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Class: Disease

URI: dismech:Disease

 classDiagram
    class Disease
    click Disease href "../Disease/"
      Disease : agent_life_cycle





        Disease --> "0..1" AgentLifeCycle : agent_life_cycle
        click AgentLifeCycle href "../AgentLifeCycle/"



      Disease : animal_models





        Disease --> "*" AnimalModel : animal_models
        click AnimalModel href "../AnimalModel/"



      Disease : biochemical





        Disease --> "*" Biochemical : biochemical
        click Biochemical href "../Biochemical/"



      Disease : categories

      Disease : category

      Disease : classifications





        Disease --> "0..1" DiseaseClassifications : classifications
        click DiseaseClassifications href "../DiseaseClassifications/"



      Disease : clinical_trials





        Disease --> "*" ClinicalTrial : clinical_trials
        click ClinicalTrial href "../ClinicalTrial/"



      Disease : computational_models





        Disease --> "*" ComputationalModel : computational_models
        click ComputationalModel href "../ComputationalModel/"



      Disease : creation_date

      Disease : curation_history





        Disease --> "*" CurationEvent : curation_history
        click CurationEvent href "../CurationEvent/"



      Disease : datasets





        Disease --> "*" Dataset : datasets
        click Dataset href "../Dataset/"



      Disease : definitions





        Disease --> "*" Definition : definitions
        click Definition href "../Definition/"



      Disease : description

      Disease : diagnosis





        Disease --> "*" Diagnosis : diagnosis
        click Diagnosis href "../Diagnosis/"



      Disease : differential_diagnoses





        Disease --> "*" DifferentialDiagnosis : differential_diagnoses
        click DifferentialDiagnosis href "../DifferentialDiagnosis/"



      Disease : disease_term





        Disease --> "0..1" DiseaseDescriptor : disease_term
        click DiseaseDescriptor href "../DiseaseDescriptor/"



      Disease : environmental





        Disease --> "*" Environmental : environmental
        click Environmental href "../Environmental/"



      Disease : epidemiology





        Disease --> "*" EpidemiologyInfo : epidemiology
        click EpidemiologyInfo href "../EpidemiologyInfo/"



      Disease : genetic





        Disease --> "*" Genetic : genetic
        click Genetic href "../Genetic/"



      Disease : has_subtypes





        Disease --> "*" Subtype : has_subtypes
        click Subtype href "../Subtype/"



      Disease : histopathology





        Disease --> "*" HistopathologyFinding : histopathology
        click HistopathologyFinding href "../HistopathologyFinding/"



      Disease : infectious_agent





        Disease --> "*" InfectiousAgent : infectious_agent
        click InfectiousAgent href "../InfectiousAgent/"



      Disease : inheritance





        Disease --> "*" Inheritance : inheritance
        click Inheritance href "../Inheritance/"



      Disease : mappings





        Disease --> "0..1" DiseaseMappings : mappings
        click DiseaseMappings href "../DiseaseMappings/"



      Disease : mechanistic_hypotheses





        Disease --> "*" MechanisticHypothesis : mechanistic_hypotheses
        click MechanisticHypothesis href "../MechanisticHypothesis/"



      Disease : modeling_considerations





        Disease --> "*" ModelingConsideration : modeling_considerations
        click ModelingConsideration href "../ModelingConsideration/"



      Disease : name

      Disease : notes

      Disease : parents

      Disease : pathophysiology





        Disease --> "*" Pathophysiology : pathophysiology
        click Pathophysiology href "../Pathophysiology/"



      Disease : phenotypes





        Disease --> "*" Phenotype : phenotypes
        click Phenotype href "../Phenotype/"



      Disease : prevalence





        Disease --> "*" Prevalence : prevalence
        click Prevalence href "../Prevalence/"



      Disease : progression





        Disease --> "*" ProgressionInfo : progression
        click ProgressionInfo href "../ProgressionInfo/"



      Disease : references





        Disease --> "*" PublicationReference : references
        click PublicationReference href "../PublicationReference/"



      Disease : review_notes

      Disease : stages





        Disease --> "*" Stage : stages
        click Stage href "../Stage/"



      Disease : synonyms

      Disease : transmission





        Disease --> "*" Transmission : transmission
        click Transmission href "../Transmission/"



      Disease : treatments





        Disease --> "*" Treatment : treatments
        click Treatment href "../Treatment/"



      Disease : updated_date

      Disease : variants





        Disease --> "*" Variant : variants
        click Variant href "../Variant/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 Preferred name for the disease direct
disease_term 0..1
DiseaseDescriptor		 The MONDO disease term for this disease direct
creation_date 0..1 recommended
String		 Timestamp for initial creation of this disease entry direct
updated_date 0..1 recommended
String		 Timestamp for the latest substantive update to this disease entry direct
description 0..1
String		 direct
references *
PublicationReference		 Top-level list of references with their key findings for this disease direct
category 0..1
String		 direct
parents *
String		 direct
has_subtypes *
Subtype		 direct
prevalence *
Prevalence		 direct
progression *
ProgressionInfo		 direct
pathophysiology *
Pathophysiology		 direct
mechanistic_hypotheses *
MechanisticHypothesis		 Disease-level mechanistic hypotheses that group and annotate causal edges direct
phenotypes *
Phenotype		 direct
histopathology *
HistopathologyFinding		 Histopathologic findings including microscopic morphology, architectural patt... direct
biochemical *
Biochemical		 direct
stages *
Stage		 direct
genetic *
Genetic		 direct
variants *
Variant		 direct
environmental *
Environmental		 direct
treatments *
Treatment		 direct
categories *
String		 direct
infectious_agent *
InfectiousAgent		 direct
agent_life_cycle 0..1
AgentLifeCycle		 direct
transmission *
Transmission		 direct
modeling_considerations *
ModelingConsideration		 direct
epidemiology *
EpidemiologyInfo		 direct
diagnosis *
Diagnosis		 direct
differential_diagnoses *
DifferentialDiagnosis		 Differential diagnoses - similar diseases that must be ruled out direct
synonyms *
String		 direct
inheritance *
Inheritance		 direct
animal_models *
AnimalModel		 direct
datasets * recommended
Dataset		 Publicly available datasets relevant to disease research direct
clinical_trials *
ClinicalTrial		 Clinical trials relevant to disease treatment and research direct
computational_models *
ComputationalModel		 Computational models (metabolic, mechanistic, ML, digital twins) for this dis... direct
classifications 0..1
DiseaseClassifications		 Classification assignments for this disease from various nosologies direct
definitions *
Definition		 Definitions or diagnostic criteria for this disease direct
mappings 0..1
DiseaseMappings		 External identifier mappings for this disease (SSSOM-inspired) direct
notes 0..1
String		 direct
review_notes 0..1
String		 direct
curation_history *
CurationEvent		 Audit trail of AI-assisted curation events direct

Usages

used by used in type used
DiseaseCollection diseases range Disease

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Disease
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- disease_term
- creation_date
- updated_date
- description
- references
- category
- parents
- has_subtypes
- prevalence
- progression
- pathophysiology
- mechanistic_hypotheses
- phenotypes
- histopathology
- biochemical
- stages
- genetic
- variants
- environmental
- treatments
- categories
- infectious_agent
- agent_life_cycle
- transmission
- modeling_considerations
- epidemiology
- diagnosis
- differential_diagnoses
- synonyms
- inheritance
- animal_models
- datasets
- clinical_trials
- computational_models
- classifications
- definitions
- mappings
- notes
- review_notes
- curation_history
slot_usage:
  name:
    name: name
    description: Preferred name for the disease
    required: true
  creation_date:
    name: creation_date
    description: Timestamp for initial creation of this disease entry. Keep this stable
      after first set.
  updated_date:
    name: updated_date
    description: Timestamp for the latest substantive update to this disease entry.
      Update this whenever curated content changes.

Induced

name: Disease
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  name:
    name: name
    description: Preferred name for the disease
    required: true
  creation_date:
    name: creation_date
    description: Timestamp for initial creation of this disease entry. Keep this stable
      after first set.
  updated_date:
    name: updated_date
    description: Timestamp for the latest substantive update to this disease entry.
      Update this whenever curated content changes.
attributes:
  name:
    name: name
    description: Preferred name for the disease
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Disease
    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
  disease_term:
    name: disease_term
    description: The MONDO disease term for this disease
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: disease_term
    owner: Disease
    domain_of:
    - DifferentialDiagnosis
    - Disease
    range: DiseaseDescriptor
    inlined: true
  creation_date:
    name: creation_date
    description: Timestamp for initial creation of this disease entry. Keep this stable
      after first set.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: creation_date
    owner: Disease
    domain_of:
    - Disease
    - ComorbidityAssociation
    range: string
    recommended: true
    pattern: ^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(?:\.\d+)?(?:Z|[+\-]\d{2}:\d{2})$
  updated_date:
    name: updated_date
    description: Timestamp for the latest substantive update to this disease entry.
      Update this whenever curated content changes.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: updated_date
    owner: Disease
    domain_of:
    - Disease
    - ComorbidityAssociation
    range: string
    recommended: true
    pattern: ^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(?:\.\d+)?(?:Z|[+\-]\d{2}:\d{2})$
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Disease
    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
  references:
    name: references
    description: Top-level list of references with their key findings for this disease
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: references
    owner: Disease
    domain_of:
    - Disease
    range: PublicationReference
    multivalued: true
    inlined: true
    inlined_as_list: true
  category:
    name: category
    examples:
    - value: Hematologic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: category
    owner: Disease
    domain_of:
    - Phenotype
    - Disease
    - AnimalModel
    range: string
  parents:
    name: parents
    examples:
    - value: '[''Bacterial Infection'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: parents
    owner: Disease
    domain_of:
    - Disease
    range: string
    multivalued: true
  has_subtypes:
    name: has_subtypes
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: has_subtypes
    owner: Disease
    domain_of:
    - Disease
    - InfectiousAgent
    range: Subtype
    multivalued: true
    inlined: true
    inlined_as_list: true
  prevalence:
    name: prevalence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: prevalence
    owner: Disease
    domain_of:
    - Disease
    range: Prevalence
    multivalued: true
    inlined: true
    inlined_as_list: true
  progression:
    name: progression
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: progression
    owner: Disease
    domain_of:
    - Disease
    range: ProgressionInfo
    multivalued: true
    inlined: true
    inlined_as_list: true
  pathophysiology:
    name: pathophysiology
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: pathophysiology
    owner: Disease
    domain_of:
    - Disease
    - Stage
    - ComorbidityHypothesis
    range: Pathophysiology
    multivalued: true
    inlined: true
    inlined_as_list: true
  mechanistic_hypotheses:
    name: mechanistic_hypotheses
    description: Disease-level mechanistic hypotheses that group and annotate causal
      edges
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mechanistic_hypotheses
    owner: Disease
    domain_of:
    - Disease
    range: MechanisticHypothesis
    multivalued: true
    inlined: true
    inlined_as_list: true
  phenotypes:
    name: phenotypes
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: phenotypes
    owner: Disease
    domain_of:
    - DifferentialDiagnosis
    - Disease
    - ComorbidityAssociation
    range: Phenotype
    multivalued: true
    inlined: true
    inlined_as_list: true
  histopathology:
    name: histopathology
    description: Histopathologic findings including microscopic morphology, architectural
      patterns, cellular features, growth patterns, and histologic grading.
    comments:
    - Separate from phenotypes as these are tissue-level microscopic observations
    - Use NCIT Morphologic Finding (C35867) or Histologic Grade (C18000) terms
    - '{''For cancer'': ''includes grade, differentiation, growth patterns, necrosis''}'
    - '{''For other diseases'': ''may include architectural changes, cellular infiltrates''}'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: histopathology
    owner: Disease
    domain_of:
    - Disease
    range: HistopathologyFinding
    multivalued: true
    inlined: true
    inlined_as_list: true
  biochemical:
    name: biochemical
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: biochemical
    owner: Disease
    domain_of:
    - Disease
    range: Biochemical
    multivalued: true
    inlined: true
    inlined_as_list: true
  stages:
    name: stages
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: stages
    owner: Disease
    domain_of:
    - Disease
    range: Stage
    multivalued: true
    inlined: true
    inlined_as_list: true
  genetic:
    name: genetic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genetic
    owner: Disease
    domain_of:
    - Disease
    range: Genetic
    multivalued: true
    inlined: true
    inlined_as_list: true
  variants:
    name: variants
    comments:
    - can currently be used at gene or disease level, TODO - decide the best level
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: variants
    owner: Disease
    domain_of:
    - Genetic
    - Disease
    range: Variant
    multivalued: true
    inlined: true
    inlined_as_list: true
  environmental:
    name: environmental
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: environmental
    owner: Disease
    domain_of:
    - Disease
    range: Environmental
    multivalued: true
    inlined: true
    inlined_as_list: true
  treatments:
    name: treatments
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: treatments
    owner: Disease
    domain_of:
    - Disease
    range: Treatment
    multivalued: true
    inlined: true
    inlined_as_list: true
  categories:
    name: categories
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: categories
    owner: Disease
    domain_of:
    - Disease
    range: string
    multivalued: true
  infectious_agent:
    name: infectious_agent
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: infectious_agent
    owner: Disease
    domain_of:
    - Disease
    range: InfectiousAgent
    multivalued: true
    inlined: true
    inlined_as_list: true
  agent_life_cycle:
    name: agent_life_cycle
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: agent_life_cycle
    owner: Disease
    domain_of:
    - Disease
    range: AgentLifeCycle
  transmission:
    name: transmission
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: transmission
    owner: Disease
    domain_of:
    - Disease
    range: Transmission
    multivalued: true
    inlined: true
    inlined_as_list: true
  modeling_considerations:
    name: modeling_considerations
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: modeling_considerations
    owner: Disease
    domain_of:
    - Disease
    range: ModelingConsideration
    multivalued: true
    inlined: true
    inlined_as_list: true
  epidemiology:
    name: epidemiology
    examples:
    - value: '[''Global'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: epidemiology
    owner: Disease
    domain_of:
    - Disease
    range: EpidemiologyInfo
    multivalued: true
    inlined: true
    inlined_as_list: true
  diagnosis:
    name: diagnosis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: diagnosis
    owner: Disease
    domain_of:
    - Disease
    range: Diagnosis
    multivalued: true
    inlined: true
    inlined_as_list: true
  differential_diagnoses:
    name: differential_diagnoses
    description: Differential diagnoses - similar diseases that must be ruled out
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: differential_diagnoses
    owner: Disease
    domain_of:
    - Disease
    range: DifferentialDiagnosis
    recommended: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  synonyms:
    name: synonyms
    examples:
    - value: '[''CYFRA 21-1'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: synonyms
    owner: Disease
    domain_of:
    - Pathophysiology
    - Biochemical
    - Environmental
    - Disease
    - Variant
    range: string
    multivalued: true
  inheritance:
    name: inheritance
    examples:
    - value: Autosomal Dominant
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: inheritance
    owner: Disease
    domain_of:
    - Subtype
    - Genetic
    - Disease
    range: Inheritance
    multivalued: true
    inlined: true
    inlined_as_list: true
  animal_models:
    name: animal_models
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: animal_models
    owner: Disease
    domain_of:
    - Disease
    range: AnimalModel
    multivalued: true
    inlined: true
    inlined_as_list: true
  datasets:
    name: datasets
    description: Publicly available datasets relevant to disease research
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: datasets
    owner: Disease
    domain_of:
    - Disease
    range: Dataset
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  clinical_trials:
    name: clinical_trials
    description: Clinical trials relevant to disease treatment and research
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: clinical_trials
    owner: Disease
    domain_of:
    - Disease
    range: ClinicalTrial
    recommended: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  computational_models:
    name: computational_models
    description: Computational models (metabolic, mechanistic, ML, digital twins)
      for this disease
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: computational_models
    owner: Disease
    domain_of:
    - Disease
    range: ComputationalModel
    multivalued: true
    inlined: true
    inlined_as_list: true
  classifications:
    name: classifications
    description: Classification assignments for this disease from various nosologies
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: classifications
    owner: Disease
    domain_of:
    - Disease
    range: DiseaseClassifications
    inlined: true
  definitions:
    name: definitions
    description: Definitions or diagnostic criteria for this disease
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: definitions
    owner: Disease
    domain_of:
    - Disease
    range: Definition
    multivalued: true
    inlined: true
    inlined_as_list: true
  mappings:
    name: mappings
    description: External identifier mappings for this disease (SSSOM-inspired)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mappings
    owner: Disease
    domain_of:
    - Disease
    range: DiseaseMappings
    inlined: 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: Disease
    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
  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: Disease
    domain_of:
    - ClinicalTrial
    - Subtype
    - ProgressionInfo
    - Phenotype
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - Treatment
    range: string
  curation_history:
    name: curation_history
    description: Audit trail of AI-assisted curation events
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: curation_history
    owner: Disease
    domain_of:
    - Disease
    range: CurationEvent
    multivalued: true
    inlined: true
    inlined_as_list: true