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Class: Diagnosis

URI: dismech:class/Diagnosis

 classDiagram
    class Diagnosis
    click Diagnosis href "../../classes/Diagnosis/"
      Diagnosis : description

      Diagnosis : diagnosis_term





        Diagnosis --> "0..1" TreatmentDescriptor : diagnosis_term
        click TreatmentDescriptor href "../../classes/TreatmentDescriptor/"



      Diagnosis : evidence





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



      Diagnosis : markers

      Diagnosis : measurements





        Diagnosis --> "*" MeasurementDescriptor : measurements
        click MeasurementDescriptor href "../../classes/MeasurementDescriptor/"



      Diagnosis : name

      Diagnosis : notes

      Diagnosis : presence

      Diagnosis : reference_ranges





        Diagnosis --> "*" ReferenceRange : reference_ranges
        click ReferenceRange href "../../classes/ReferenceRange/"



      Diagnosis : results

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
diagnosis_term 0..1
TreatmentDescriptor		 The NCIT term for this diagnostic procedure direct
measurements *
MeasurementDescriptor		 The measurements a diagnostic test consists of, each bound to LOINC direct
reference_ranges *
ReferenceRange		 Decision thresholds this disease owns for a measurement named in measurements... direct
presence 0..1
String		 direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct
results 0..1
String		 direct
markers 0..1
String		 Free-text list of the analytes a test reads direct
description 0..1
String		 direct

Usages

used by used in type used
Disease diagnosis range Diagnosis

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Diagnosis
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- diagnosis_term
- measurements
- reference_ranges
- presence
- evidence
- notes
- results
- markers
- description
slot_usage:
  reference_ranges:
    name: reference_ranges
    description: 'Decision thresholds this disease owns for a measurement named in
      measurements: a diagnostic cut-off, a staging or severity grading (MoCA below
      26, PHQ-9 5/10/15/20, GOLD FEV1 bands). Each range names its measurement through
      loinc_term and carries the cut-offs as interpretation_bands. This is not the
      place for a population reference interval, which is true of everyone and belongs
      to no disease.'
  markers:
    name: markers
    description: Free-text list of the analytes a test reads. Superseded by measurements,
      which binds each one to LOINC; keep existing values, and put new tests in measurements.

Induced

name: Diagnosis
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  reference_ranges:
    name: reference_ranges
    description: 'Decision thresholds this disease owns for a measurement named in
      measurements: a diagnostic cut-off, a staging or severity grading (MoCA below
      26, PHQ-9 5/10/15/20, GOLD FEV1 bands). Each range names its measurement through
      loinc_term and carries the cut-offs as interpretation_bands. This is not the
      place for a population reference interval, which is true of everyone and belongs
      to no disease.'
  markers:
    name: markers
    description: Free-text list of the analytes a test reads. Superseded by measurements,
      which binds each one to LOINC; keep existing values, and put new tests in measurements.
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Diagnosis
    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
  diagnosis_term:
    name: diagnosis_term
    description: The NCIT term for this diagnostic procedure
    comments:
    - NCIT includes diagnostic procedures under Clinical Intervention or Procedure
      (C25218)
    - Use qualifiers with UBERON terms to specify anatomical location (e.g., right
      heart catheterization)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: diagnosis_term
    owner: Diagnosis
    domain_of:
    - Diagnosis
    range: TreatmentDescriptor
    inlined: true
  measurements:
    name: measurements
    description: 'The measurements a diagnostic test consists of, each bound to LOINC.
      The diagnosis_term says what kind of procedure the test is (an NCIT clinical
      intervention: enzyme assay, molecular genetic testing); measurements say which
      observables it reads: hexosaminidase A activity in leukocytes, a CFTR sequencing
      panel, the PHQ-9 total score. The same action/thing split as treatment_term
      and therapeutic_agent.'
    comments:
    - One entry per distinct measurement. A two-analyte test is two entries.
    - Bind the LOINC Part or the panel / total-score code for the measurement's identity,
      not a method- or specimen-specific code; LOINC has dozens of codes for one assay,
      and binding method codes here puts the same test on different codes in different
      entries. Method codes belong in a definitions[] phenotype algorithm.
    - preferred_term is the curator's name for the measurement in this disease ("sweat
      chloride"); term.label is the Long Common Name.
    - Decision thresholds the disease owns (a diagnostic cut-off, a severity grading)
      go in the sibling reference_ranges, keyed on the same LOINC code via loinc_term.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: measurements
    owner: Diagnosis
    domain_of:
    - Diagnosis
    range: MeasurementDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  reference_ranges:
    name: reference_ranges
    description: 'Decision thresholds this disease owns for a measurement named in
      measurements: a diagnostic cut-off, a staging or severity grading (MoCA below
      26, PHQ-9 5/10/15/20, GOLD FEV1 bands). Each range names its measurement through
      loinc_term and carries the cut-offs as interpretation_bands. This is not the
      place for a population reference interval, which is true of everyone and belongs
      to no disease.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: reference_ranges
    owner: Diagnosis
    domain_of:
    - Biochemical
    - Diagnosis
    range: ReferenceRange
    multivalued: true
    inlined: true
    inlined_as_list: true
  presence:
    name: presence
    examples:
    - value: Positive
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: presence
    owner: Diagnosis
    domain_of:
    - Biochemical
    - Genetic
    - Environmental
    - Diagnosis
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Diagnosis
    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: Diagnosis
    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
  results:
    name: results
    examples:
    - value: Identifies MEFV mutations
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: results
    owner: Diagnosis
    domain_of:
    - Diagnosis
    range: string
  markers:
    name: markers
    description: Free-text list of the analytes a test reads. Superseded by measurements,
      which binds each one to LOINC; keep existing values, and put new tests in measurements.
    examples:
    - value: CRP, ESR, SAA
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: markers
    owner: Diagnosis
    domain_of:
    - Diagnosis
    range: string
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Diagnosis
    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