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Class: Measurement

FHIR mapping: Observation (https://www.hl7.org/fhir/observation.html)

URI: phenopackets:Measurement

erDiagram Measurement { string description } Value { } Quantity { double value } OntologyClass { string id string label } TimeElement { string timestamp } TimeInterval { string end string start } GestationalAge { integer days integer weeks } AgeRange { } Age { string iso8601duration } Procedure { } ComplexValue { } TypedQuantity { } Measurement ||--|o OntologyClass : "assay" Measurement ||--|o ComplexValue : "complexValue" Measurement ||--|o Procedure : "procedure" Measurement ||--|o TimeElement : "timeObserved" Measurement ||--|o Value : "value" Value ||--|o OntologyClass : "ontologyClass" Value ||--|o Quantity : "quantity" Quantity ||--|o ReferenceRange : "referenceRange" Quantity ||--|o OntologyClass : "unit" TimeElement ||--|o Age : "age" TimeElement ||--|o AgeRange : "ageRange" TimeElement ||--|o GestationalAge : "gestationalAge" TimeElement ||--|o TimeInterval : "interval" TimeElement ||--|o OntologyClass : "ontologyClass" AgeRange ||--|o Age : "end" AgeRange ||--|o Age : "start" Procedure ||--|o OntologyClass : "bodySite" Procedure ||--|o OntologyClass : "code" Procedure ||--|o TimeElement : "performed" ComplexValue ||--}o TypedQuantity : "typedQuantities" TypedQuantity ||--|o Quantity : "quantity" TypedQuantity ||--|o OntologyClass : "type"

Slots

Name Cardinality and Range Description Inheritance
assay 0..1
OntologyClass		 An ontology class which describes the assay used to produce the measurement direct
complexValue 0..1
ComplexValue		 direct
description 0..1
String		 Free-text description of the feature direct
procedure 0..1
Procedure		 Clinical procedure performed on the subject in order to produce the measureme... direct
timeObserved 0..1
TimeElement		 The time at which the measurement was made direct
value 0..1
Value		 direct

Usages

used by used in type used
Phenopacket measurements range Measurement
Biosample measurements range Measurement

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type Mapped Value
self phenopackets:Measurement
native phenopackets:Measurement

LinkML Source

Direct

name: Measurement
description: 'FHIR mapping: Observation (https://www.hl7.org/fhir/observation.html)'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  assay:
    name: assay
    annotations:
      rank:
        tag: rank
        value: 2
    description: 'An ontology class which describes the assay used to produce the
      measurement. For example "body temperature" (CMO:0000015) or "Platelets [#/volume]
      in Blood" (LOINC:26515-7) FHIR mapping: Observation.code'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Measurement
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  complexValue:
    name: complexValue
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Measurement
    range: ComplexValue
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 1
    description: Free-text description of the feature. Note this is not a acceptable
      place to document/describe the phenotype - the type and onset etc... fields
      should be used for this purpose.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  procedure:
    name: procedure
    annotations:
      rank:
        tag: rank
        value: 6
    description: Clinical procedure performed on the subject in order to produce the
      measurement.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Measurement
    - Biosample
    - MedicalAction
    range: Procedure
  timeObserved:
    name: timeObserved
    annotations:
      rank:
        tag: rank
        value: 5
    description: The time at which the measurement was made
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Measurement
    range: TimeElement
    inlined: true
    inlined_as_list: true
  value:
    name: value
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Measurement
    - Quantity
    - Any
    - IndefiniteRange
    - Number
    - Expression
    - Extension
    range: Value
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        value:
          name: value
          required: true
    - slot_conditions:
        complexValue:
          name: complexValue
          required: true

Induced

name: Measurement
description: 'FHIR mapping: Observation (https://www.hl7.org/fhir/observation.html)'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  assay:
    name: assay
    annotations:
      rank:
        tag: rank
        value: 2
    description: 'An ontology class which describes the assay used to produce the
      measurement. For example "body temperature" (CMO:0000015) or "Platelets [#/volume]
      in Blood" (LOINC:26515-7) FHIR mapping: Observation.code'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: assay
    owner: Measurement
    domain_of:
    - Measurement
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  complexValue:
    name: complexValue
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: complexValue
    owner: Measurement
    domain_of:
    - Measurement
    range: ComplexValue
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 1
    description: Free-text description of the feature. Note this is not a acceptable
      place to document/describe the phenotype - the type and onset etc... fields
      should be used for this purpose.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: description
    owner: Measurement
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  procedure:
    name: procedure
    annotations:
      rank:
        tag: rank
        value: 6
    description: Clinical procedure performed on the subject in order to produce the
      measurement.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: procedure
    owner: Measurement
    domain_of:
    - Measurement
    - Biosample
    - MedicalAction
    range: Procedure
  timeObserved:
    name: timeObserved
    annotations:
      rank:
        tag: rank
        value: 5
    description: The time at which the measurement was made
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: timeObserved
    owner: Measurement
    domain_of:
    - Measurement
    range: TimeElement
    inlined: true
    inlined_as_list: true
  value:
    name: value
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: value
    owner: Measurement
    domain_of:
    - Measurement
    - Quantity
    - Any
    - IndefiniteRange
    - Number
    - Expression
    - Extension
    range: Value
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        value:
          name: value
          required: true
    - slot_conditions:
        complexValue:
          name: complexValue
          required: true