: true
  collector:
    name: collector
    description: The organization responsible for collecting a given sample.
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    alias: collector
    owner: Sample
    domain_of:
    - Sample
    range: string
    multivalued: true
  id:
    name: id
    description: A unique identifier for a thing
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: Sample
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for a thing
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: Sample
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A human-readable description for a thing
    from_schema: https://w3id.org/sdsc-ordes/modos-schema
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: Sample
    domain_of:
    - NamedThing
    range: string