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Class: Pathophysiology

URI: dismech:Pathophysiology

 classDiagram
    class Pathophysiology
    click Pathophysiology href "../Pathophysiology/"
      Pathophysiology : assays





        Pathophysiology --> "*" AssayDescriptor : assays
        click AssayDescriptor href "../AssayDescriptor/"



      Pathophysiology : biological_processes





        Pathophysiology --> "*" BiologicalProcessDescriptor : biological_processes
        click BiologicalProcessDescriptor href "../BiologicalProcessDescriptor/"



      Pathophysiology : cell_types





        Pathophysiology --> "*" CellTypeDescriptor : cell_types
        click CellTypeDescriptor href "../CellTypeDescriptor/"



      Pathophysiology : cellular_components





        Pathophysiology --> "*" CellularComponentDescriptor : cellular_components
        click CellularComponentDescriptor href "../CellularComponentDescriptor/"



      Pathophysiology : chemical_entities





        Pathophysiology --> "*" ChemicalEntityDescriptor : chemical_entities
        click ChemicalEntityDescriptor href "../ChemicalEntityDescriptor/"



      Pathophysiology : consequence

      Pathophysiology : consequences

      Pathophysiology : description

      Pathophysiology : downstream





        Pathophysiology --> "*" CausalEdge : downstream
        click CausalEdge href "../CausalEdge/"



      Pathophysiology : evidence





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



      Pathophysiology : examples

      Pathophysiology : frequency





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



      Pathophysiology : gene





        Pathophysiology --> "0..1" GeneDescriptor : gene
        click GeneDescriptor href "../GeneDescriptor/"



      Pathophysiology : gene_products





        Pathophysiology --> "*" GeneProductDescriptor : gene_products
        click GeneProductDescriptor href "../GeneProductDescriptor/"



      Pathophysiology : genes





        Pathophysiology --> "*" GeneDescriptor : genes
        click GeneDescriptor href "../GeneDescriptor/"



      Pathophysiology : locations





        Pathophysiology --> "*" AnatomicalEntityDescriptor : locations
        click AnatomicalEntityDescriptor href "../AnatomicalEntityDescriptor/"



      Pathophysiology : mechanisms

      Pathophysiology : name

      Pathophysiology : notes

      Pathophysiology : pathways





        Pathophysiology --> "*" BiologicalProcessDescriptor : pathways
        click BiologicalProcessDescriptor href "../BiologicalProcessDescriptor/"



      Pathophysiology : protein_complexes





        Pathophysiology --> "*" ProteinComplexDescriptor : protein_complexes
        click ProteinComplexDescriptor href "../ProteinComplexDescriptor/"



      Pathophysiology : role

      Pathophysiology : subtypes

      Pathophysiology : synonyms

      Pathophysiology : triggers





        Pathophysiology --> "*" TriggerDescriptor : triggers
        click TriggerDescriptor href "../TriggerDescriptor/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
cell_types *
CellTypeDescriptor		 direct
evidence * recommended
EvidenceItem		 direct
biological_processes *
BiologicalProcessDescriptor		 direct
locations *
AnatomicalEntityDescriptor		 direct
examples *
String		 direct
role 0..1
String		 direct
synonyms *
String		 direct
consequence 0..1
String		 direct
consequences *
String		 direct
gene 0..1
GeneDescriptor		 direct
pathways *
BiologicalProcessDescriptor		 direct
downstream *
CausalEdge		 direct
genes *
GeneDescriptor		 direct
subtypes *
String		 direct
cellular_components *
CellularComponentDescriptor		 direct
protein_complexes *
ProteinComplexDescriptor		 Protein complexes that gene products participate in direct
chemical_entities *
ChemicalEntityDescriptor		 direct
gene_products *
GeneProductDescriptor		 Gene products (proteins, fusion proteins, oncoproteins) involved in this path... direct
triggers *
TriggerDescriptor		 direct
assays *
AssayDescriptor		 direct
mechanisms *
String		 direct
notes 0..1
String		 direct
frequency 0..1
Any or 
FrequencyEnum or 
FrequencyQuantity		 direct

Usages

used by used in type used
Disease pathophysiology range Pathophysiology
Stage pathophysiology range Pathophysiology
ComorbidityHypothesis pathophysiology range Pathophysiology

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Pathophysiology
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- cell_types
- evidence
- biological_processes
- locations
- examples
- role
- synonyms
- consequence
- consequences
- gene
- pathways
- downstream
- genes
- subtypes
- cellular_components
- protein_complexes
- chemical_entities
- gene_products
- triggers
- assays
- mechanisms
- notes
- frequency

Induced

name: Pathophysiology
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: Pathophysiology
    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: Pathophysiology
    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
  cell_types:
    name: cell_types
    examples:
    - value: '[{preferred_term: Macrophage}, {preferred_term: T Cell}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: cell_types
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    - Biochemical
    range: CellTypeDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Pathophysiology
    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
  biological_processes:
    name: biological_processes
    examples:
    - value: '[{preferred_term: TNF-alpha Production}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: biological_processes
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: BiologicalProcessDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  locations:
    name: locations
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: locations
    owner: Pathophysiology
    domain_of:
    - Subtype
    - Pathophysiology
    range: AnatomicalEntityDescriptor
    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: Pathophysiology
    domain_of:
    - Pathophysiology
    - Genetic
    - Environmental
    - Stage
    - Treatment
    range: string
    multivalued: true
  role:
    name: role
    examples:
    - value: Primary
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: role
    owner: Pathophysiology
    domain_of:
    - HostDescriptor
    - Pathophysiology
    - Stage
    - Treatment
    range: string
  synonyms:
    name: synonyms
    examples:
    - value: '[''CYFRA 21-1'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: synonyms
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    - Biochemical
    - Environmental
    - Disease
    - Variant
    range: string
    multivalued: true
  consequence:
    name: consequence
    examples:
    - value: Leads to abnormal sexual development and bone maturation.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: consequence
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: string
  consequences:
    name: consequences
    todos:
    - unify consequences and consequence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: consequences
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: string
    multivalued: true
  gene:
    name: gene
    examples:
    - value: '{preferred_term: MEFV}'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene
    owner: Pathophysiology
    domain_of:
    - GeneticContext
    - Pathophysiology
    - Variant
    range: GeneDescriptor
    inlined: true
  pathways:
    name: pathways
    examples:
    - value: '[{preferred_term: Wnt Pathway}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: pathways
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: BiologicalProcessDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  downstream:
    name: downstream
    examples:
    - value: '[{target: Tissue Damage, causal_link_type: INDIRECT_UNKNOWN_INTERMEDIATES,
        hypothesis_groups: [canonical_model]}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: downstream
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: CausalEdge
    multivalued: true
    inlined: true
    inlined_as_list: true
  genes:
    name: genes
    examples:
    - value: '[{preferred_term: HLA-DQ2}, {preferred_term: INS}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genes
    owner: Pathophysiology
    domain_of:
    - GeneticContext
    - Dataset
    - Subtype
    - Pathophysiology
    - AnimalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  subtypes:
    name: subtypes
    examples:
    - value: '[''DENV-1'', ''DENV-2'', ''DENV-3'', ''DENV-4'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtypes
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: string
    multivalued: true
  cellular_components:
    name: cellular_components
    examples:
    - value: '[{preferred_term: Peroxisome}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: cellular_components
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: CellularComponentDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_complexes:
    name: protein_complexes
    description: Protein complexes that gene products participate in
    examples:
    - value: '[{preferred_term: FA nuclear complex, term: {id: "GO:0043240", label:
        "Fanconi anaemia nuclear complex"}}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: protein_complexes
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: ProteinComplexDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  chemical_entities:
    name: chemical_entities
    examples:
    - value: '[{preferred_term: Plasmalogen}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: chemical_entities
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: ChemicalEntityDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  gene_products:
    name: gene_products
    description: Gene products (proteins, fusion proteins, oncoproteins) involved
      in this pathophysiology mechanism. Use NCIT terms for specific proteins.
    examples:
    - value: '[{preferred_term: BCR-ABL1 fusion protein, term: {id: NCIT:C16325, label:
        BCR/ABL1 Fusion Protein}}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene_products
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: GeneProductDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  triggers:
    name: triggers
    examples:
    - value: '[{preferred_term: Viral Infections}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: triggers
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: TriggerDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  assays:
    name: assays
    examples:
    - value: '[{preferred_term: Elevated Blood Glucose}]'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: assays
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    - Biochemical
    range: AssayDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  mechanisms:
    name: mechanisms
    examples:
    - value: '[''Thrombocytopenia'', ''Platelet Dysfunction'', ''Disseminated Intravascular
        Coagulation (DIC)'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mechanisms
    owner: Pathophysiology
    domain_of:
    - Pathophysiology
    range: string
    multivalued: 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: Pathophysiology
    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
  frequency:
    name: frequency
    examples:
    - value: Occasional
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: frequency
    owner: Pathophysiology
    domain_of:
    - PhenotypeContext
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity