Class: Phenotype

URI: dismech:class/Phenotype

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

      Phenotype : context

      Phenotype : description

      Phenotype : diagnostic

      Phenotype : electrophysiology





        Phenotype --> "0..1" ElectrophysiologyContext : electrophysiology
        click ElectrophysiologyContext href "../../classes/ElectrophysiologyContext/"



      Phenotype : evidence





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



      Phenotype : frequency





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



      Phenotype : name

      Phenotype : notes

      Phenotype : phenotype_contexts





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



      Phenotype : phenotype_term





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



      Phenotype : reports_on





        Phenotype --> "*" PhenotypeReadout : reports_on
        click PhenotypeReadout href "../../classes/PhenotypeReadout/"



      Phenotype : review_notes

      Phenotype : sequelae





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



      Phenotype : severity





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



      Phenotype : subtype

      Phenotype : subtypes

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 FrequencyEnum or FrequencyQuantity or Any		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 or Any or SeverityQualifierEnum		direct
notes	0..1 String		direct
subtype	0..1 String		direct
subtypes	* String	Names of subtypes (foreign keys to this disease's `has_subtypes[]	direct
phenotype_contexts	* PhenotypeContext	Context-specific qualifications of this phenotype's frequency, severity, or o...	direct
electrophysiology	0..1 ElectrophysiologyContext	Optional electrophysiologic post-composition sidecar for a phenotype whose ph...	direct
reports_on	* PhenotypeReadout	Links an investigation-readout phenotype (e	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
- subtypes
- phenotype_contexts
- electrophysiology
- reports_on

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:
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    - Grouping
    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:
    - ExperimentalReadout
    - ReferenceRangeBand
    - Phenotype
    - ImagingFinding
    - LogicalCriterion
    - DifferentiatingMechanism
    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
    - ImagingFinding
    - 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
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    range: string
  diagnostic:
    name: diagnostic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: diagnostic
    owner: Phenotype
    domain_of:
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    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
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    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
    - ImagingFinding
    - 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:
    - Descriptor
    - PhenotypeContext
    - ReferenceRangeBand
    - Phenotype
    range: Any
    any_of:
    - range: SeverityQualifierEnum
    - 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
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    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
    - ImagingFinding
    - Genetic
    range: string
  subtypes:
    name: subtypes
    description: Names of subtypes (foreign keys to this disease's `has_subtypes[].name`)
      associated with a phenotype, biochemical finding, pathophysiology node, or other
      subtyped entry. Use this multivalued form when an item is characteristic of
      more than one subtype with overlapping features. For single-subtype associations,
      the scalar `subtype` slot may still be used.
    examples:
    - value: '[''DENV-1'', ''DENV-2'', ''DENV-3'', ''DENV-4'']'
    - value: '[''Type 1'', ''Type 2'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtypes
    owner: Phenotype
    domain_of:
    - Pathophysiology
    - Phenotype
    - Biochemical
    range: string
    multivalued: true
  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
  electrophysiology:
    name: electrophysiology
    description: Optional electrophysiologic post-composition sidecar for a phenotype
      whose phenotype_term is an EEG/EMG/EKG finding (HP:0002353 / HP:0003457 / HP:0003115
      subtrees). Carries modality plus the ictal and recording-state axes a flat HP
      term cannot express. Electrophysiologic findings are HP phenotypes, so they
      stay in `phenotypes`; this only post-composes them.
    comments:
    - Use on EEG/EMG/EKG phenotypes; leave absent otherwise
    - Not for acquisition protocol, per-patient tracings, or decision support
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: electrophysiology
    owner: Phenotype
    domain_of:
    - Phenotype
    range: ElectrophysiologyContext
    inlined: true
  reports_on:
    name: reports_on
    description: Links an investigation-readout phenotype (e.g. an abnormal electrophysiology
      or clinical-test finding such as HP:0000512 Abnormal electroretinogram) to the
      pathograph node whose underlying state it measures or reflects. The target is
      a named pathophysiology or phenotype node in the same disease file. These are
      observational readout links, not causal disease-progression edges, so they let
      an otherwise-disconnected test-result phenotype attach to the mechanism it reports
      on without asserting that the mechanism "causes" the test result.
    comments:
    - Use on investigation/test-result phenotypes (electrophysiology, functional testing,
      laboratory findings) that report on an underlying mechanism rather than participating
      causally
    - Target names should match a pathophysiology or phenotype entry name in the same
      disease file
    - Rendered as a dashed observational edge (mechanism -.-> readout), like biomarker
      readouts
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: reports_on
    owner: Phenotype
    domain_of:
    - Phenotype
    range: PhenotypeReadout
    multivalued: true
    inlined: true
    inlined_as_list: true