Class: AgentSubtypeDescriptor

A descriptor for a taxonomic stratum below a named infectious agent - subspecies, serovar, serotype, or biotype - bindable to NCBITaxon.

Distinct from SubtypeDescriptor, which grounds a disease subtype to MONDO or NCIT. An agent stratum is an organism, not a disease, so it binds through OrganismTerm and inherits that binding from OrganismDescriptor unchanged.

URI: dismech:class/AgentSubtypeDescriptor

 classDiagram
    class AgentSubtypeDescriptor
    click AgentSubtypeDescriptor href "../../classes/AgentSubtypeDescriptor/"
      OrganismDescriptor <|-- AgentSubtypeDescriptor
        click OrganismDescriptor href "../../classes/OrganismDescriptor/"

      AgentSubtypeDescriptor : clinical_course





        AgentSubtypeDescriptor --> "0..1" ClinicalCourseEnum : clinical_course
        click ClinicalCourseEnum href "../../enums/ClinicalCourseEnum/"



      AgentSubtypeDescriptor : description

      AgentSubtypeDescriptor : laterality





        AgentSubtypeDescriptor --> "0..1" LateralityEnum : laterality
        click LateralityEnum href "../../enums/LateralityEnum/"



      AgentSubtypeDescriptor : located_in





        AgentSubtypeDescriptor --> "0..1" AnatomicalEntityDescriptor : located_in
        click AnatomicalEntityDescriptor href "../../classes/AnatomicalEntityDescriptor/"



      AgentSubtypeDescriptor : modifier





        AgentSubtypeDescriptor --> "0..1" ModifierEnum : modifier
        click ModifierEnum href "../../enums/ModifierEnum/"



      AgentSubtypeDescriptor : onset





        AgentSubtypeDescriptor --> "0..1" OnsetDescriptor : onset
        click OnsetDescriptor href "../../classes/OnsetDescriptor/"



      AgentSubtypeDescriptor : preferred_term

      AgentSubtypeDescriptor : qualifiers





        AgentSubtypeDescriptor --> "*" Qualifier : qualifiers
        click Qualifier href "../../classes/Qualifier/"



      AgentSubtypeDescriptor : severity





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



      AgentSubtypeDescriptor : spatial_extent





        AgentSubtypeDescriptor --> "0..1" SpatialExtentEnum : spatial_extent
        click SpatialExtentEnum href "../../enums/SpatialExtentEnum/"



      AgentSubtypeDescriptor : temporality





        AgentSubtypeDescriptor --> "0..1" TemporalityEnum : temporality
        click TemporalityEnum href "../../enums/TemporalityEnum/"



      AgentSubtypeDescriptor : term





        AgentSubtypeDescriptor --> "0..1 _recommended_" Term : term
        click Term href "../../classes/Term/"

Inheritance

• Descriptor
  • OrganismDescriptor
    • AgentSubtypeDescriptor

Slots

Name	Cardinality and Range	Description	Inheritance
preferred_term	1 String	The preferred human-readable term for this descriptor	Descriptor
description	0..1 String	A description of the descriptor	Descriptor
term	0..1 recommended Term	NCBITaxon term reference	Descriptor
modifier	0..1 ModifierEnum	Directional, functional, or qualitative modifier for a descriptor (e	Descriptor
located_in	0..1 AnatomicalEntityDescriptor	Anatomical location where this entity/process occurs or procedure is performe...	Descriptor
laterality	0..1 LateralityEnum	Laterality qualifier (left, right, or bilateral)	Descriptor
spatial_extent	0..1 SpatialExtentEnum	The spatial extent or distribution pattern applicable to this descriptor (e	Descriptor
onset	0..1 OnsetDescriptor	Structured age of onset descriptor	Descriptor
temporality	0..1 TemporalityEnum	Temporal qualifier for this descriptor (e	Descriptor
clinical_course	0..1 ClinicalCourseEnum	Clinical course qualifier for this descriptor (e	Descriptor
severity	0..1 SeverityQualifierEnum or  Any or  String		Descriptor
qualifiers	* Qualifier	List of predicate-value pairs for formal post-composition	Descriptor

Usages

used by	used in	type	used
AgentSubtype	subtype_term	range	AgentSubtypeDescriptor

Comments

• Bind only at a rank NCBITaxon genuinely carries. Where the only candidate node is the parent species, omit the term rather than binding it - an agent stratum bound to its own parent asserts nothing and reads as grounded.
• Pathotypes (ETEC, MRSA, toxigenic C. difficile) are defined by virulence gene content rather than phylogeny and have no NCBITaxon node. They are carried structurally, by naming the defining determinant in the subtype description, and must not be bound here.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: AgentSubtypeDescriptor
description: 'A descriptor for a taxonomic stratum below a named infectious agent
  - subspecies, serovar, serotype, or biotype - bindable to NCBITaxon.

  Distinct from SubtypeDescriptor, which grounds a *disease* subtype to MONDO or NCIT.
  An agent stratum is an organism, not a disease, so it binds through OrganismTerm
  and inherits that binding from OrganismDescriptor unchanged.'
comments:
- Bind only at a rank NCBITaxon genuinely carries. Where the only candidate node is
  the parent species, omit the term rather than binding it - an agent stratum bound
  to its own parent asserts nothing and reads as grounded.
- Pathotypes (ETEC, MRSA, toxigenic C. difficile) are defined by virulence gene content
  rather than phylogeny and have no NCBITaxon node. They are carried structurally,
  by naming the defining determinant in the subtype description, and must not be bound
  here.
from_schema: https://w3id.org/monarch-initiative/dismech
is_a: OrganismDescriptor

Induced

name: AgentSubtypeDescriptor
description: 'A descriptor for a taxonomic stratum below a named infectious agent
  - subspecies, serovar, serotype, or biotype - bindable to NCBITaxon.

  Distinct from SubtypeDescriptor, which grounds a *disease* subtype to MONDO or NCIT.
  An agent stratum is an organism, not a disease, so it binds through OrganismTerm
  and inherits that binding from OrganismDescriptor unchanged.'
comments:
- Bind only at a rank NCBITaxon genuinely carries. Where the only candidate node is
  the parent species, omit the term rather than binding it - an agent stratum bound
  to its own parent asserts nothing and reads as grounded.
- Pathotypes (ETEC, MRSA, toxigenic C. difficile) are defined by virulence gene content
  rather than phylogeny and have no NCBITaxon node. They are carried structurally,
  by naming the defining determinant in the subtype description, and must not be bound
  here.
from_schema: https://w3id.org/monarch-initiative/dismech
is_a: OrganismDescriptor
attributes:
  preferred_term:
    name: preferred_term
    description: The preferred human-readable term for this descriptor. This may be
      more specific or nuanced than the linked ontology term label when the ontology
      does not fully capture the desired granularity. Note that postcomposition using
      the modifier slot may be appropriate for capturing the semantics of the preferred
      term.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: preferred_term
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - ConditionDescriptor
    range: string
    required: true
  description:
    name: description
    description: A description of the descriptor. This may typically be redundant
      with the `term` object, but the description is more human-readable and may be
      used to communicate nuances not captured by the rigid standardization of the
      term object.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: AgentSubtypeDescriptor
    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
    recommended: false
  term:
    name: term
    description: NCBITaxon term reference
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: term
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - TermMapping
    - ConditionDescriptor
    - GOEnrichmentTerm
    range: Term
    bindings:
    - range: OrganismTerm
      obligation_level: REQUIRED
      binds_value_of: id
    recommended: true
    inlined: true
  modifier:
    name: modifier
    description: Directional, functional, or qualitative modifier for a descriptor
      (e.g., increased, decreased, abnormal, gain of function, loss of function).
      See ModifierEnum for the boundary between the quantitative INCREASED/DECREASED
      values and the GAIN_OF_FUNCTION/LOSS_OF_FUNCTION values.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: modifier
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - ImagingFinding
    - DifferentiatingMechanism
    range: ModifierEnum
  located_in:
    name: located_in
    description: Anatomical location where this entity/process occurs or procedure
      is performed
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: located_in
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - ImagingFinding
    range: AnatomicalEntityDescriptor
    inlined: true
  laterality:
    name: laterality
    description: Laterality qualifier (left, right, or bilateral)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: laterality
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - ImagingFinding
    range: LateralityEnum
  spatial_extent:
    name: spatial_extent
    description: The spatial extent or distribution pattern applicable to this descriptor
      (e.g., focal, diffuse, extensive)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: spatial_extent
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - ImagingFinding
    range: SpatialExtentEnum
  onset:
    name: onset
    description: Structured age of onset descriptor. Combines an HPO onset category
      with optional quantitative age data (mean, min, max in years) and free-text
      notes.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: onset
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - PhenotypeContext
    range: OnsetDescriptor
    inlined: true
  temporality:
    name: temporality
    description: Temporal qualifier for this descriptor (e.g., acute, chronic, recurrent)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: temporality
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    range: TemporalityEnum
  clinical_course:
    name: clinical_course
    description: Clinical course qualifier for this descriptor (e.g., progressive,
      stable)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: clinical_course
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    range: ClinicalCourseEnum
  severity:
    name: severity
    examples:
    - value: Severe
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: severity
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    - PhenotypeContext
    - ReferenceRangeBand
    - Phenotype
    range: Any
    any_of:
    - range: SeverityQualifierEnum
    - range: string
  qualifiers:
    name: qualifiers
    description: List of predicate-value pairs for formal post-composition. Allows
      OWL-like expressivity with controlled predicates (e.g., RO relations) and values.
    deprecated: Prefer explicit slots like located_in and laterality instead of generic
      qualifiers
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: qualifiers
    owner: AgentSubtypeDescriptor
    domain_of:
    - Descriptor
    range: Qualifier
    multivalued: true
    inlined: true
    inlined_as_list: true