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Class: SpecimenStorageActivity

_An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the _

intrinsic physical nature of a specimen.

URI: bdchm:SpecimenStorageActivity

classDiagram class SpecimenStorageActivity Entity <|-- SpecimenStorageActivity SpecimenStorageActivity : container SpecimenStorageActivity --> SpecimenContainer : container SpecimenStorageActivity : date_ended SpecimenStorageActivity --> TimePoint : date_ended SpecimenStorageActivity : date_started SpecimenStorageActivity --> TimePoint : date_started SpecimenStorageActivity : duration SpecimenStorageActivity --> Quantity : duration SpecimenStorageActivity : id SpecimenStorageActivity : method_type

Inheritance

  • Entity
    • SpecimenStorageActivity

Slots

Name Cardinality and Range Description Inheritance
date_started 0..1
TimePoint		 The date when the activity began (in this case, a storage event) direct
date_ended 0..1
TimePoint		 The date when the activity ended (in this case, a storage event) direct
duration 0..1
Quantity		 The length of time over which the activity was performed direct
method_type 0..1
String		 A specific type of method or procedure performed to store the specimen direct
container 0..*
SpecimenContainer		 A container in which the specimen is held or affixed during its storage direct
id 1..1
Uriorcurie		 The 'logical' identifier of the entity within the system of record Entity

Usages

used by used in type used
Specimen storage_activity range SpecimenStorageActivity

Comments

  • Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each.

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/nhlbidatastage/bdchm

Mappings

Mapping Type Mapped Value
self bdchm:SpecimenStorageActivity
native bdchm:SpecimenStorageActivity

LinkML Source

Direct

name: SpecimenStorageActivity
description: "An activity in which a specimen is stored or maintained in a particular\
  \ location, container, or state. Unlike 'processing' activities, storage does not\
  \ alter the \nintrinsic physical nature of a specimen."
comments:
- Think of the StorageActivity as being one of many possible periods when the specimen
  was stored at some location and in some state or condition.  We may want to capture
  storage dates and conditions for each.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  date_started:
    name: date_started
    description: The date when the activity began (in this case, a storage event).
    comments:
    - To allow for more precise specification of dates when an activity was performed,
      we provide date_started and date_ended attributes.  If source data only provides
      a single date, it SHOULD be entered as both the date_started and date_ended.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    range: TimePoint
    required: false
  date_ended:
    name: date_ended
    description: The date when the activity ended (in this case, a storage event).
    comments:
    - To allow for more precise specification of dates when an activity was performed,
      we provide date_started and date_ended attributes.  If source data only provides
      a single date, it SHOULD be entered as both the date_started and date_ended.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    range: TimePoint
    required: false
  duration:
    name: duration
    description: The length of time over which the activity was performed.
    comments:
    - 'Quantity.unit MUST be a unit of time. '
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    range: Quantity
    required: false
  method_type:
    name: method_type
    description: A specific type of method or procedure performed to store the specimen
    examples:
    - value: ambient temperature
    - value: cut slide
    - value: fresh
    - value: frozen at -70C
    - value: frozen at -150C
    - value: frozen in liquid nitrogen
    - value: frozen in vapor phase
    - value: paraffin block
    - value: RNAlater at 4C
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    values_from:
    - crdch:enum_CRDCH_SpecimenStorageActivity_method_type
    multivalued: false
    range: string
    required: false
  container:
    name: container
    description: A container in which the specimen is held or affixed during its storage.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: SpecimenContainer
    required: false
    inlined: true
    inlined_as_list: true

Induced

name: SpecimenStorageActivity
description: "An activity in which a specimen is stored or maintained in a particular\
  \ location, container, or state. Unlike 'processing' activities, storage does not\
  \ alter the \nintrinsic physical nature of a specimen."
comments:
- Think of the StorageActivity as being one of many possible periods when the specimen
  was stored at some location and in some state or condition.  We may want to capture
  storage dates and conditions for each.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  date_started:
    name: date_started
    description: The date when the activity began (in this case, a storage event).
    comments:
    - To allow for more precise specification of dates when an activity was performed,
      we provide date_started and date_ended attributes.  If source data only provides
      a single date, it SHOULD be entered as both the date_started and date_ended.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: date_started
    owner: SpecimenStorageActivity
    domain_of:
    - ResearchStudy
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - SpecimenTransportActivity
    range: TimePoint
    required: false
  date_ended:
    name: date_ended
    description: The date when the activity ended (in this case, a storage event).
    comments:
    - To allow for more precise specification of dates when an activity was performed,
      we provide date_started and date_ended attributes.  If source data only provides
      a single date, it SHOULD be entered as both the date_started and date_ended.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: date_ended
    owner: SpecimenStorageActivity
    domain_of:
    - ResearchStudy
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - SpecimenTransportActivity
    range: TimePoint
    required: false
  duration:
    name: duration
    description: The length of time over which the activity was performed.
    comments:
    - 'Quantity.unit MUST be a unit of time. '
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: duration
    owner: SpecimenStorageActivity
    domain_of:
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - SpecimenTransportActivity
    range: Quantity
    required: false
  method_type:
    name: method_type
    description: A specific type of method or procedure performed to store the specimen
    examples:
    - value: ambient temperature
    - value: cut slide
    - value: fresh
    - value: frozen at -70C
    - value: frozen at -150C
    - value: frozen in liquid nitrogen
    - value: frozen in vapor phase
    - value: paraffin block
    - value: RNAlater at 4C
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    values_from:
    - crdch:enum_CRDCH_SpecimenStorageActivity_method_type
    multivalued: false
    alias: method_type
    owner: SpecimenStorageActivity
    domain_of:
    - DimensionalObservation
    - DimensionalObservationSet
    - SpecimenQualityObservation
    - SpecimenQuantityObservation
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    range: string
    required: false
  container:
    name: container
    description: A container in which the specimen is held or affixed during its storage.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: container
    owner: SpecimenStorageActivity
    domain_of:
    - SpecimenStorageActivity
    range: SpecimenContainer
    required: false
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: The 'logical' identifier of the entity within the system of record.  The
      simple value of this attribute stands for an identifier of this data object
      within the system, it can be used as a reference from other objects within the
      same system (i.e. primary and foreign keys), and it should be unique per type
      of object. The same data object copied to a different system will likely have
      a different "id" in the new system since "id" values are system specific and
      do not represent persistent business identifiers. Business identifiers are assigned
      outside the information system and are captured in the "identifier" field. The
      "id" field is more likely to be a serially or randomly generated value that
      is assigned to the data object as it is created in a system.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    slot_uri: schema:identifier
    identifier: true
    alias: id
    owner: SpecimenStorageActivity
    domain_of:
    - Entity
    range: uriorcurie
    required: true