Class: Biospecimen Retention (BiospecimenRetention)

The continued possession, cataloging, and storage of collected biological specimens beyond their initial use.

URI: https://example.org/usdm/v4/linkml/BiospecimenRetention

 classDiagram
    class BiospecimenRetention
    click BiospecimenRetention href "../../classes/BiospecimenRetention/"
      BiospecimenRetention : description

      BiospecimenRetention : extensionAttributes





        BiospecimenRetention --> "*" ExtensionAttribute : extensionAttributes
        click ExtensionAttribute href "../../classes/ExtensionAttribute/"



      BiospecimenRetention : id

      BiospecimenRetention : includesDNA

      BiospecimenRetention : isRetained

      BiospecimenRetention : label

      BiospecimenRetention : name

Class Properties

Property Value
Class URI usdm:BiospecimenRetention

Slots

Name Cardinality and Range Description Inheritance
id 1
string		 direct
name 1
string		 The literal identifier (i.e., distinctive designation) of the biospecimen retention. direct
label 0..1
string		 The short descriptive designation for the biospecimen retention. direct
description 0..1
string		 A narrative representation of the biospecimen retention. direct
isRetained 1
boolean		 An indication as to whether biospecimens were retained. direct
includesDNA 0..1
boolean		 An indication as to whether retained biospecimens contain DNA. direct
extensionAttributes *
ExtensionAttribute		 direct

Usages

used by used in type used
InterventionalStudyDesign biospecimenRetentions range BiospecimenRetention
ObservationalStudyDesign biospecimenRetentions range BiospecimenRetention
StudyDesign biospecimenRetentions range BiospecimenRetention

Identifier and Mapping Information

Schema Source

  • from schema: https://example.org/usdm/v4/linkml

Mappings

Mapping Type Mapped Value
self https://example.org/usdm/v4/linkml/BiospecimenRetention
native https://example.org/usdm/v4/linkml/BiospecimenRetention
exact ncit:C215505

Examples

Example: BiospecimenRetention-02-Standard-Instance

id: retention-med-002
name: Pharmacogenomic Storage
label: PGx Retention
description: Long-term storage of whole blood samples for future genomic research as specified in the informed consent.
isRetained: true
includesDNA: true

Example: BiospecimenRetention-01-Minimal-Data-Instance

id: retention-min-001
name: Standard Serum Retention
isRetained: true

Example: BiospecimenRetention-03-Detailed-Instance

id: retention-det-003
name: Biobank Appendix A
label: Optional Longitudinal Storage
description: Retention of residual tissue samples for exploratory biomarker analysis.
isRetained: true
includesDNA: true
notes:
  - id: note-retention-001
    text: Samples are stored at -80 degrees Celsius at the central repository.
extensionAttributes:
  - id: ext-retention-01
    url: https://example.org/usdm/ext/storage-facility-id
    valueString: FAC-9982
  - id: ext-retention-02
    url: https://example.org/usdm/ext/consent-version
    valueInteger: 4

LinkML Source

Direct

name: BiospecimenRetention
description: The continued possession, cataloging, and storage of collected biological
  specimens beyond their initial use.
title: Biospecimen Retention
from_schema: https://example.org/usdm/v4/linkml
exact_mappings:
- ncit:C215505
rank: 1000
attributes:
  id:
    name: id
    from_schema: https://example.org/usdm/v4/linkml
    identifier: true
    domain_of:
    - Abbreviation
    - Activity
    - Address
    - AdministrableProduct
    - AdministrableProductProperty
    - Administration
    - AliasCode
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - Code
    - CommentAnnotation
    - ConditionAssignment
    - DocumentContentReference
    - Duration
    - EligibilityCriterion
    - Encounter
    - Estimand
    - ExtensionAttribute
    - ExtensionClass
    - GeographicScope
    - GovernanceDate
    - Identifier
    - Indication
    - Ingredient
    - Masking
    - MedicalDevice
    - NarrativeContent
    - NarrativeContentItem
    - Organization
    - ParameterMap
    - PersonName
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - QuantityRange
    - ResponseCode
    - ScheduleTimeline
    - ScheduleTimelineExit
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyAmendmentImpact
    - StudyAmendmentReason
    - StudyArm
    - StudyCell
    - StudyChange
    - StudyDefinitionDocument
    - StudyDefinitionDocumentVersion
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - StudyTitle
    - StudyVersion
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: true
  name:
    name: name
    description: The literal identifier (i.e., distinctive designation) of the biospecimen
      retention.
    title: Biospecimen Retention Name
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C215645
    domain_of:
    - Activity
    - AdministrableProduct
    - AdministrableProductProperty
    - Administration
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - EligibilityCriterion
    - Encounter
    - Estimand
    - GovernanceDate
    - Indication
    - MedicalDevice
    - NarrativeContent
    - NarrativeContentItem
    - Organization
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - ResponseCode
    - ScheduleTimeline
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyArm
    - StudyChange
    - StudyDefinitionDocument
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: true
  label:
    name: label
    description: The short descriptive designation for the biospecimen retention.
    title: Biospecimen Retention Label
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C215646
    domain_of:
    - Activity
    - AdministrableProduct
    - Administration
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - EligibilityCriterion
    - Encounter
    - Estimand
    - GovernanceDate
    - Indication
    - MedicalDevice
    - Organization
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - ResponseCode
    - ScheduleTimeline
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyArm
    - StudyChange
    - StudyDefinitionDocument
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: false
  description:
    name: description
    description: A narrative representation of the biospecimen retention.
    title: Biospecimen Retention Description
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C181231
    domain_of:
    - Activity
    - AdministrableProduct
    - Administration
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConceptCategory
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - EligibilityCriterion
    - Encounter
    - Estimand
    - GovernanceDate
    - Indication
    - MedicalDevice
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - ScheduleTimeline
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyArm
    - StudyChange
    - StudyDefinitionDocument
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: false
  isRetained:
    name: isRetained
    description: An indication as to whether biospecimens were retained.
    title: Biospecimen Retention Indicator
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C164620
    rank: 1000
    domain_of:
    - BiospecimenRetention
    range: boolean
    required: true
  includesDNA:
    name: includesDNA
    description: An indication as to whether retained biospecimens contain DNA.
    title: Biospecimen Retention Includes DNA Indicator
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C127777
    rank: 1000
    domain_of:
    - BiospecimenRetention
    range: boolean
    required: false
  extensionAttributes:
    name: extensionAttributes
    from_schema: https://example.org/usdm/v4/linkml
    domain_of:
    - Abbreviation
    - Activity
    - Address
    - AdministrableProduct
    - AdministrableProductIdentifier
    - AdministrableProductProperty
    - Administration
    - AliasCode
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - Characteristic
    - Code
    - CommentAnnotation
    - Condition
    - ConditionAssignment
    - DocumentContentReference
    - Duration
    - EligibilityCriterion
    - EligibilityCriterionItem
    - Encounter
    - Endpoint
    - Estimand
    - ExtensionAttribute
    - ExtensionClass
    - GeographicScope
    - GovernanceDate
    - Indication
    - Ingredient
    - IntercurrentEvent
    - InterventionalStudyDesign
    - Masking
    - MedicalDevice
    - MedicalDeviceIdentifier
    - NarrativeContent
    - NarrativeContentItem
    - Objective
    - ObservationalStudyDesign
    - Organization
    - ParameterMap
    - PersonName
    - Procedure
    - ProductOrganizationRole
    - Quantity
    - Range
    - ReferenceIdentifier
    - ResponseCode
    - ScheduleTimeline
    - ScheduleTimelineExit
    - ScheduledActivityInstance
    - ScheduledDecisionInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyAmendmentImpact
    - StudyAmendmentReason
    - StudyArm
    - StudyCell
    - StudyChange
    - StudyCohort
    - StudyDefinitionDocument
    - StudyDefinitionDocumentVersion
    - StudyDesignPopulation
    - StudyElement
    - StudyEpoch
    - StudyIdentifier
    - StudyIntervention
    - StudyRole
    - StudySite
    - StudyTitle
    - StudyVersion
    - SubjectEnrollment
    - Substance
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: ExtensionAttribute
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
class_uri: usdm:BiospecimenRetention

Induced

name: BiospecimenRetention
description: The continued possession, cataloging, and storage of collected biological
  specimens beyond their initial use.
title: Biospecimen Retention
from_schema: https://example.org/usdm/v4/linkml
exact_mappings:
- ncit:C215505
rank: 1000
attributes:
  id:
    name: id
    from_schema: https://example.org/usdm/v4/linkml
    identifier: true
    alias: id
    owner: BiospecimenRetention
    domain_of:
    - Abbreviation
    - Activity
    - Address
    - AdministrableProduct
    - AdministrableProductProperty
    - Administration
    - AliasCode
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - Code
    - CommentAnnotation
    - ConditionAssignment
    - DocumentContentReference
    - Duration
    - EligibilityCriterion
    - Encounter
    - Estimand
    - ExtensionAttribute
    - ExtensionClass
    - GeographicScope
    - GovernanceDate
    - Identifier
    - Indication
    - Ingredient
    - Masking
    - MedicalDevice
    - NarrativeContent
    - NarrativeContentItem
    - Organization
    - ParameterMap
    - PersonName
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - QuantityRange
    - ResponseCode
    - ScheduleTimeline
    - ScheduleTimelineExit
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyAmendmentImpact
    - StudyAmendmentReason
    - StudyArm
    - StudyCell
    - StudyChange
    - StudyDefinitionDocument
    - StudyDefinitionDocumentVersion
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - StudyTitle
    - StudyVersion
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: true
  name:
    name: name
    description: The literal identifier (i.e., distinctive designation) of the biospecimen
      retention.
    title: Biospecimen Retention Name
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C215645
    alias: name
    owner: BiospecimenRetention
    domain_of:
    - Activity
    - AdministrableProduct
    - AdministrableProductProperty
    - Administration
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - EligibilityCriterion
    - Encounter
    - Estimand
    - GovernanceDate
    - Indication
    - MedicalDevice
    - NarrativeContent
    - NarrativeContentItem
    - Organization
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - ResponseCode
    - ScheduleTimeline
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyArm
    - StudyChange
    - StudyDefinitionDocument
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: true
  label:
    name: label
    description: The short descriptive designation for the biospecimen retention.
    title: Biospecimen Retention Label
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C215646
    alias: label
    owner: BiospecimenRetention
    domain_of:
    - Activity
    - AdministrableProduct
    - Administration
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - EligibilityCriterion
    - Encounter
    - Estimand
    - GovernanceDate
    - Indication
    - MedicalDevice
    - Organization
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - ResponseCode
    - ScheduleTimeline
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyArm
    - StudyChange
    - StudyDefinitionDocument
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: false
  description:
    name: description
    description: A narrative representation of the biospecimen retention.
    title: Biospecimen Retention Description
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C181231
    alias: description
    owner: BiospecimenRetention
    domain_of:
    - Activity
    - AdministrableProduct
    - Administration
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConceptCategory
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - EligibilityCriterion
    - Encounter
    - Estimand
    - GovernanceDate
    - Indication
    - MedicalDevice
    - PopulationDefinition
    - Procedure
    - ProductOrganizationRole
    - ScheduleTimeline
    - ScheduledInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyArm
    - StudyChange
    - StudyDefinitionDocument
    - StudyDesign
    - StudyElement
    - StudyEpoch
    - StudyIntervention
    - StudyRole
    - StudySite
    - SubjectEnrollment
    - Substance
    - SyntaxTemplate
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: string
    required: false
  isRetained:
    name: isRetained
    description: An indication as to whether biospecimens were retained.
    title: Biospecimen Retention Indicator
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C164620
    rank: 1000
    alias: isRetained
    owner: BiospecimenRetention
    domain_of:
    - BiospecimenRetention
    range: boolean
    required: true
  includesDNA:
    name: includesDNA
    description: An indication as to whether retained biospecimens contain DNA.
    title: Biospecimen Retention Includes DNA Indicator
    from_schema: https://example.org/usdm/v4/linkml
    exact_mappings:
    - ncit:C127777
    rank: 1000
    alias: includesDNA
    owner: BiospecimenRetention
    domain_of:
    - BiospecimenRetention
    range: boolean
    required: false
  extensionAttributes:
    name: extensionAttributes
    from_schema: https://example.org/usdm/v4/linkml
    alias: extensionAttributes
    owner: BiospecimenRetention
    domain_of:
    - Abbreviation
    - Activity
    - Address
    - AdministrableProduct
    - AdministrableProductIdentifier
    - AdministrableProductProperty
    - Administration
    - AliasCode
    - AnalysisPopulation
    - AssignedPerson
    - BiomedicalConcept
    - BiomedicalConceptCategory
    - BiomedicalConceptProperty
    - BiomedicalConceptSurrogate
    - BiospecimenRetention
    - Characteristic
    - Code
    - CommentAnnotation
    - Condition
    - ConditionAssignment
    - DocumentContentReference
    - Duration
    - EligibilityCriterion
    - EligibilityCriterionItem
    - Encounter
    - Endpoint
    - Estimand
    - ExtensionAttribute
    - ExtensionClass
    - GeographicScope
    - GovernanceDate
    - Indication
    - Ingredient
    - IntercurrentEvent
    - InterventionalStudyDesign
    - Masking
    - MedicalDevice
    - MedicalDeviceIdentifier
    - NarrativeContent
    - NarrativeContentItem
    - Objective
    - ObservationalStudyDesign
    - Organization
    - ParameterMap
    - PersonName
    - Procedure
    - ProductOrganizationRole
    - Quantity
    - Range
    - ReferenceIdentifier
    - ResponseCode
    - ScheduleTimeline
    - ScheduleTimelineExit
    - ScheduledActivityInstance
    - ScheduledDecisionInstance
    - Strength
    - Study
    - StudyAmendment
    - StudyAmendmentImpact
    - StudyAmendmentReason
    - StudyArm
    - StudyCell
    - StudyChange
    - StudyCohort
    - StudyDefinitionDocument
    - StudyDefinitionDocumentVersion
    - StudyDesignPopulation
    - StudyElement
    - StudyEpoch
    - StudyIdentifier
    - StudyIntervention
    - StudyRole
    - StudySite
    - StudyTitle
    - StudyVersion
    - SubjectEnrollment
    - Substance
    - SyntaxTemplateDictionary
    - Timing
    - TransitionRule
    range: ExtensionAttribute
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
class_uri: usdm:BiospecimenRetention