Class: Sample (Sample)

Biospecimen data

classDiagram class Sample click Sample href "../Sample" AccessControlledRecord <|-- Sample click AccessControlledRecord href "../AccessControlledRecord" Sample : aliquots Sample --> "*" Aliquot : aliquots click Aliquot href "../Aliquot" Sample : availablity_status Sample --> "0..1" EnumAvailabilityStatus : availablity_status click EnumAvailabilityStatus href "../EnumAvailabilityStatus" Sample : biospecimen_collection Sample --> "0..1" BiospecimenCollection : biospecimen_collection click BiospecimenCollection href "../BiospecimenCollection" Sample : external_id Sample : has_access_policy Sample --> "0..1" AccessPolicy : has_access_policy click AccessPolicy href "../AccessPolicy" Sample : id Sample : parent_sample Sample --> "0..1" Sample : parent_sample click Sample href "../Sample" Sample : processing Sample : quantity_number Sample : quantity_units Sample : sample_type Sample : storage_method

Inheritance

Thing
- AccessControlledRecord
  - Sample

Slots

Name	Cardinality and Range	Description	Inheritance
biospecimen_collection	0..1 BiospecimenCollection	Biospecimen Collection that generated this sample	direct
parent_sample	0..1 Sample	Sample from which this sample is derived	direct
sample_type	1 Uriorcurie	Type of material of which this Sample is comprised	direct
processing	* Uriorcurie	Processing that was applied to the Parent Sample or from the Biospecimen Coll...	direct
availablity_status	0..1 EnumAvailabilityStatus	Can this Sample be requested for further analysis?	direct
storage_method	* Uriorcurie	Sample storage method, eg, Frozen or with additives	direct
quantity_number	0..1 Float	The total quantity of the specimen	direct
quantity_units	0..1 Uriorcurie	The structured term defining the units of the quantity	direct
aliquots	* Aliquot	Aliquot(s) from this Sample	direct
has_access_policy	0..1 AccessPolicy	Which access policy applies to this element?	AccessControlledRecord
id	1 String	ID associated with a class	Thing
external_id	* Uriorcurie	Other identifiers for this entity, eg, from the submitting study or in system...	Thing

Usages

used by	used in	type	used
Subject	has_sample	range	Sample
Sample	parent_sample	range	Sample
File	sample	range	Sample

Identifier and Mapping Information

Schema Source

from schema: https://anvilproject.org/acr-harmonized-data-model

Mappings

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

LinkML Source

Direct

name: Sample
description: Biospecimen data
title: Sample
from_schema: https://anvilproject.org/acr-harmonized-data-model
is_a: AccessControlledRecord
slots:
- biospecimen_collection
- parent_sample
- sample_type
- processing
- availablity_status
- storage_method
- quantity_number
- quantity_units
- aliquots

Induced

name: Sample
description: Biospecimen data
title: Sample
from_schema: https://anvilproject.org/acr-harmonized-data-model
is_a: AccessControlledRecord
attributes:
  biospecimen_collection:
    name: biospecimen_collection
    description: Biospecimen Collection that generated this sample.
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: biospecimen_collection
    owner: Sample
    domain_of:
    - Sample
    range: BiospecimenCollection
    required: false
    multivalued: false
    inlined: true
  parent_sample:
    name: parent_sample
    description: Sample from which this sample is derived
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: parent_sample
    owner: Sample
    domain_of:
    - Sample
    range: Sample
    required: false
    multivalued: false
    inlined: false
  sample_type:
    name: sample_type
    description: Type of material of which this Sample is comprised
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    identifier: false
    alias: sample_type
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: true
    multivalued: false
  processing:
    name: processing
    description: Processing that was applied to the Parent Sample or from the Biospecimen
      Collection that yielded this distinct sample
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    identifier: false
    alias: processing
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: true
  availablity_status:
    name: availablity_status
    description: Can this Sample be requested for further analysis?
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: availablity_status
    owner: Sample
    domain_of:
    - Sample
    - Aliquot
    range: EnumAvailabilityStatus
    required: false
  storage_method:
    name: storage_method
    description: Sample storage method, eg, Frozen or with additives
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: storage_method
    owner: Sample
    domain_of:
    - Sample
    range: uriorcurie
    required: false
    multivalued: true
  quantity_number:
    name: quantity_number
    description: The total quantity of the specimen
    title: Quantity
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: quantity_number
    owner: Sample
    domain_of:
    - Sample
    - Aliquot
    range: float
  quantity_units:
    name: quantity_units
    description: The structured term defining the units of the quantity.
    title: Quantity Units
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: quantity_units
    owner: Sample
    domain_of:
    - Sample
    - Aliquot
    range: uriorcurie
  aliquots:
    name: aliquots
    description: Aliquot(s) from this Sample.
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: aliquots
    owner: Sample
    domain_of:
    - Sample
    range: Aliquot
    required: false
    multivalued: true
    inlined: true
  has_access_policy:
    name: has_access_policy
    description: Which access policy applies to this element?
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: has_access_policy
    owner: Sample
    domain_of:
    - AccessControlledRecord
    range: AccessPolicy
    inlined: false
  id:
    name: id
    description: ID associated with a class
    title: ID
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    identifier: true
    alias: id
    owner: Sample
    domain_of:
    - Thing
    range: string
    required: true
    multivalued: false
  external_id:
    name: external_id
    description: Other identifiers for this entity, eg, from the submitting study
      or in systems link dbGaP
    title: External Identifiers
    from_schema: https://anvilproject.org/acr-harmonized-data-model
    rank: 1000
    alias: external_id
    owner: Sample
    domain_of:
    - Thing
    range: uriorcurie
    required: false
    multivalued: true