Class: Subtype

URI: dismech:class/Subtype

 classDiagram
    class Subtype
    click Subtype href "../../classes/Subtype/"
      Subtype <|-- AgentSubtype
        click AgentSubtype href "../../classes/AgentSubtype/"

      Subtype : children

      Subtype : classification

      Subtype : curated_in

      Subtype : description

      Subtype : display_name

      Subtype : evidence





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



      Subtype : genes





        Subtype --> "*" GeneDescriptor : genes
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      Subtype : geography





        Subtype --> "*" GeographyTerm : geography
        click GeographyTerm href "../../enums/GeographyTerm/"



      Subtype : inheritance





        Subtype --> "*" Inheritance : inheritance
        click Inheritance href "../../classes/Inheritance/"



      Subtype : locations





        Subtype --> "*" AnatomicalEntityDescriptor : locations
        click AnatomicalEntityDescriptor href "../../classes/AnatomicalEntityDescriptor/"



      Subtype : mappings





        Subtype --> "0..1" DiseaseMappings : mappings
        click DiseaseMappings href "../../classes/DiseaseMappings/"



      Subtype : name

      Subtype : review_notes

      Subtype : subtype_frequency

      Subtype : subtype_term





        Subtype --> "0..1" SubtypeDescriptor : subtype_term
        click SubtypeDescriptor href "../../classes/SubtypeDescriptor/"

Inheritance

Subtype
- AgentSubtype

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 String		direct
display_name	0..1 String	Human-readable display name for a subtype, used when the name (which serves a...	direct
subtype_term	0..1 SubtypeDescriptor	The ontology term grounding this subtype or cancer facet value	direct
mappings	0..1 DiseaseMappings	External identifier mappings for this disease or subtype (SSSOM-inspired)	direct
description	0..1 String		direct
evidence	* recommended EvidenceItem		direct
review_notes	0..1 String		direct
locations	* AnatomicalEntityDescriptor		direct
geography	* GeographyTerm		direct
classification	0..1 String	Classification scheme this subtype belongs to (e	direct
curated_in	0..1 String	File stem of the `kb/disorders/` entry in which this subtype is curated in fu...	direct
children	* String	Names of other subtypes in this list that are members/children of this groupi...	direct
genes	* GeneDescriptor		direct
subtype_frequency	0..1 FrequencyEnum or FrequencyQuantity or String	Frequency of this subtype among all cases of the parent disease (e	direct
inheritance	* Inheritance		direct

Usages

used by	used in	type	used
Disease	has_subtypes	range	Subtype

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Subtype
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- display_name
- subtype_term
- mappings
- description
- evidence
- review_notes
- locations
- geography
- classification
- curated_in
- children
- genes
- subtype_frequency
- inheritance

Induced

name: Subtype
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Subtype
    domain_of:
    - GenomicRegion
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    - Grouping
    - ModuleCollection
    range: string
    required: true
  display_name:
    name: display_name
    description: Human-readable display name for a subtype, used when the name (which
      serves as the FK target) is too terse for comfortable display. Optional; when
      absent, renderers should fall back to name.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: display_name
    owner: Subtype
    domain_of:
    - Subtype
    - Grouping
    - GroupingMember
    - ModuleCollection
    range: string
  subtype_term:
    name: subtype_term
    description: The ontology term grounding this subtype or cancer facet value. Prefer
      MONDO when available; use NCIT for oncology-specific subtype refinement when
      needed.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype_term
    owner: Subtype
    domain_of:
    - Subtype
    range: SubtypeDescriptor
    inlined: true
  mappings:
    name: mappings
    description: External identifier mappings for this disease or subtype (SSSOM-inspired)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mappings
    owner: Subtype
    domain_of:
    - Subtype
    - Disease
    - Grouping
    range: DiseaseMappings
    inlined: true
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Subtype
    domain_of:
    - Descriptor
    - DietaryModification
    - GenomicRegion
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Subtype
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: Subtype
    domain_of:
    - ClinicalTrial
    - Subtype
    - ProgressionInfo
    - Pathophysiology
    - Phenotype
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  locations:
    name: locations
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: locations
    owner: Subtype
    domain_of:
    - Subtype
    - Pathophysiology
    range: AnatomicalEntityDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  geography:
    name: geography
    examples:
    - value: '[''Philippines'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: geography
    owner: Subtype
    domain_of:
    - Subtype
    range: GeographyTerm
    multivalued: true
  classification:
    name: classification
    description: Classification scheme this subtype belongs to (e.g., 'complementation_group',
      'pathway_tier', 'histological', 'molecular', 'clinical_phenotype').
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: classification
    owner: Subtype
    domain_of:
    - Subtype
    - LogicalCriterion
    range: string
  curated_in:
    name: curated_in
    description: File stem of the `kb/disorders/` entry in which this subtype is curated
      in full (`Rocky_Mountain_Spotted_Fever`), when the stratum has been promoted
      to its own Disease entry -- the *pointer* subtype of design decisions §3a (L4)
      and §3e (rung 4). The parent keeps the row so the stratum stays discoverable
      and other sections can still scope to it, but the mechanism, phenotype and treatment
      content lives in the named entry, and a consumer counting diseases should not
      count the pointer. The value is the same identifier a cross-file entity reference
      uses and must resolve to an existing file; `just check-granularity` reports
      a dangling pointer and, where both are bound, a `subtype_term` that disagrees
      with the target's `disease_term`. Omit on a subtype curated here.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: curated_in
    owner: Subtype
    domain_of:
    - Subtype
    range: string
  children:
    name: children
    description: Names of other subtypes in this list that are members/children of
      this grouping subtype. Used to express cross-scheme relationships (e.g., a pathway_tier
      subtype grouping complementation_group subtypes).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: children
    owner: Subtype
    domain_of:
    - Subtype
    range: string
    multivalued: true
  genes:
    name: genes
    examples:
    - value: '[{preferred_term: HLA-DQ2}, {preferred_term: INS}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genes
    owner: Subtype
    domain_of:
    - GeneticContext
    - Dataset
    - ExperimentalPerturbation
    - Subtype
    - GeneClassificationCollection
    - Pathophysiology
    - AnimalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  subtype_frequency:
    name: subtype_frequency
    description: Frequency of this subtype among all cases of the parent disease (e.g.,
      '60-70%', '~15%'). Distinct from phenotype frequency.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype_frequency
    owner: Subtype
    domain_of:
    - Subtype
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  inheritance:
    name: inheritance
    examples:
    - value: Autosomal Dominant
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: inheritance
    owner: Subtype
    domain_of:
    - Subtype
    - Genetic
    - Disease
    range: Inheritance
    multivalued: true
    inlined: true
    inlined_as_list: true