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Class: PhenotypeContext

A context-specific annotation qualifying how a phenotype manifests under particular conditions. Each context can specify a genetic context, demographic stratum, or disease subtype, along with frequency, severity, onset, and supporting evidence specific to that context.

When no context qualifier slots are set (no genetic_context, sex, population, age_range, or subtype), the context provides evidence for the overall/default frequency claim, addressing the evidence separation problem (issue #112).

URI: dismech:PhenotypeContext

 classDiagram
    class PhenotypeContext
    click PhenotypeContext href "../PhenotypeContext/"
      PhenotypeContext : age_range

      PhenotypeContext : evidence





        PhenotypeContext --> "*" EvidenceItem : evidence
        click EvidenceItem href "../EvidenceItem/"



      PhenotypeContext : frequency





        PhenotypeContext --> "0..1" Any : frequency
        click Any href "../Any/"



      PhenotypeContext : genetic_context





        PhenotypeContext --> "0..1" GeneticContext : genetic_context
        click GeneticContext href "../GeneticContext/"



      PhenotypeContext : notes

      PhenotypeContext : onset





        PhenotypeContext --> "0..1" OnsetDescriptor : onset
        click OnsetDescriptor href "../OnsetDescriptor/"



      PhenotypeContext : population

      PhenotypeContext : severity

      PhenotypeContext : sex





        PhenotypeContext --> "0..1" SexEnum : sex
        click SexEnum href "../SexEnum/"



      PhenotypeContext : subtype

Slots

Name Cardinality and Range Description Inheritance
frequency 0..1
Any or 
FrequencyEnum or 
FrequencyQuantity		 direct
severity 0..1
String		 direct
onset 0..1
OnsetDescriptor		 Structured age of onset descriptor direct
notes 0..1
String		 direct
evidence * recommended
EvidenceItem		 Evidence supporting the frequency, severity, or onset claims made in this spe... direct
genetic_context 0..1
GeneticContext		 The genetic context under which this qualification applies direct
sex 0..1
SexEnum		 Sex-specific stratum, if applicable direct
population 0..1
String		 Population or cohort description (e direct
age_range 0..1
String		 Age range or stratification, if applicable direct
subtype 0..1
String		 direct

Usages

used by used in type used
Phenotype phenotype_contexts range PhenotypeContext

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type Mapped Value
self dismech:PhenotypeContext
native dismech:PhenotypeContext

LinkML Source

Direct

name: PhenotypeContext
description: 'A context-specific annotation qualifying how a phenotype manifests under
  particular conditions. Each context can specify a genetic context, demographic stratum,
  or disease subtype, along with frequency, severity, onset, and supporting evidence
  specific to that context.

  When no context qualifier slots are set (no genetic_context, sex, population, age_range,
  or subtype), the context provides evidence for the overall/default frequency claim,
  addressing the evidence separation problem (issue #112).'
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- frequency
- severity
- onset
- notes
- evidence
- genetic_context
- sex
- population
- age_range
- subtype
slot_usage:
  sex:
    name: sex
    range: SexEnum
  evidence:
    name: evidence
    description: Evidence supporting the frequency, severity, or onset claims made
      in this specific context. Distinct from the D2P evidence on the parent Phenotype.

Induced

name: PhenotypeContext
description: 'A context-specific annotation qualifying how a phenotype manifests under
  particular conditions. Each context can specify a genetic context, demographic stratum,
  or disease subtype, along with frequency, severity, onset, and supporting evidence
  specific to that context.

  When no context qualifier slots are set (no genetic_context, sex, population, age_range,
  or subtype), the context provides evidence for the overall/default frequency claim,
  addressing the evidence separation problem (issue #112).'
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  sex:
    name: sex
    range: SexEnum
  evidence:
    name: evidence
    description: Evidence supporting the frequency, severity, or onset claims made
      in this specific context. Distinct from the D2P evidence on the parent Phenotype.
attributes:
  frequency:
    name: frequency
    examples:
    - value: Occasional
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: frequency
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  severity:
    name: severity
    examples:
    - value: Severe
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: severity
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - Phenotype
    range: string
  onset:
    name: onset
    description: Structured age of onset descriptor. Combines an HPO onset category
      with optional quantitative age data (mean, min, max in years) and free-text
      notes.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: onset
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    range: OnsetDescriptor
    inlined: true
  notes:
    name: notes
    examples:
    - value: Contagious stage where symptoms appear and the bacteria can be spread
        to others.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: notes
    owner: PhenotypeContext
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    range: string
  evidence:
    name: evidence
    description: Evidence supporting the frequency, severity, or onset claims made
      in this specific context. Distinct from the D2P evidence on the parent Phenotype.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - Finding
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  genetic_context:
    name: genetic_context
    description: The genetic context under which this qualification applies. May specify
      genes, mutation types, zygosity, complementation groups, or complex genotypes.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genetic_context
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    range: GeneticContext
    inlined: true
  sex:
    name: sex
    description: Sex-specific stratum, if applicable
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: sex
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - Demographics
    range: SexEnum
  population:
    name: population
    description: Population or cohort description (e.g., for prevalence or association
      signals)
    examples:
    - value: Global
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: population
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - Prevalence
    - AssociationSignal
    range: string
  age_range:
    name: age_range
    description: Age range or stratification, if applicable
    examples:
    - value: Childhood-Adolescence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: age_range
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - ProgressionInfo
    - Demographics
    range: string
  subtype:
    name: subtype
    examples:
    - value: Eyelid Myoclonia with Absences
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype
    owner: PhenotypeContext
    domain_of:
    - PhenotypeContext
    - Prevalence
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: string