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Class: Treatment

URI: dismech:Treatment

 classDiagram
    class Treatment
    click Treatment href "../Treatment/"
      Treatment : context

      Treatment : description

      Treatment : evidence





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



      Treatment : examples

      Treatment : mechanism





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



      Treatment : name

      Treatment : notes

      Treatment : regimen_term





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



      Treatment : review_notes

      Treatment : role

      Treatment : target_mechanisms





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



      Treatment : target_phenotypes





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



      Treatment : treatment_term





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

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
treatment_term 0..1
TreatmentDescriptor		 The MAXO term for this treatment/medical action direct
regimen_term 0..1
RegimenDescriptor		 The NCIT term for this treatment regimen 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
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct
context 0..1
String		 direct
review_notes 0..1
String		 direct
role 0..1
String		 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
- treatment_term
- regimen_term
- target_phenotypes
- target_mechanisms
- 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:
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - 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
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Treatment
    domain_of:
    - Descriptor
    - GeneticContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - 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
  treatment_term:
    name: treatment_term
    description: The MAXO term for this treatment/medical action
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: treatment_term
    owner: Treatment
    domain_of:
    - 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
  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)
    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
    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
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Treatment
    domain_of:
    - PhenotypeContext
    - Dataset
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - 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
  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
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    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
    - 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
    - Phenotype
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  role:
    name: role
    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