Class: Biospecimen (Biospecimen)

A Biospecimen Collected from A Participant

classDiagram class Biospecimen click Biospecimen href "../Biospecimen" Thing <|-- Biospecimen click Thing href "../Thing" Biospecimen : ageAtBiospecimenCollection Biospecimen : biospecimenStorage Biospecimen : collectionExternalId Biospecimen : collectionGlobalId Biospecimen : collectionSampleType Biospecimen : concentration Biospecimen : concentrationUnit Biospecimen : containerAvailability Biospecimen --> "0..1" EnumAvailability : containerAvailability click EnumAvailability href "../EnumAvailability" Biospecimen : containerExternalId Biospecimen : containerGlobalId Biospecimen : laboratoryProcedure Biospecimen : parentSampleExternalId Biospecimen : parentSampleGlobalId Biospecimen : parentSampleType Biospecimen : participantExternalId Biospecimen : participantGlobalId Biospecimen : sampleAvailability Biospecimen --> "1" EnumAvailability : sampleAvailability click EnumAvailability href "../EnumAvailability" Biospecimen : sampleExternalId Biospecimen : sampleGlobalId Biospecimen : sampleType Biospecimen : studyCode Biospecimen --> "1" EnumStudyCode : studyCode click EnumStudyCode href "../EnumStudyCode" Biospecimen : volume Biospecimen : volumeUnit

Inheritance

Thing
- Biospecimen

Slots

Name	Cardinality and Range	Description	Inheritance
studyCode	1 EnumStudyCode	Unique identifier for the study (generally a short acronym)	direct
participantGlobalId	1 String	Unique INCLUDE global identifier for the participant, assigned by DCC	direct
participantExternalId	1 String	Unique, de-identified identifier for the participant, assigned by data contri...	direct
sampleGlobalId	1 String	INCLUDE global identifier for sample, assigned by DCC	direct
sampleExternalId	1 String	Unique identifier for sample, assigned by data contributor	direct
sampleType	1 String	Type of biological material comprising the Sample (e	direct
ageAtBiospecimenCollection	0..1 Integer	Age in days of participant at time of biospecimen collection	direct
parentSampleGlobalId	0..1 String	INCLUDE global identifier for the direct parent from which Sample was derived...	direct
parentSampleExternalId	0..1 String	Identifier for the direct parent from which Sample was derived, processed, po...	direct
parentSampleType	0..1 String	Type of biological material comprising the Parent Sample (e	direct
collectionGlobalId	0..1 String	INCLUDE global identifier for the eldest sample in a lineage, assigned by DCC	direct
collectionExternalId	0..1 String	Identifier for the eldest sample in a lineage of processed, pooled, or aliquo...	direct
collectionSampleType	0..1 String	Type of biological material comprising the Collected Sample (e	direct
containerGlobalId	0..1 String	INCLUDE global identifier for specific container/aliquot of sample, assigned ...	direct
containerExternalId	0..1 String	Identifier for specific container/aliquot of sample, assigned by data contrib...	direct
volume	0..1 Float	Amount of sample in container	direct
volumeUnit	0..1 String	Unit of sample volume	direct
concentration	0..1 Float	Concentration of sample in container	direct
concentrationUnit	0..1 String	Unit of sample concentration	direct
laboratoryProcedure	0..1 String	Procedure by which Sample was derived from Parent Sample (e	direct
biospecimenStorage	0..1 String	Method by which Container is stored (e	direct
sampleAvailability	1 EnumAvailability	Whether or not the Sample (any Container thereof) is potentially available fo...	direct
containerAvailability	0..1 EnumAvailability	Whether or not the specific Container is potentially available for sharing th...	direct

Identifier and Mapping Information

Annotations

property	value
required	True

Schema Source

from schema: https://w3id.org/include

Mappings

Mapping Type	Mapped Value
self	include:Biospecimen
native	include:Biospecimen

LinkML Source

Direct

name: Biospecimen
definition_uri: include:Biospecimen
annotations:
  required:
    tag: required
    value: 'True'
  requires_component:
    tag: requires_component
    value: Study,Participant,DataFile
description: A Biospecimen Collected from A Participant
title: Biospecimen
from_schema: https://w3id.org/include
is_a: Thing
slots:
- studyCode
- participantGlobalId
- participantExternalId
- sampleGlobalId
- sampleExternalId
- sampleType
- ageAtBiospecimenCollection
- parentSampleGlobalId
- parentSampleExternalId
- parentSampleType
- collectionGlobalId
- collectionExternalId
- collectionSampleType
- containerGlobalId
- containerExternalId
- volume
- volumeUnit
- concentration
- concentrationUnit
- laboratoryProcedure
- biospecimenStorage
- sampleAvailability
- containerAvailability

Induced

name: Biospecimen
definition_uri: include:Biospecimen
annotations:
  required:
    tag: required
    value: 'True'
  requires_component:
    tag: requires_component
    value: Study,Participant,DataFile
description: A Biospecimen Collected from A Participant
title: Biospecimen
from_schema: https://w3id.org/include
is_a: Thing
attributes:
  studyCode:
    name: studyCode
    definition_uri: include:studyCode
    description: Unique identifier for the study (generally a short acronym)
    title: Study Code
    from_schema: https://w3id.org/include
    rank: 1000
    alias: studyCode
    owner: Biospecimen
    domain_of:
    - Biospecimen
    - DataFile
    - Participant
    - Condition
    - Study
    - Dataset
    - DatasetManifest
    range: enum_studyCode
    required: true
  participantGlobalId:
    name: participantGlobalId
    definition_uri: include:participantGlobalId
    description: Unique INCLUDE global identifier for the participant, assigned by
      DCC
    title: Participant Global ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: participantGlobalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    - DataFile
    - Participant
    - Condition
    range: string
    required: true
  participantExternalId:
    name: participantExternalId
    definition_uri: include:participantExternalId
    description: Unique, de-identified identifier for the participant, assigned by
      data contributor. External IDs must be two steps removed from personal information
      in the study records.
    title: Participant External ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: participantExternalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    - DataFile
    - Participant
    - Condition
    range: string
    required: true
  sampleGlobalId:
    name: sampleGlobalId
    definition_uri: include:sampleGlobalId
    description: INCLUDE global identifier for sample, assigned by DCC
    title: Sample Global ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: sampleGlobalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    - DataFile
    range: string
    required: true
  sampleExternalId:
    name: sampleExternalId
    definition_uri: include:sampleExternalId
    description: Unique identifier for sample, assigned by data contributor. A sample
      is a unique biological material; two samples with two different IDs are biologically
      distinct.
    title: Sample External ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: sampleExternalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    - DataFile
    range: string
    required: true
  sampleType:
    name: sampleType
    definition_uri: include:sampleType
    description: Type of biological material comprising the Sample (e.g. Plasma, White
      blood cells, Red blood cells, DNA, RNA, Peripheral blood mononuclear cells,
      CD4+ Tconv cells, NK cells, Monocytes, CD8+ T cells, B cells, Granulocytes,
      Treg cells)
    title: Sample Type
    from_schema: https://w3id.org/include
    rank: 1000
    alias: sampleType
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
    required: true
  ageAtBiospecimenCollection:
    name: ageAtBiospecimenCollection
    definition_uri: include:ageAtBiospecimenCollection
    description: Age in days of participant at time of biospecimen collection
    title: Age At Biospecimen Collection
    from_schema: https://w3id.org/include
    rank: 1000
    alias: ageAtBiospecimenCollection
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: integer
  parentSampleGlobalId:
    name: parentSampleGlobalId
    definition_uri: include:parentSampleGlobalId
    description: INCLUDE global identifier for the direct parent from which Sample
      was derived, assigned by DCC
    title: Parent Sample Global ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: parentSampleGlobalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  parentSampleExternalId:
    name: parentSampleExternalId
    definition_uri: include:parentSampleExternalId
    description: Identifier for the direct parent from which Sample was derived, processed,
      pooled, etc. (if applicable); assigned by data contributor
    title: Parent Sample External ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: parentSampleExternalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  parentSampleType:
    name: parentSampleType
    definition_uri: include:parentSampleType
    description: Type of biological material comprising the Parent Sample (e.g. Peripheral
      Whole Blood, Derived Cell Line, Saliva, Whole blood, WBCs)
    title: Parent Sample Type
    from_schema: https://w3id.org/include
    rank: 1000
    alias: parentSampleType
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  collectionGlobalId:
    name: collectionGlobalId
    definition_uri: include:collectionGlobalId
    description: INCLUDE global identifier for the eldest sample in a lineage, assigned
      by DCC
    title: Collection Global ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: collectionGlobalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  collectionExternalId:
    name: collectionExternalId
    definition_uri: include:collectionExternalId
    description: Identifier for the eldest sample in a lineage of processed, pooled,
      or aliquoted samples - typically the material actually collected from the Participant.
      This may be the same as Parent Sample ID or Sample ID (if no processing was
      performed). Assigned by data contributor.
    title: Collection External ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: collectionExternalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  collectionSampleType:
    name: collectionSampleType
    definition_uri: include:collectionSampleType
    description: Type of biological material comprising the Collected Sample (e.g.
      Whole blood, Not reported, Saliva, Derived cell line)
    title: Collection Sample Type
    from_schema: https://w3id.org/include
    rank: 1000
    alias: collectionSampleType
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  containerGlobalId:
    name: containerGlobalId
    definition_uri: include:containerGlobalId
    description: INCLUDE global identifier for specific container/aliquot of sample,
      assigned by DCC
    title: Container Global ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: containerGlobalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  containerExternalId:
    name: containerExternalId
    definition_uri: include:containerExternalId
    description: Identifier for specific container/aliquot of sample, assigned by
      data contributor. For example, distinct aliquots of a sample will have the same
      Sample ID but different Container IDs.
    title: Container External ID
    from_schema: https://w3id.org/include
    rank: 1000
    alias: containerExternalId
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  volume:
    name: volume
    definition_uri: include:volume
    description: Amount of sample in container
    title: Volume
    from_schema: https://w3id.org/include
    rank: 1000
    alias: volume
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: float
  volumeUnit:
    name: volumeUnit
    definition_uri: include:volumeUnit
    description: Unit of sample volume
    title: Volume Unit
    from_schema: https://w3id.org/include
    rank: 1000
    alias: volumeUnit
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  concentration:
    name: concentration
    definition_uri: include:concentration
    description: Concentration of sample in container
    title: Concentration
    from_schema: https://w3id.org/include
    rank: 1000
    alias: concentration
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: float
  concentrationUnit:
    name: concentrationUnit
    definition_uri: include:concentrationUnit
    description: Unit of sample concentration
    title: Concentration Unit
    from_schema: https://w3id.org/include
    rank: 1000
    alias: concentrationUnit
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  laboratoryProcedure:
    name: laboratoryProcedure
    definition_uri: include:laboratoryProcedure
    description: Procedure by which Sample was derived from Parent Sample (e.g. Centrifugation,
      RBC lysis, Lyse/fix buffer, FACS, PAXgene DNA, PAXgene RNA, Qiagen Allprep,
      Ficoll)
    title: Laboratory Procedure
    from_schema: https://w3id.org/include
    rank: 1000
    alias: laboratoryProcedure
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  biospecimenStorage:
    name: biospecimenStorage
    definition_uri: include:biospecimenStorage
    description: Method by which Container is stored (e.g. Minus 80 degrees Celsius,
      Liquid nitrogen storage)
    title: Biospecimen Storage
    from_schema: https://w3id.org/include
    rank: 1000
    alias: biospecimenStorage
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: string
  sampleAvailability:
    name: sampleAvailability
    definition_uri: include:sampleAvailability
    description: Whether or not the Sample (any Container thereof) is potentially
      available for sharing through the Virtual Biorepository
    title: Sample Availability
    from_schema: https://w3id.org/include
    rank: 1000
    alias: sampleAvailability
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: enum_Availability
    required: true
  containerAvailability:
    name: containerAvailability
    definition_uri: include:containerAvailability
    description: Whether or not the specific Container is potentially available for
      sharing through the Virtual Biorepository
    title: Container Availability
    from_schema: https://w3id.org/include
    rank: 1000
    alias: containerAvailability
    owner: Biospecimen
    domain_of:
    - Biospecimen
    range: enum_Availability