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Class: AgentSubtype

A taxonomic stratum below a named infectious agent: a subspecies, serovar, serotype, or biotype of the organism named by the parent InfectiousAgent.

Identical to Subtype except that subtype_term binds NCBITaxon rather than MONDO/NCIT, because the thing being grounded is an organism rather than a disease. Splitting it out is what lets an agent stratum be grounded at all: the disease-level binding is rooted at MONDO:0000001 and NCIT:C2991, so a serovar or biotype nested under an agent was previously forced to remain name-only free text.

URI: dismech:class/AgentSubtype

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

      AgentSubtype : children

      AgentSubtype : classification

      AgentSubtype : curated_in

      AgentSubtype : description

      AgentSubtype : display_name

      AgentSubtype : evidence





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



      AgentSubtype : genes





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



      AgentSubtype : geography





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



      AgentSubtype : inheritance





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



      AgentSubtype : locations





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



      AgentSubtype : mappings





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



      AgentSubtype : name

      AgentSubtype : review_notes

      AgentSubtype : subtype_frequency

      AgentSubtype : subtype_term





        AgentSubtype --> "0..1" AgentSubtypeDescriptor : subtype_term
        click AgentSubtypeDescriptor href "../../classes/AgentSubtypeDescriptor/"

Inheritance

Slots

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

Usages

used by used in type used
InfectiousAgent has_subtypes range AgentSubtype

Comments

  • This class carries the organism axis only. A stratum that needs to be referenced by a phenotype, treatment, prevalence or progression record must instead be a disease-level has_subtypes entry, because the subtype foreign key resolves against the disease-level list alone.
  • inheritance and genes are inherited from Subtype and describe human genetics. They do not apply to an agent stratum; leave them unset.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: AgentSubtype
description: 'A taxonomic stratum below a named infectious agent: a subspecies, serovar,
  serotype, or biotype of the organism named by the parent InfectiousAgent.

  Identical to Subtype except that subtype_term binds NCBITaxon rather than MONDO/NCIT,
  because the thing being grounded is an organism rather than a disease. Splitting
  it out is what lets an agent stratum be grounded at all: the disease-level binding
  is rooted at MONDO:0000001 and NCIT:C2991, so a serovar or biotype nested under
  an agent was previously forced to remain name-only free text.'
comments:
- This class carries the organism axis only. A stratum that needs to be referenced
  by a phenotype, treatment, prevalence or progression record must instead be a disease-level
  has_subtypes entry, because the subtype foreign key resolves against the disease-level
  list alone.
- inheritance and genes are inherited from Subtype and describe human genetics. They
  do not apply to an agent stratum; leave them unset.
from_schema: https://w3id.org/monarch-initiative/dismech
is_a: Subtype
slot_usage:
  subtype_term:
    name: subtype_term
    description: The NCBITaxon term grounding this agent stratum. Omit it rather than
      binding the parent species when NCBITaxon carries no node at this rank.
    range: AgentSubtypeDescriptor

Induced

name: AgentSubtype
description: 'A taxonomic stratum below a named infectious agent: a subspecies, serovar,
  serotype, or biotype of the organism named by the parent InfectiousAgent.

  Identical to Subtype except that subtype_term binds NCBITaxon rather than MONDO/NCIT,
  because the thing being grounded is an organism rather than a disease. Splitting
  it out is what lets an agent stratum be grounded at all: the disease-level binding
  is rooted at MONDO:0000001 and NCIT:C2991, so a serovar or biotype nested under
  an agent was previously forced to remain name-only free text.'
comments:
- This class carries the organism axis only. A stratum that needs to be referenced
  by a phenotype, treatment, prevalence or progression record must instead be a disease-level
  has_subtypes entry, because the subtype foreign key resolves against the disease-level
  list alone.
- inheritance and genes are inherited from Subtype and describe human genetics. They
  do not apply to an agent stratum; leave them unset.
from_schema: https://w3id.org/monarch-initiative/dismech
is_a: Subtype
slot_usage:
  subtype_term:
    name: subtype_term
    description: The NCBITaxon term grounding this agent stratum. Omit it rather than
      binding the parent species when NCBITaxon carries no node at this rank.
    range: AgentSubtypeDescriptor
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: AgentSubtype
    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: AgentSubtype
    domain_of:
    - Subtype
    - Grouping
    - GroupingMember
    - ModuleCollection
    range: string
  subtype_term:
    name: subtype_term
    description: The NCBITaxon term grounding this agent stratum. Omit it rather than
      binding the parent species when NCBITaxon carries no node at this rank.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype_term
    owner: AgentSubtype
    domain_of:
    - Subtype
    range: AgentSubtypeDescriptor
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    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: AgentSubtype
    domain_of:
    - Subtype
    range: string
    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: AgentSubtype
    domain_of:
    - Subtype
    - Genetic
    - Disease
    range: Inheritance
    multivalued: true
    inlined: true
    inlined_as_list: true