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Class: SpecimenQuantityObservation

A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement.

URI: bdchm:SpecimenQuantityObservation

classDiagram class SpecimenQuantityObservation Observation <|-- SpecimenQuantityObservation SpecimenQuantityObservation : age_at_observation SpecimenQuantityObservation : associated_participant SpecimenQuantityObservation --> Participant : associated_participant SpecimenQuantityObservation : associated_visit SpecimenQuantityObservation --> Visit : associated_visit SpecimenQuantityObservation : category SpecimenQuantityObservation : focus SpecimenQuantityObservation --> Entity : focus SpecimenQuantityObservation : id SpecimenQuantityObservation : method_type SpecimenQuantityObservation : observation_type SpecimenQuantityObservation : performed_by SpecimenQuantityObservation --> Organization : performed_by SpecimenQuantityObservation : value_boolean SpecimenQuantityObservation : value_enum SpecimenQuantityObservation --> BaseEnum : value_enum SpecimenQuantityObservation : value_quantity SpecimenQuantityObservation --> Quantity : value_quantity SpecimenQuantityObservation : value_string

Inheritance

Slots

Name Cardinality and Range Description Inheritance
age_at_observation 0..1
Integer		 The Participant's age (expressed in days) when the Observation was made Observation
category 0..1
String		 The general category of observation described Observation
observation_type 1..1
String		 The type of Observation being represented (e Observation
method_type 0..1
String		 A type of method used in generating the Observation result Observation
focus 0..1
Entity		 The entity or entities directly observed/measured in generating an observatio... Observation
associated_participant 0..1
Participant		 The patient that the observation is about (if not the direct focus) Observation
associated_visit 0..1
Visit		 A reference to the Visit during which this Observation was recorded Observation
performed_by 0..1
Organization		 The organization or group that performed the observation activity Observation
value_string 0..1
String		 A slot to hold a string value for an Observation Observation
value_boolean 0..1
Boolean		 A slot to hold a boolean value for an Observation Observation
value_quantity 0..1
Quantity		 A slot to hold a Quantity value for an Observation Observation
value_enum 0..1
BaseEnum		 A slot to hold an enumerated value for an Observation Observation
id 1..1
Uriorcurie		 The 'logical' identifier of the entity within the system of record Entity

Usages

used by used in type used
Specimen quantity_measure range SpecimenQuantityObservation

Comments

  • At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a "key" field defines the type of observation made, and the "value" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: SpecimenQuantityObservation
description: A structured object that describes a single data item about the quantity
  of a Specimen, as generated through a point-in-time observation or measurement.
comments:
- At the core of an Observation is a flexible key-value pair (or a structured collection
  of key-value pairs), where a "key" field defines the type of observation made, and
  the "value" field describes the value or outcome of the observation. The fact that
  the type of observation captured is defined in the data allow Observation to convey
  a broad range of observation data.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Observation

Induced

name: SpecimenQuantityObservation
description: A structured object that describes a single data item about the quantity
  of a Specimen, as generated through a point-in-time observation or measurement.
comments:
- At the core of an Observation is a flexible key-value pair (or a structured collection
  of key-value pairs), where a "key" field defines the type of observation made, and
  the "value" field describes the value or outcome of the observation. The fact that
  the type of observation captured is defined in the data allow Observation to convey
  a broad range of observation data.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Observation
attributes:
  age_at_observation:
    name: age_at_observation
    description: The Participant's age (expressed in days) when the Observation was
      made.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: age_at_observation
    owner: SpecimenQuantityObservation
    domain_of:
    - Observation
    range: integer
    unit:
      ucum_code: d
  category:
    name: category
    description: The general category of observation described
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    values_from:
    - crdch:enum_CRDCH_Observation_category
    multivalued: false
    alias: category
    owner: SpecimenQuantityObservation
    domain_of:
    - ObservationSet
    - Observation
    range: string
    required: false
  observation_type:
    name: observation_type
    description: The type of Observation being represented (e.g. 'diastolic blood
      pressure')
    comments:
    - This field holds the "key" in the core key-value pair comprised of the observation_type
      field and the relevant value(s) field.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_Observation_observation_type
    multivalued: false
    alias: observation_type
    owner: SpecimenQuantityObservation
    domain_of:
    - Observation
    range: string
    required: true
  method_type:
    name: method_type
    description: A type of method used in generating the Observation result.
    comments:
    - This may be a type of observational, measurement, experimental, or computational
      method specifying how to generate data (e.g. "manual counting", "bright field
      microscopy",). Or a Guideline or SOP specifying how to interpret data and/or
      encode the result of an  Observation (e.g. a Cancer Staging system such as that
      defined by the AJCC, or variant interpretation guideline such as that provided
      by the ACMG).
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    values_from:
    - crdch:enum_CRDCH_Observation_method_type
    multivalued: false
    alias: method_type
    owner: SpecimenQuantityObservation
    domain_of:
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - ObservationSet
    - Observation
    range: string
    required: false
  focus:
    name: focus
    description: The entity or entities directly observed/measured in generating an
      observation result.
    comments:
    - The "focus", "subject", and "specimen" fields are useful when data creators
      want an Observation object to stand on its own, so it can point back to the
      entities it is about.  These fields are not needed when an Observation is embedded
      in a Specimen or other entity, where focus, subject, and specimen can be determined
      from context.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: focus
    owner: SpecimenQuantityObservation
    domain_of:
    - Document
    - ObservationSet
    - Observation
    range: Entity
    required: false
  associated_participant:
    name: associated_participant
    description: The patient that the observation is about (if not the direct focus).  e.g.
      observations are often made on specimens derived from a patient, or other entities
      related to a patient, that ultimately tell us something about the patient of
      interest.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: associated_participant
    owner: SpecimenQuantityObservation
    domain_of:
    - Demography
    - Visit
    - Condition
    - Procedure
    - Exposure
    - File
    - ObservationSet
    - Observation
    range: Participant
    required: false
  associated_visit:
    name: associated_visit
    description: A reference to the Visit during which this Observation was recorded.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    alias: associated_visit
    owner: SpecimenQuantityObservation
    domain_of:
    - QuestionnaireResponse
    - Condition
    - Procedure
    - Exposure
    - ObservationSet
    - Observation
    range: Visit
  performed_by:
    name: performed_by
    description: The organization or group that performed the observation activity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    alias: performed_by
    owner: SpecimenQuantityObservation
    domain_of:
    - SpecimenCreationActivity
    - ObservationSet
    - Observation
    range: Organization
    required: false
  value_string:
    name: value_string
    description: A slot to hold a string value for an Observation.
    comments:
    - One and only one of the value(x) fields must be populated.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: value_string
    owner: SpecimenQuantityObservation
    domain_of:
    - Observation
    range: string
    required: false
  value_boolean:
    name: value_boolean
    description: A slot to hold a boolean value for an Observation.
    comments:
    - One and only one of the value(x) fields must be populated.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: value_boolean
    owner: SpecimenQuantityObservation
    domain_of:
    - Observation
    range: boolean
    required: false
  value_quantity:
    name: value_quantity
    description: A slot to hold a Quantity value for an Observation.
    comments:
    - One and only one of the value(x) fields must be populated.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: value_quantity
    owner: SpecimenQuantityObservation
    domain_of:
    - Observation
    range: Quantity
    required: false
  value_enum:
    name: value_enum
    description: A slot to hold an enumerated value for an Observation.
    comments:
    - One and only one of the value(x) fields must be populated.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: false
    alias: value_enum
    owner: SpecimenQuantityObservation
    domain_of:
    - Observation
    range: BaseEnum
    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: SpecimenQuantityObservation
    domain_of:
    - Entity
    range: uriorcurie
    required: true