Class: PhenotypicFeature

An individual phenotypic feature, observed as either present or absent (negated), with possible onset, modifiers and frequency FHIR mapping: Condition (https://www.hl7.org/fhir/condition.html) or Observation (https://www.hl7.org/fhir/observation.html)

URI: phenopackets:PhenotypicFeature

erDiagram PhenotypicFeature { string description boolean excluded } OntologyClass { string id string label } TimeElement { string timestamp } TimeInterval { string end string start } GestationalAge { integer days integer weeks } AgeRange { } Age { string iso8601duration } Evidence { } ExternalReference { string description string id string reference } PhenotypicFeature ||--}o Evidence : "evidence" PhenotypicFeature ||--}o OntologyClass : "modifiers" PhenotypicFeature ||--|o TimeElement : "onset" PhenotypicFeature ||--|o TimeElement : "resolution" PhenotypicFeature ||--|o OntologyClass : "severity" PhenotypicFeature ||--|o OntologyClass : "type" 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" Evidence ||--|o OntologyClass : "evidenceCode" Evidence ||--|o ExternalReference : "reference"

Slots

Name	Cardinality and Range	Description	Inheritance
description	0..1 String	Free-text description of the phenotype	direct
evidence	0..* Evidence	Evidences for how the phenotype was determined	direct
excluded	0..1 Boolean	Flag to indicate whether the phenotype was observed or not	direct
modifiers	0..* OntologyClass	subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 -...	direct
onset	0..1 TimeElement	the values of this will come from the HPO onset hierarchy i	direct
resolution	0..1 TimeElement		direct
severity	0..1 OntologyClass	Severity of the condition e	direct
type	0..1 OntologyClass	The primary ontology class which describes the phenotype	direct

Usages

used by	used in	type	used
Phenopacket	phenotypicFeatures	range	PhenotypicFeature
Biosample	phenotypicFeatures	range	PhenotypicFeature

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: PhenotypicFeature
description: 'An individual phenotypic feature, observed as either present or absent
  (negated), with possible onset, modifiers and frequency FHIR mapping: Condition
  (https://www.hl7.org/fhir/condition.html) or Observation (https://www.hl7.org/fhir/observation.html)'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 1
    description: Free-text description of the phenotype. 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
  evidence:
    name: evidence
    annotations:
      rank:
        tag: rank
        value: 8
    description: Evidences for how the phenotype was determined.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - PhenotypicFeature
    range: Evidence
  excluded:
    name: excluded
    annotations:
      rank:
        tag: rank
        value: 3
    description: Flag to indicate whether the phenotype was observed or not. Default
      is 'false', in other words the phenotype was observed. Therefore it is only
      required in cases to indicate that the phenotype was looked for, but found to
      be absent. More formally, this modifier indicates the logical negation of the
      OntologyClass used in the 'type' field. *CAUTION* It is imperative to check
      this field for correct interpretation of the phenotype!
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - PhenotypicFeature
    - Disease
    range: boolean
  modifiers:
    name: modifiers
    annotations:
      rank:
        tag: rank
        value: 5
    description: subclasses of HP:0012823 ! Clinical modifier apart from Severity
      HP:0012824 - Severity
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - PhenotypicFeature
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  onset:
    name: onset
    annotations:
      rank:
        tag: rank
        value: 6
    description: 'the values of this will come from the HPO onset hierarchy i.e. subclasses
      of HP:0003674 FHIR mapping: Condition.onset'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  resolution:
    name: resolution
    annotations:
      rank:
        tag: rank
        value: 7
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  severity:
    name: severity
    annotations:
      rank:
        tag: rank
        value: 4
    description: 'Severity of the condition e.g. subclasses of HP:0012824-Severity
      or SNOMED:272141005-Severities FHIR mapping: Condition.severity'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - PhenotypicFeature
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  type:
    name: type
    annotations:
      rank:
        tag: rank
        value: 2
    description: 'The primary ontology class which describes the phenotype. For example
      "HP:0001363"  "Craniosynostosis" FHIR mapping: Condition.identifier'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - TypedQuantity
    - PhenotypicFeature
    range: OntologyClass
    inlined: true
    inlined_as_list: true

Induced

name: PhenotypicFeature
description: 'An individual phenotypic feature, observed as either present or absent
  (negated), with possible onset, modifiers and frequency FHIR mapping: Condition
  (https://www.hl7.org/fhir/condition.html) or Observation (https://www.hl7.org/fhir/observation.html)'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 1
    description: Free-text description of the phenotype. 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: PhenotypicFeature
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  evidence:
    name: evidence
    annotations:
      rank:
        tag: rank
        value: 8
    description: Evidences for how the phenotype was determined.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: evidence
    owner: PhenotypicFeature
    domain_of:
    - PhenotypicFeature
    range: Evidence
  excluded:
    name: excluded
    annotations:
      rank:
        tag: rank
        value: 3
    description: Flag to indicate whether the phenotype was observed or not. Default
      is 'false', in other words the phenotype was observed. Therefore it is only
      required in cases to indicate that the phenotype was looked for, but found to
      be absent. More formally, this modifier indicates the logical negation of the
      OntologyClass used in the 'type' field. *CAUTION* It is imperative to check
      this field for correct interpretation of the phenotype!
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: excluded
    owner: PhenotypicFeature
    domain_of:
    - PhenotypicFeature
    - Disease
    range: boolean
  modifiers:
    name: modifiers
    annotations:
      rank:
        tag: rank
        value: 5
    description: subclasses of HP:0012823 ! Clinical modifier apart from Severity
      HP:0012824 - Severity
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: modifiers
    owner: PhenotypicFeature
    domain_of:
    - PhenotypicFeature
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  onset:
    name: onset
    annotations:
      rank:
        tag: rank
        value: 6
    description: 'the values of this will come from the HPO onset hierarchy i.e. subclasses
      of HP:0003674 FHIR mapping: Condition.onset'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: onset
    owner: PhenotypicFeature
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  resolution:
    name: resolution
    annotations:
      rank:
        tag: rank
        value: 7
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: resolution
    owner: PhenotypicFeature
    domain_of:
    - PhenotypicFeature
    - Disease
    range: TimeElement
    inlined: true
    inlined_as_list: true
  severity:
    name: severity
    annotations:
      rank:
        tag: rank
        value: 4
    description: 'Severity of the condition e.g. subclasses of HP:0012824-Severity
      or SNOMED:272141005-Severities FHIR mapping: Condition.severity'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: severity
    owner: PhenotypicFeature
    domain_of:
    - PhenotypicFeature
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  type:
    name: type
    annotations:
      rank:
        tag: rank
        value: 2
    description: 'The primary ontology class which describes the phenotype. For example
      "HP:0001363"  "Craniosynostosis" FHIR mapping: Condition.identifier'
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: type
    owner: PhenotypicFeature
    domain_of:
    - TypedQuantity
    - PhenotypicFeature
    range: OntologyClass
    inlined: true
    inlined_as_list: true