Class: SpecimenProcessingActivity

An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen.

URI: bdchm:SpecimenProcessingActivity

classDiagram class SpecimenProcessingActivity Entity <|-- SpecimenProcessingActivity SpecimenProcessingActivity : activity_type SpecimenProcessingActivity --> SpecimenProcessingActivityTypeEnum : activity_type SpecimenProcessingActivity : additive SpecimenProcessingActivity --> Substance : additive SpecimenProcessingActivity : date_ended SpecimenProcessingActivity --> TimePoint : date_ended SpecimenProcessingActivity : date_started SpecimenProcessingActivity --> TimePoint : date_started SpecimenProcessingActivity : duration SpecimenProcessingActivity --> Quantity : duration SpecimenProcessingActivity : id SpecimenProcessingActivity : method_type

Inheritance

Entity
- SpecimenProcessingActivity

Slots

Name	Cardinality and Range	Description	Inheritance
activity_type	0..1 SpecimenProcessingActivityTypeEnum	The high-level type of processing activity	direct
date_started	0..1 TimePoint	The date when the activity began (in this case, a specimen processing event)	direct
date_ended	0..1 TimePoint	The date when the activity began (in this case, a specimen processing event)	direct
duration	0..* 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 process the specimen	direct
additive	0..* Substance	A type of material or reagent used as input when processing the specimen	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	processing_activity	range	SpecimenProcessingActivity

Comments

"Processing" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: SpecimenProcessingActivity
description: An activity that modifies the physical structure, composition, or state
  of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result
  in the generation of new entities - they take a single specimen as input, and output
  that same specimen.
comments:
- '"Processing" as defined here alters the physical nature of a specimen, such that
  storage or transport activities do not qualify as processing activities. When instantiating
  this class, create a separate instances for each type/method of processing performed
  (e.g. each method of fixation, freezing, labeling, etc. that is applied).'
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  activity_type:
    name: activity_type
    description: The high-level type of processing activity
    examples:
    - value: Fixation
    - value: Freezing
    - value: Mounting
    - value: Preservation
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    range: SpecimenProcessingActivityTypeEnum
    required: false
  date_started:
    name: date_started
    description: The date when the activity began (in this case, a specimen processing
      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 began (in this case, a specimen processing
      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.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    range: Quantity
    required: false
    inlined: true
    inlined_as_list: true
  method_type:
    name: method_type
    description: A specific type of method or procedure performed to process the specimen
    examples:
    - value: Snap Freezing
    - value: Cryopreservation in liquid nitrogen (dead tissue)
    - value: Cryopreservation in dry ice (dead tissue)
    - value: Formalin fixed paraffin embedded (FFPE)
    - value: Formalin fixed-unbuffered
    - value: Formalin fixed-buffered
    - value: OCT
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    values_from:
    - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type
    multivalued: false
    range: string
    required: false
  additive:
    name: additive
    description: A type of material or reagent used as input when processing the specimen
    examples:
    - value: Formalin
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: true
    range: Substance
    required: false
    inlined: true
    inlined_as_list: true

Induced

name: SpecimenProcessingActivity
description: An activity that modifies the physical structure, composition, or state
  of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result
  in the generation of new entities - they take a single specimen as input, and output
  that same specimen.
comments:
- '"Processing" as defined here alters the physical nature of a specimen, such that
  storage or transport activities do not qualify as processing activities. When instantiating
  this class, create a separate instances for each type/method of processing performed
  (e.g. each method of fixation, freezing, labeling, etc. that is applied).'
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  activity_type:
    name: activity_type
    description: The high-level type of processing activity
    examples:
    - value: Fixation
    - value: Freezing
    - value: Mounting
    - value: Preservation
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: activity_type
    owner: SpecimenProcessingActivity
    domain_of:
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    range: SpecimenProcessingActivityTypeEnum
    required: false
  date_started:
    name: date_started
    description: The date when the activity began (in this case, a specimen processing
      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: SpecimenProcessingActivity
    domain_of:
    - ResearchStudy
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - SpecimenTransportActivity
    range: TimePoint
    required: false
  date_ended:
    name: date_ended
    description: The date when the activity began (in this case, a specimen processing
      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: SpecimenProcessingActivity
    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.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: duration
    owner: SpecimenProcessingActivity
    domain_of:
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - SpecimenTransportActivity
    range: Quantity
    required: false
    inlined: true
    inlined_as_list: true
  method_type:
    name: method_type
    description: A specific type of method or procedure performed to process the specimen
    examples:
    - value: Snap Freezing
    - value: Cryopreservation in liquid nitrogen (dead tissue)
    - value: Cryopreservation in dry ice (dead tissue)
    - value: Formalin fixed paraffin embedded (FFPE)
    - value: Formalin fixed-unbuffered
    - value: Formalin fixed-buffered
    - value: OCT
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    values_from:
    - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type
    multivalued: false
    alias: method_type
    owner: SpecimenProcessingActivity
    domain_of:
    - DimensionalObservation
    - DimensionalObservationSet
    - SpecimenQualityObservation
    - SpecimenQuantityObservation
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    range: string
    required: false
  additive:
    name: additive
    description: A type of material or reagent used as input when processing the specimen
    examples:
    - value: Formalin
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: true
    alias: additive
    owner: SpecimenProcessingActivity
    domain_of:
    - SpecimenContainer
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    range: Substance
    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: SpecimenProcessingActivity
    domain_of:
    - Entity
    range: uriorcurie
    required: true