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Class: Treatment

URI: dismech:class/Treatment

 classDiagram
    class Treatment
    click Treatment href "../../classes/Treatment/"
      Treatment : action_category





        Treatment --> "0..1" MedicalActionCategoryEnum : action_category
        click MedicalActionCategoryEnum href "../../enums/MedicalActionCategoryEnum/"



      Treatment : aso_details





        Treatment --> "0..1" OligonucleotideDetail : aso_details
        click OligonucleotideDetail href "../../classes/OligonucleotideDetail/"



      Treatment : context

      Treatment : delivery_system





        Treatment --> "0..1" DeliverySystem : delivery_system
        click DeliverySystem href "../../classes/DeliverySystem/"



      Treatment : description

      Treatment : dosing_interval

      Treatment : dosing_interval_days

      Treatment : effect_modifiers





        Treatment --> "*" TreatmentEffectModifier : effect_modifiers
        click TreatmentEffectModifier href "../../classes/TreatmentEffectModifier/"



      Treatment : evidence





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



      Treatment : examples

      Treatment : mechanism





        Treatment --> "*" Mechanism : mechanism
        click Mechanism href "../../classes/Mechanism/"



      Treatment : name

      Treatment : notes

      Treatment : oligonucleotide_details





        Treatment --> "0..1" OligonucleotideDetail : oligonucleotide_details
        click OligonucleotideDetail href "../../classes/OligonucleotideDetail/"



      Treatment : pdb_structures





        Treatment --> "*" ProteinStructure : pdb_structures
        click ProteinStructure href "../../classes/ProteinStructure/"



      Treatment : regimen_term





        Treatment --> "0..1" RegimenDescriptor : regimen_term
        click RegimenDescriptor href "../../classes/RegimenDescriptor/"



      Treatment : review_notes

      Treatment : role

      Treatment : target_mechanisms





        Treatment --> "*" TreatmentMechanismTarget : target_mechanisms
        click TreatmentMechanismTarget href "../../classes/TreatmentMechanismTarget/"



      Treatment : target_phenotypes





        Treatment --> "*" PhenotypeDescriptor : target_phenotypes
        click PhenotypeDescriptor href "../../classes/PhenotypeDescriptor/"



      Treatment : therapeutic_modality





        Treatment --> "0..1" TherapeuticModalityEnum : therapeutic_modality
        click TherapeuticModalityEnum href "../../enums/TherapeuticModalityEnum/"



      Treatment : treatment_term





        Treatment --> "0..1" TreatmentDescriptor : treatment_term
        click TreatmentDescriptor href "../../classes/TreatmentDescriptor/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
action_category 0..1
MedicalActionCategoryEnum		 Optional high-level category for a clinical action in the treatments section direct
treatment_term 0..1
TreatmentDescriptor		 The NCIT term for this treatment/medical action direct
regimen_term 0..1
RegimenDescriptor		 The NCIT term for this treatment regimen direct
therapeutic_modality 0..1
TherapeuticModalityEnum		 Broad therapeutic platform/modality of a treatment (e direct
delivery_system 0..1
DeliverySystem		 Structured detail of how this treatment's active agent reaches its target: th... direct
oligonucleotide_details 0..1
OligonucleotideDetail		 Structured detail specific to nucleic-acid treatments that act by base-pairin... direct
aso_details 0..1
OligonucleotideDetail		 Deprecated alias of oligonucleotide_details, retained so entries authored bef... direct
dosing_interval 0..1
String		 Human-readable maintenance dosing interval as stated by the label or trial (e direct
dosing_interval_days 0..1
Float		 The maintenance dosing interval normalized to days, so treatments are compara... direct
effect_modifiers *
TreatmentEffectModifier		 Reported differences in a treatment's effect across patient subgroups (age, s... direct
target_phenotypes *
PhenotypeDescriptor		 Phenotypes that this treatment or trial addresses or targets direct
target_mechanisms *
TreatmentMechanismTarget		 Pathophysiology mechanism nodes that this treatment targets or modulates direct
pdb_structures *
ProteinStructure		 Experimental or predicted 3D protein structures relevant to this treatment's ... direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct
context 0..1
String		 direct
review_notes 0..1
String		 direct
role 0..1
String		 Free-text role of this item within its section (e direct
mechanism *
Mechanism		 direct
examples *
String		 direct

Usages

used by used in type used
Disease treatments range Treatment

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Treatment
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- action_category
- treatment_term
- regimen_term
- therapeutic_modality
- delivery_system
- oligonucleotide_details
- aso_details
- dosing_interval
- dosing_interval_days
- effect_modifiers
- target_phenotypes
- target_mechanisms
- pdb_structures
- evidence
- notes
- context
- review_notes
- role
- mechanism
- examples

Induced

name: Treatment
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: Treatment
    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
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Treatment
    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
  action_category:
    name: action_category
    description: Optional high-level category for a clinical action in the treatments
      section. Use THERAPEUTIC for actions that treat, prevent, mitigate, or manage
      disease mechanisms or symptoms; use non-therapeutic categories for screening,
      diagnosis, monitoring, and counseling or informational interventions.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: action_category
    owner: Treatment
    domain_of:
    - Treatment
    range: MedicalActionCategoryEnum
  treatment_term:
    name: treatment_term
    description: The NCIT term for this treatment/medical action
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: treatment_term
    owner: Treatment
    domain_of:
    - ExperimentalPerturbation
    - Treatment
    range: TreatmentDescriptor
    inlined: true
  regimen_term:
    name: regimen_term
    description: The NCIT term for this treatment regimen
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regimen_term
    owner: Treatment
    domain_of:
    - Treatment
    range: RegimenDescriptor
    inlined: true
  therapeutic_modality:
    name: therapeutic_modality
    description: Broad therapeutic platform/modality of a treatment (e.g., small molecule,
      monoclonal antibody, antisense oligonucleotide, gene therapy). Complements treatment_term
      (the NCIT action) and therapeutic_agent (the specific drug) by classifying the
      kind of therapeutic, enabling cross-disease queries by platform. Prefer this
      enum-backed slot over the free-text role slot for modality.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: therapeutic_modality
    owner: Treatment
    domain_of:
    - Treatment
    range: TherapeuticModalityEnum
  delivery_system:
    name: delivery_system
    description: 'Structured detail of how this treatment''s active agent reaches
      its target: the formulation platform, any targeting ligand on the carrier, the
      receptor that ligand binds, and the cell type the carrier is aimed at. Populate
      for any modality whose carrier is part of the therapeutic identity - an mRNA
      lipid nanoparticle, an albumin-bound or liposomal small molecule, an AAV vector
      - not only for oligonucleotides. Supersedes the delivery_platform and conjugation
      slots nested in oligonucleotide_details, which remain valid for entries authored
      before this slot existed.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: delivery_system
    owner: Treatment
    domain_of:
    - Treatment
    range: DeliverySystem
    inlined: true
  oligonucleotide_details:
    name: oligonucleotide_details
    description: Structured detail specific to nucleic-acid treatments that act by
      base-pairing with a target RNA. Populate when therapeutic_modality is ANTISENSE_OLIGONUCLEOTIDE
      or SIRNA.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: oligonucleotide_details
    owner: Treatment
    domain_of:
    - Treatment
    range: OligonucleotideDetail
    inlined: true
  aso_details:
    name: aso_details
    description: Deprecated alias of oligonucleotide_details, retained so entries
      authored before the slot was generalized continue to validate.
    deprecated: Renamed to oligonucleotide_details, which covers siRNA as well as
      antisense oligonucleotides. Existing entries carrying aso_details remain valid;
      do not populate it on new treatments.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: aso_details
    owner: Treatment
    domain_of:
    - Treatment
    range: OligonucleotideDetail
    inlined: true
  dosing_interval:
    name: dosing_interval
    description: Human-readable maintenance dosing interval as stated by the label
      or trial (e.g., "once every 3 weeks", "twice yearly"). Record loading or induction
      doses in the treatment description rather than here.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: dosing_interval
    owner: Treatment
    domain_of:
    - Treatment
    range: string
  dosing_interval_days:
    name: dosing_interval_days
    description: The maintenance dosing interval normalized to days, so treatments
      are comparable across entries (3 weeks = 21; monthly = 30; quarterly = 90; twice
      yearly = 182.5). Populate alongside dosing_interval, which keeps the source
      phrasing.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: dosing_interval_days
    owner: Treatment
    domain_of:
    - Treatment
    range: float
  effect_modifiers:
    name: effect_modifiers
    description: 'Reported differences in a treatment''s effect across patient subgroups
      (age, sex, baseline severity, genotype, ...). One entry per stratum, outcome
      and source: the same stratum can show a larger effect on one outcome and none
      on another. Absent means no subgroup difference has been curated, not that none
      exists.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: effect_modifiers
    owner: Treatment
    domain_of:
    - Treatment
    range: TreatmentEffectModifier
    multivalued: true
    inlined: true
    inlined_as_list: true
  target_phenotypes:
    name: target_phenotypes
    description: Phenotypes that this treatment or trial addresses or targets
    comments:
    - Should reference phenotype names defined in the same disease's phenotypes list
    - Enables linking treatments/trials to the symptoms/manifestations they aim to
      manage
    - Each phenotype can include ontology term references (HP)
    - Use only for THERAPEUTIC actions; non-therapeutic actions need a future dedicated
      observation/screening link instead of treatment-style target links
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target_phenotypes
    owner: Treatment
    domain_of:
    - ClinicalTrial
    - Treatment
    range: PhenotypeDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  target_mechanisms:
    name: target_mechanisms
    description: Pathophysiology mechanism nodes that this treatment targets or modulates.
      Links a treatment to specific steps in the disease's causal graph, enabling
      inference about which downstream phenotypes should respond to therapy.
    comments:
    - Target names should match pathophysiology entry names in the same disease file
    - Complements target_phenotypes by explaining WHERE in the causal chain the drug
      acts
    - Analogous to DrugMechDB paths but anchored to dismech pathophysiology nodes
    - Use only for THERAPEUTIC actions; non-therapeutic actions such as screening,
      monitoring, diagnostics, and counseling or informational interventions should
      not link to pathophysiology nodes
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target_mechanisms
    owner: Treatment
    domain_of:
    - Treatment
    range: TreatmentMechanismTarget
    multivalued: true
    inlined: true
    inlined_as_list: true
  pdb_structures:
    name: pdb_structures
    description: Experimental or predicted 3D protein structures relevant to this
      treatment's mechanism of action. Typically co-crystal structures of the drug
      bound to its target protein, or AlphaFold predictions of the drug target.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: pdb_structures
    owner: Treatment
    domain_of:
    - Pathophysiology
    - Treatment
    range: ProteinStructure
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Treatment
    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
  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: Treatment
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassification
    - GeneClassificationCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - Transmission
    - Diagnosis
    - VariantPopulationEffect
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
  context:
    name: context
    examples:
    - value: Pregnancy
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: context
    owner: Treatment
    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: Treatment
    domain_of:
    - ClinicalTrial
    - Subtype
    - ProgressionInfo
    - Pathophysiology
    - Phenotype
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  role:
    name: role
    description: 'Free-text role of this item within its section (e.g. a pathophysiology
      node''s place in the cascade, or a host''s role in a parasite life cycle). Deliberately
      unconstrained: the KB carries ~90 distinct values on pathophysiology nodes alone,
      many of them descriptive rather than categorical, so narrowing this to an enum
      would retire legitimate content and invalidate in-flight curation (cf. the retired-enum-value
      hazard, dismech#10061).'
    comments:
    - '`role` is never read as a claim. For neoplasms in particular, an initiating-sounding
      role does NOT identify the cell of origin: that derivation reads `genetic_context.variant_origin:
      SOMATIC` on the lesion node, or an `environmental_effect: TRIGGERS` link for
      non-mutational initiation (design decisions 3d). An earlier version did read
      this slot and mis-fired. See docs/cancer-cell-of-origin.md and `just check-cancer-origin`.'
    examples:
    - value: Primary
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: role
    owner: Treatment
    domain_of:
    - HostDescriptor
    - Pathophysiology
    - Stage
    - Treatment
    range: string
  mechanism:
    name: mechanism
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mechanism
    owner: Treatment
    domain_of:
    - Treatment
    range: Mechanism
    multivalued: true
    inlined: true
    inlined_as_list: true
  examples:
    name: examples
    examples:
    - value: '[''Kaposi Sarcoma'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: examples
    owner: Treatment
    domain_of:
    - Pathophysiology
    - Genetic
    - Environmental
    - Stage
    - Treatment
    range: string
    multivalued: true