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Class: Subtype

URI: dismech:class/Subtype

 classDiagram
    class Subtype
    click Subtype href "../../classes/Subtype/"
      Subtype : children

      Subtype : classification

      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/"

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
children *
String		 Names of other subtypes in this list that are members/children of this groupi... direct
genes *
GeneDescriptor		 direct
subtype_frequency 0..1
String or 
FrequencyEnum or 
FrequencyQuantity		 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
InfectiousAgent 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
- 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:
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ExternalAssertion
    - 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
  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
    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
    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
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ProteinStructure
    - ExternalAssertion
    - 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
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Subtype
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ExternalAssertion
    - 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
  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
    - 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
    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
    - Subtype
    - 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