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Class: Observation

A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel.

URI: bdchm:Observation

classDiagram class Observation click Observation href "../Observation" Entity <|-- Observation click Entity href "../Entity" Observation <|-- DimensionalObservation click DimensionalObservation href "../DimensionalObservation" Observation <|-- SpecimenQualityObservation click SpecimenQualityObservation href "../SpecimenQualityObservation" Observation <|-- SpecimenQuantityObservation click SpecimenQuantityObservation href "../SpecimenQuantityObservation" Observation <|-- MeasurementObservation click MeasurementObservation href "../MeasurementObservation" Observation <|-- SdohObservation click SdohObservation href "../SdohObservation" Observation : age_at_observation Observation : associated_participant Observation --> "0..1" Participant : associated_participant click Participant href "../Participant" Observation : associated_visit Observation --> "0..1" Visit : associated_visit click Visit href "../Visit" Observation : category Observation : focus Observation --> "0..1" Entity : focus click Entity href "../Entity" Observation : id Observation : method_type Observation : observation_type Observation --> "1" BaseObservationTypeEnum : observation_type click BaseObservationTypeEnum href "../BaseObservationTypeEnum" Observation : performed_by Observation --> "0..1" Organization : performed_by click Organization href "../Organization" Observation : value_boolean Observation : value_enum Observation --> "0..1" BaseEnum : value_enum click BaseEnum href "../BaseEnum" Observation : value_quantity Observation --> "0..1" Quantity : value_quantity click Quantity href "../Quantity" Observation : value_string

Inheritance

Slots

Name Cardinality and Range Description Inheritance
associated_visit 0..1
Visit		 A reference to the Visit that is associated with this record direct
associated_participant 0..1
Participant		 A reference to the Participant that is associated with this record direct
age_at_observation 0..1
Integer		 The Participant's age (expressed in days) when the Observation was made direct
category 0..1
String		 The general category of observation described direct
observation_type 1
BaseObservationTypeEnum		 The type of Observation being represented (e direct
method_type 0..1
String		 A type of method used in generating the Observation result direct
focus 0..1
Entity		 The entity or entities directly observed/measured in generating an observatio... direct
performed_by 0..1
Organization		 The organization or group that performed the observation activity direct
value_string 0..1
String		 A slot to hold a string value for an Observation direct
value_boolean 0..1
Boolean		 A slot to hold a boolean value for an Observation direct
value_quantity 0..1
Quantity		 A slot to hold a Quantity value for an Observation direct
value_enum 0..1
BaseEnum		 A slot to hold an enumerated value for an Observation direct
id 1
Uriorcurie		 The 'logical' identifier of the entity within the system of record Entity

Usages

used by used in type used
ObservationSet observations range Observation

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Observation
description: A data structure with key (observation_type) and value (value) attributes
  that represents a single observation, such as the hematocrit component of a complete
  blood count panel.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
slots:
- associated_visit
- associated_participant
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
    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
    domain_of:
    - ObservationSet
    - Observation
    range: string
    required: false
    multivalued: 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
    domain_of:
    - Observation
    - MeasurementObservation
    range: BaseObservationTypeEnum
    required: true
    multivalued: false
  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
    domain_of:
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - ObservationSet
    - Observation
    range: string
    required: false
    multivalued: 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
    domain_of:
    - Document
    - ObservationSet
    - Observation
    range: Entity
    required: false
    multivalued: false
  performed_by:
    name: performed_by
    description: The organization or group that performed the observation activity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    domain_of:
    - SpecimenCreationActivity
    - ObservationSet
    - Observation
    range: Organization
    required: false
    multivalued: 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
    domain_of:
    - Observation
    range: string
    required: false
    multivalued: 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
    domain_of:
    - Observation
    range: boolean
    required: false
    multivalued: 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
    domain_of:
    - Observation
    range: Quantity
    required: false
    multivalued: 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
    domain_of:
    - Observation
    range: BaseEnum
    required: false
    multivalued: false

Induced

name: Observation
description: A data structure with key (observation_type) and value (value) attributes
  that represents a single observation, such as the hematocrit component of a complete
  blood count panel.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
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: Observation
    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
    alias: category
    owner: Observation
    domain_of:
    - ObservationSet
    - Observation
    range: string
    required: false
    multivalued: 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
    alias: observation_type
    owner: Observation
    domain_of:
    - Observation
    - MeasurementObservation
    range: BaseObservationTypeEnum
    required: true
    multivalued: false
  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
    alias: method_type
    owner: Observation
    domain_of:
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - ObservationSet
    - Observation
    range: string
    required: false
    multivalued: 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
    alias: focus
    owner: Observation
    domain_of:
    - Document
    - ObservationSet
    - Observation
    range: Entity
    required: false
    multivalued: false
  performed_by:
    name: performed_by
    description: The organization or group that performed the observation activity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    alias: performed_by
    owner: Observation
    domain_of:
    - SpecimenCreationActivity
    - ObservationSet
    - Observation
    range: Organization
    required: false
    multivalued: 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
    alias: value_string
    owner: Observation
    domain_of:
    - Observation
    range: string
    required: false
    multivalued: 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
    alias: value_boolean
    owner: Observation
    domain_of:
    - Observation
    range: boolean
    required: false
    multivalued: 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
    alias: value_quantity
    owner: Observation
    domain_of:
    - Observation
    range: Quantity
    required: false
    multivalued: 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
    alias: value_enum
    owner: Observation
    domain_of:
    - Observation
    range: BaseEnum
    required: false
    multivalued: false
  associated_visit:
    name: associated_visit
    description: A reference to the Visit that is associated with this record.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: associated_visit
    owner: Observation
    domain_of:
    - Demography
    - QuestionnaireResponse
    - Condition
    - Procedure
    - ImagingStudy
    - Exposure
    - ObservationSet
    - Observation
    range: Visit
  associated_participant:
    name: associated_participant
    description: A reference to the Participant that is associated with this record.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    alias: associated_participant
    owner: Observation
    domain_of:
    - Demography
    - Visit
    - Condition
    - Procedure
    - ImagingStudy
    - Exposure
    - File
    - ObservationSet
    - Observation
    range: Participant
  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: Observation
    domain_of:
    - Entity
    range: uriorcurie
    required: true