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Class: HistopathologyFinding

A histopathologic finding from microscopic examination of tissue. Includes morphologic features, architectural patterns, cellular characteristics, growth patterns, and histologic grading.

URI: dismech:HistopathologyFinding

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

      HistopathologyFinding : description

      HistopathologyFinding : diagnostic

      HistopathologyFinding : evidence





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



      HistopathologyFinding : finding_term





        HistopathologyFinding --> "0..1" HistopathologyFindingDescriptor : finding_term
        click HistopathologyFindingDescriptor href "../HistopathologyFindingDescriptor/"



      HistopathologyFinding : frequency





        HistopathologyFinding --> "0..1" Any : frequency
        click Any href "../Any/"



      HistopathologyFinding : name

      HistopathologyFinding : notes

      HistopathologyFinding : subtype

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 Name of the histopathologic finding direct
finding_term 0..1
HistopathologyFindingDescriptor		 Ontology term for a histopathologic finding (from NCIT or HP) direct
description 0..1
String		 Detailed description of the finding and its clinical significance direct
frequency 0..1
Any or 
FrequencyEnum or 
FrequencyQuantity		 How frequently this finding is observed in the disease direct
diagnostic 0..1
Boolean		 Whether this finding is pathognomonic or highly diagnostic direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct
context 0..1
String		 Context in which this finding is observed (e direct
subtype 0..1
String		 direct

Usages

used by used in type used
Disease histopathology range HistopathologyFinding

Comments

  • {'For cancers': 'tumor grade, differentiation, growth patterns, necrosis, rosettes'}
  • {'For other diseases': 'inflammatory infiltrates, architectural distortion, fibrosis'}
  • Separate from phenotypes as these are microscopic observations requiring biopsy

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: HistopathologyFinding
description: A histopathologic finding from microscopic examination of tissue. Includes
  morphologic features, architectural patterns, cellular characteristics, growth patterns,
  and histologic grading.
comments:
- '{''For cancers'': ''tumor grade, differentiation, growth patterns, necrosis, rosettes''}'
- '{''For other diseases'': ''inflammatory infiltrates, architectural distortion,
  fibrosis''}'
- Separate from phenotypes as these are microscopic observations requiring biopsy
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- finding_term
- description
- frequency
- diagnostic
- evidence
- notes
- context
- subtype
slot_usage:
  name:
    name: name
    description: Name of the histopathologic finding
    examples:
    - value: Flexner-Wintersteiner Rosettes
    - value: Spindle Cell Morphology
    - value: High Grade (Fuhrman Grade 3-4)
  description:
    name: description
    description: Detailed description of the finding and its clinical significance
  frequency:
    name: frequency
    description: How frequently this finding is observed in the disease
  diagnostic:
    name: diagnostic
    description: Whether this finding is pathognomonic or highly diagnostic
  context:
    name: context
    description: Context in which this finding is observed (e.g., specific subtype)

Induced

name: HistopathologyFinding
description: A histopathologic finding from microscopic examination of tissue. Includes
  morphologic features, architectural patterns, cellular characteristics, growth patterns,
  and histologic grading.
comments:
- '{''For cancers'': ''tumor grade, differentiation, growth patterns, necrosis, rosettes''}'
- '{''For other diseases'': ''inflammatory infiltrates, architectural distortion,
  fibrosis''}'
- Separate from phenotypes as these are microscopic observations requiring biopsy
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  name:
    name: name
    description: Name of the histopathologic finding
    examples:
    - value: Flexner-Wintersteiner Rosettes
    - value: Spindle Cell Morphology
    - value: High Grade (Fuhrman Grade 3-4)
  description:
    name: description
    description: Detailed description of the finding and its clinical significance
  frequency:
    name: frequency
    description: How frequently this finding is observed in the disease
  diagnostic:
    name: diagnostic
    description: Whether this finding is pathognomonic or highly diagnostic
  context:
    name: context
    description: Context in which this finding is observed (e.g., specific subtype)
attributes:
  name:
    name: name
    description: Name of the histopathologic finding
    examples:
    - value: Flexner-Wintersteiner Rosettes
    - value: Spindle Cell Morphology
    - value: High Grade (Fuhrman Grade 3-4)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: HistopathologyFinding
    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
  finding_term:
    name: finding_term
    description: Ontology term for a histopathologic finding (from NCIT or HP)
    comments:
    - Use NCIT terms from Morphologic Finding (C35867) or Histologic Grade (C18000)
    - Use HP terms for rosettes and cell morphology abnormalities (HP:0025461 descendants)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: finding_term
    owner: HistopathologyFinding
    domain_of:
    - HistopathologyFinding
    range: HistopathologyFindingDescriptor
    inlined: true
  description:
    name: description
    description: Detailed description of the finding and its clinical significance
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: HistopathologyFinding
    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
  frequency:
    name: frequency
    description: How frequently this finding is observed in the disease
    examples:
    - value: Occasional
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: frequency
    owner: HistopathologyFinding
    domain_of:
    - PhenotypeContext
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  diagnostic:
    name: diagnostic
    description: Whether this finding is pathognomonic or highly diagnostic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: diagnostic
    owner: HistopathologyFinding
    domain_of:
    - Phenotype
    - HistopathologyFinding
    range: boolean
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: HistopathologyFinding
    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: HistopathologyFinding
    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
    description: Context in which this finding is observed (e.g., specific subtype)
    examples:
    - value: Pregnancy
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: context
    owner: HistopathologyFinding
    domain_of:
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  subtype:
    name: subtype
    examples:
    - value: Eyelid Myoclonia with Absences
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype
    owner: HistopathologyFinding
    domain_of:
    - PhenotypeContext
    - Prevalence
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: string