Skip to content

Class: ObservationSet

A structured object to hold related Observations in a set.

URI: bdchm:ObservationSet

classDiagram class ObservationSet Entity <|-- ObservationSet ObservationSet <|-- DimensionalObservationSet ObservationSet <|-- MeasurementObservationSet ObservationSet <|-- SdohObservationSet ObservationSet : associated_participant ObservationSet --> Participant : associated_participant ObservationSet : associated_visit ObservationSet --> Visit : associated_visit ObservationSet : category ObservationSet : focus ObservationSet --> Entity : focus ObservationSet : id ObservationSet : method_type ObservationSet : observations ObservationSet --> Observation : observations ObservationSet : performed_by ObservationSet --> Organization : performed_by

Inheritance

Slots

Name Cardinality and Range Description Inheritance
observations 0..*
Observation		 A set of one or more observations direct
category 0..1
String		 The general category of observation set described direct
focus 0..*
Entity		 The entity or entities directly observed/measured in generating an observatio... direct
associated_participant 0..1
Participant		 The Participant that the observation is about (if not the direct focus) direct
associated_visit 0..1
Visit		 A reference to the Visit during which this Observation was recorded direct
method_type 0..*
String		 The type of method used in generating the ObservationSet direct
performed_by 0..1
Organization		 The organization or group that performed the observation activity direct
id 1..1
Uriorcurie		 The 'logical' identifier of the entity within the system of record Entity

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ObservationSet
description: A structured object to hold related Observations in a set.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
slots:
- observations
attributes:
  category:
    name: category
    description: The general category of observation set described
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_ObservationSet_category
    multivalued: false
    range: string
    required: false
  focus:
    name: focus
    description: The entity or entities directly observed/measured in generating an
      observation result.
    comments:
    - The "focus", and "associated_participant" 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 an entity, where focus, subject, and specimen can be determined from context.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: true
    range: Entity
    required: false
    inlined: true
    inlined_as_list: true
  associated_participant:
    name: associated_participant
    description: The Participant that the observation is about (if not the direct
      focus).  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
    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
    range: Visit
  method_type:
    name: method_type
    description: The type of method used in generating the ObservationSet
    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_ObservationSet_method_type
    multivalued: true
    range: string
    required: false
  performed_by:
    name: performed_by
    description: The organization or group that performed the observation activity.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: false
    range: Organization
    required: false

Induced

name: ObservationSet
description: A structured object to hold related Observations in a set.
from_schema: https://w3id.org/nhlbidatastage/bdchm
is_a: Entity
attributes:
  category:
    name: category
    description: The general category of observation set described
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    values_from:
    - crdch:enum_CRDCH_ObservationSet_category
    multivalued: false
    alias: category
    owner: ObservationSet
    domain_of:
    - 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", and "associated_participant" 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 an entity, where focus, subject, and specimen can be determined from context.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    multivalued: true
    alias: focus
    owner: ObservationSet
    domain_of:
    - Document
    - ObservationSet
    - Observation
    range: Entity
    required: false
    inlined: true
    inlined_as_list: true
  associated_participant:
    name: associated_participant
    description: The Participant that the observation is about (if not the direct
      focus).  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: ObservationSet
    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: ObservationSet
    domain_of:
    - QuestionnaireResponse
    - Condition
    - Procedure
    - Exposure
    - ObservationSet
    - Observation
    range: Visit
  method_type:
    name: method_type
    description: The type of method used in generating the ObservationSet
    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_ObservationSet_method_type
    multivalued: true
    alias: method_type
    owner: ObservationSet
    domain_of:
    - SpecimenProcessingActivity
    - SpecimenStorageActivity
    - ObservationSet
    - Observation
    range: string
    required: false
  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: ObservationSet
    domain_of:
    - SpecimenCreationActivity
    - ObservationSet
    - Observation
    range: Organization
    required: false
  observations:
    name: observations
    description: A set of one or more observations.
    from_schema: https://w3id.org/nhlbidatastage/bdchm
    rank: 1000
    multivalued: true
    alias: observations
    owner: ObservationSet
    domain_of:
    - ObservationSet
    range: Observation
  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: ObservationSet
    domain_of:
    - Entity
    range: uriorcurie
    required: true