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Class: SpecimenCreationActivity

The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting).

URI: bdchm:SpecimenCreationActivity

classDiagram class SpecimenCreationActivity Entity <|-- SpecimenCreationActivity SpecimenCreationActivity : activity_type SpecimenCreationActivity --> SpecimenCreationActivityTypeEnum : activity_type SpecimenCreationActivity : additive SpecimenCreationActivity --> Substance : additive SpecimenCreationActivity : collection_method_type SpecimenCreationActivity --> SpecimenCollectionMethodType : collection_method_type SpecimenCreationActivity : collection_site SpecimenCreationActivity --> BodySite : collection_site SpecimenCreationActivity : date_ended SpecimenCreationActivity --> TimePoint : date_ended SpecimenCreationActivity : date_started SpecimenCreationActivity --> TimePoint : date_started SpecimenCreationActivity : derivation_method_type SpecimenCreationActivity : id SpecimenCreationActivity : performed_by SpecimenCreationActivity --> Organization : performed_by SpecimenCreationActivity : quantity_collected SpecimenCreationActivity --> Quantity : quantity_collected SpecimenCreationActivity : specimen_order

Inheritance

  • Entity
    • SpecimenCreationActivity

Slots

Name Cardinality and Range Description Inheritance
activity_type 0..1
SpecimenCreationActivityTypeEnum		 The high-level type of creation activity direct
date_started 0..1
TimePoint		 The date when the activity began (in this case, a specimen creation event) direct
date_ended 0..1
TimePoint		 The date when the activity ended (in this case, a specimen creation event) direct
performed_by 0..1
Organization		 The organization or group that performed the activity direct
collection_method_type 0..1
SpecimenCollectionMethodType		 The type of method applied in collecting a sample from its original source direct
derivation_method_type 0..1
String		 The type of method applied to derive a new specimen from an existing one direct
additive 0..*
Substance		 A type of material or reagent used applied as input when creating a specimen direct
collection_site 0..1
BodySite		 The anatomic site from which a specimen was collected direct
quantity_collected 0..1
Quantity		 The quantity of material in the specimen as originally collected from its ori... direct
specimen_order 0..1
Integer		 A numeric value that represents the sequential order of this creation activit... 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 creation_activity range SpecimenCreationActivity

Comments

  • A creation' activity represents the entire process up to the point where the specimen is physically modified, stored, or transported.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: SpecimenCreationActivity
description: The process of creating a specimen. This may occur through observing
  and/or collecting material from an biological source or natural setting, or through
  derivation from an existing specimen (e.g. via portioning or aliquoting).
comments:
- A creation' activity represents the entire process up to the point where the specimen
  is physically modified, stored, or transported.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  activity_type:
    name: activity_type
    description: The high-level type of creation activity.
    comments:
    - At present our model collapses two types of processes through which specimens
      are created (initial collection from source, and derivation from an existing
      specimen).  The 'category' is a flag to indicate which applies to a given instance,
      so that more specific recommendations about data entry in certain fields can
      be specified.
    examples:
    - value: Collection from Source
    - value: Derivation from Specimen
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: SpecimenCreationActivityTypeEnum
    required: false
  date_started:
    name: date_started
    description: The date when the activity began (in this case, a specimen creation
      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 specimen creation
      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
  performed_by:
    name: performed_by
    description: The organization or group that performed the activity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: Organization
    required: false
  collection_method_type:
    name: collection_method_type
    description: The type of method applied in collecting a sample from its original
      source.
    comments:
    - This attribute applies only when the Specimen.category = 'original'.
    examples:
    - value: Anterior Resection of Rectum
    - value: Ascites Drainage
    - value: Excisional Biopsy
    - value: Specimen Pooling
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: SpecimenCollectionMethodType
    required: false
  derivation_method_type:
    name: derivation_method_type
    description: The type of method applied to derive a new specimen from an existing
      one.
    comments:
    - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte',
      or 'slide'.
    examples:
    - value: Vibratome
    - value: Cryosectioning
    - value: Tissuemolds
    - value: Slidingmicrotome
    - value: Sectioning
    - value: Other
    - value: Unknown
    - value: NotReported
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type
    multivalued: false
    range: string
    required: false
  additive:
    name: additive
    description: A type of material or reagent used applied as input when creating
      a specimen.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: true
    range: Substance
    required: false
  collection_site:
    name: collection_site
    description: The anatomic site from which a specimen was collected.
    comments:
    - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection
      from Source'.
    examples:
    - value: Abdomen
    - value: Abdominal Wall
    - value: Acetabulum
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: BodySite
    required: false
  quantity_collected:
    name: quantity_collected
    description: The quantity of material in the specimen as originally collected
      from its original source material (prior to downstream portioning or processing)
    comments:
    - This attribute applies only when Specimen.category='initial sample'.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: Quantity
    required: false
  specimen_order:
    name: specimen_order
    description: A numeric value that represents the sequential order of this creation
      activity relative to those producing other specimens from the same source material
      or parent specimen.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    range: integer
    required: false

Induced

name: SpecimenCreationActivity
description: The process of creating a specimen. This may occur through observing
  and/or collecting material from an biological source or natural setting, or through
  derivation from an existing specimen (e.g. via portioning or aliquoting).
comments:
- A creation' activity represents the entire process up to the point where the specimen
  is physically modified, stored, or transported.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  activity_type:
    name: activity_type
    description: The high-level type of creation activity.
    comments:
    - At present our model collapses two types of processes through which specimens
      are created (initial collection from source, and derivation from an existing
      specimen).  The 'category' is a flag to indicate which applies to a given instance,
      so that more specific recommendations about data entry in certain fields can
      be specified.
    examples:
    - value: Collection from Source
    - value: Derivation from Specimen
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: activity_type
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    range: SpecimenCreationActivityTypeEnum
    required: false
  date_started:
    name: date_started
    description: The date when the activity began (in this case, a specimen creation
      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: SpecimenCreationActivity
    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 specimen creation
      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: SpecimenCreationActivity
    domain_of:
    - ResearchStudy
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - SpecimenTransportActivity
    range: TimePoint
    required: false
  performed_by:
    name: performed_by
    description: The organization or group that performed the activity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: performed_by
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    range: Organization
    required: false
  collection_method_type:
    name: collection_method_type
    description: The type of method applied in collecting a sample from its original
      source.
    comments:
    - This attribute applies only when the Specimen.category = 'original'.
    examples:
    - value: Anterior Resection of Rectum
    - value: Ascites Drainage
    - value: Excisional Biopsy
    - value: Specimen Pooling
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: collection_method_type
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    range: SpecimenCollectionMethodType
    required: false
  derivation_method_type:
    name: derivation_method_type
    description: The type of method applied to derive a new specimen from an existing
      one.
    comments:
    - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte',
      or 'slide'.
    examples:
    - value: Vibratome
    - value: Cryosectioning
    - value: Tissuemolds
    - value: Slidingmicrotome
    - value: Sectioning
    - value: Other
    - value: Unknown
    - value: NotReported
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type
    multivalued: false
    alias: derivation_method_type
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    range: string
    required: false
  additive:
    name: additive
    description: A type of material or reagent used applied as input when creating
      a specimen.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: true
    alias: additive
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenContainer
    - SpecimenCreationActivity
    - SpecimenProcessingActivity
    range: Substance
    required: false
  collection_site:
    name: collection_site
    description: The anatomic site from which a specimen was collected.
    comments:
    - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection
      from Source'.
    examples:
    - value: Abdomen
    - value: Abdominal Wall
    - value: Acetabulum
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: collection_site
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    range: BodySite
    required: false
  quantity_collected:
    name: quantity_collected
    description: The quantity of material in the specimen as originally collected
      from its original source material (prior to downstream portioning or processing)
    comments:
    - This attribute applies only when Specimen.category='initial sample'.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: quantity_collected
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    range: Quantity
    required: false
  specimen_order:
    name: specimen_order
    description: A numeric value that represents the sequential order of this creation
      activity relative to those producing other specimens from the same source material
      or parent specimen.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: specimen_order
    owner: SpecimenCreationActivity
    domain_of:
    - SpecimenCreationActivity
    range: integer
    required: false
  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: SpecimenCreationActivity
    domain_of:
    - Entity
    range: uriorcurie
    required: true