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Class: Phenotype

URI: dismech:Phenotype

 classDiagram
    class Phenotype
    click Phenotype href "../Phenotype/"
      Phenotype : category

      Phenotype : context

      Phenotype : description

      Phenotype : diagnostic

      Phenotype : evidence





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



      Phenotype : frequency





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



      Phenotype : name

      Phenotype : notes

      Phenotype : phenotype_contexts





        Phenotype --> "*" PhenotypeContext : phenotype_contexts
        click PhenotypeContext href "../PhenotypeContext/"



      Phenotype : phenotype_term





        Phenotype --> "0..1" PhenotypeDescriptor : phenotype_term
        click PhenotypeDescriptor href "../PhenotypeDescriptor/"



      Phenotype : review_notes

      Phenotype : sequelae





        Phenotype --> "*" CausalEdge : sequelae
        click CausalEdge href "../CausalEdge/"



      Phenotype : severity

      Phenotype : subtype

Slots

Name Cardinality and Range Description Inheritance
category 0..1
String		 direct
name 1
String		 direct
phenotype_term 0..1
PhenotypeDescriptor		 The HP term for this phenotype direct
frequency 0..1
Any or 
FrequencyEnum or 
FrequencyQuantity		 direct
description 0..1
String		 direct
diagnostic 0..1
Boolean		 direct
sequelae *
CausalEdge		 direct
evidence * recommended
EvidenceItem		 direct
context 0..1
String		 direct
review_notes 0..1
String		 direct
severity 0..1
String		 direct
notes 0..1
String		 direct
subtype 0..1
String		 direct
phenotype_contexts *
PhenotypeContext		 Context-specific qualifications of this phenotype's frequency, severity, or o... direct

Usages

used by used in type used
DifferentialDiagnosis phenotypes range Phenotype
Disease phenotypes range Phenotype
ComorbidityAssociation phenotypes range Phenotype

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Phenotype
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- category
- name
- phenotype_term
- frequency
- description
- diagnostic
- sequelae
- evidence
- context
- review_notes
- severity
- notes
- subtype
- phenotype_contexts

Induced

name: Phenotype
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  category:
    name: category
    examples:
    - value: Hematologic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: category
    owner: Phenotype
    domain_of:
    - Phenotype
    - Disease
    - AnimalModel
    range: string
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Phenotype
    domain_of:
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    range: string
    required: true
  phenotype_term:
    name: phenotype_term
    description: The HP term for this phenotype
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: phenotype_term
    owner: Phenotype
    domain_of:
    - Phenotype
    range: PhenotypeDescriptor
    inlined: true
  frequency:
    name: frequency
    examples:
    - value: Occasional
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: frequency
    owner: Phenotype
    domain_of:
    - PhenotypeContext
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Phenotype
    domain_of:
    - Descriptor
    - GeneticContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: string
  diagnostic:
    name: diagnostic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: diagnostic
    owner: Phenotype
    domain_of:
    - Phenotype
    - HistopathologyFinding
    range: boolean
  sequelae:
    name: sequelae
    examples:
    - value: '[{target: Diabetic Ketoacidosis}, {target: Chronic Complications}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: sequelae
    owner: Phenotype
    domain_of:
    - Phenotype
    range: CausalEdge
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Phenotype
    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
  context:
    name: context
    examples:
    - value: Pregnancy
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: context
    owner: Phenotype
    domain_of:
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  review_notes:
    name: review_notes
    examples:
    - value: Added an additional clinically relevant subtype.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: review_notes
    owner: Phenotype
    domain_of:
    - ClinicalTrial
    - Subtype
    - ProgressionInfo
    - Phenotype
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  severity:
    name: severity
    examples:
    - value: Severe
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: severity
    owner: Phenotype
    domain_of:
    - PhenotypeContext
    - Phenotype
    range: string
  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: Phenotype
    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
  subtype:
    name: subtype
    examples:
    - value: Eyelid Myoclonia with Absences
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype
    owner: Phenotype
    domain_of:
    - PhenotypeContext
    - Prevalence
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: string
  phenotype_contexts:
    name: phenotype_contexts
    description: Context-specific qualifications of this phenotype's frequency, severity,
      or onset. Each context can optionally specify a genetic context, demographic
      stratum, or disease subtype. When no context qualifiers are set, provides evidence
      for the base frequency/severity claim (addressing the frequency-evidence separation
      problem).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: phenotype_contexts
    owner: Phenotype
    domain_of:
    - Phenotype
    range: PhenotypeContext
    multivalued: true
    inlined: true
    inlined_as_list: true