Class: Pathophysiology
URI: dismech:class/Pathophysiology
classDiagram
class Pathophysiology
click Pathophysiology href "../../classes/Pathophysiology/"
Pathophysiology : assays
Pathophysiology --> "*" AssayDescriptor : assays
click AssayDescriptor href "../../classes/AssayDescriptor/"
Pathophysiology : biological_processes
Pathophysiology --> "*" BiologicalProcessDescriptor : biological_processes
click BiologicalProcessDescriptor href "../../classes/BiologicalProcessDescriptor/"
Pathophysiology : cell_types
Pathophysiology --> "*" CellTypeDescriptor : cell_types
click CellTypeDescriptor href "../../classes/CellTypeDescriptor/"
Pathophysiology : cellular_components
Pathophysiology --> "*" CellularComponentDescriptor : cellular_components
click CellularComponentDescriptor href "../../classes/CellularComponentDescriptor/"
Pathophysiology : chemical_entities
Pathophysiology --> "*" ChemicalEntityDescriptor : chemical_entities
click ChemicalEntityDescriptor href "../../classes/ChemicalEntityDescriptor/"
Pathophysiology : conforms_to
Pathophysiology : consequence
Pathophysiology : consequences
Pathophysiology : description
Pathophysiology : downstream
Pathophysiology --> "*" CausalEdge : downstream
click CausalEdge href "../../classes/CausalEdge/"
Pathophysiology : evidence
Pathophysiology --> "* _recommended_" EvidenceItem : evidence
click EvidenceItem href "../../classes/EvidenceItem/"
Pathophysiology : examples
Pathophysiology : frequency
Pathophysiology --> "0..1" Any : frequency
click Any href "../../classes/Any/"
Pathophysiology : gene
Pathophysiology --> "0..1" GeneDescriptor : gene
click GeneDescriptor href "../../classes/GeneDescriptor/"
Pathophysiology : gene_products
Pathophysiology --> "*" GeneProductDescriptor : gene_products
click GeneProductDescriptor href "../../classes/GeneProductDescriptor/"
Pathophysiology : genes
Pathophysiology --> "*" GeneDescriptor : genes
click GeneDescriptor href "../../classes/GeneDescriptor/"
Pathophysiology : genetic_context
Pathophysiology --> "0..1" GeneticContext : genetic_context
click GeneticContext href "../../classes/GeneticContext/"
Pathophysiology : locations
Pathophysiology --> "*" AnatomicalEntityDescriptor : locations
click AnatomicalEntityDescriptor href "../../classes/AnatomicalEntityDescriptor/"
Pathophysiology : mechanism_confidence
Pathophysiology --> "0..1" MechanismConfidenceEnum : mechanism_confidence
click MechanismConfidenceEnum href "../../enums/MechanismConfidenceEnum/"
Pathophysiology : mechanisms
Pathophysiology : molecular_functions
Pathophysiology --> "*" MolecularFunctionDescriptor : molecular_functions
click MolecularFunctionDescriptor href "../../classes/MolecularFunctionDescriptor/"
Pathophysiology : name
Pathophysiology : notes
Pathophysiology : pathways
Pathophysiology --> "*" BiologicalProcessDescriptor : pathways
click BiologicalProcessDescriptor href "../../classes/BiologicalProcessDescriptor/"
Pathophysiology : pdb_structures
Pathophysiology --> "*" ProteinStructure : pdb_structures
click ProteinStructure href "../../classes/ProteinStructure/"
Pathophysiology : protein_complexes
Pathophysiology --> "*" ProteinComplexDescriptor : protein_complexes
click ProteinComplexDescriptor href "../../classes/ProteinComplexDescriptor/"
Pathophysiology : role
Pathophysiology : subtypes
Pathophysiology : synonyms
Pathophysiology : triggers
Pathophysiology --> "*" TriggerDescriptor : triggers
click TriggerDescriptor href "../../classes/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 | |
| molecular_functions | * MolecularFunctionDescriptor |
direct | |
| locations | * AnatomicalEntityDescriptor |
direct | |
| examples | * String |
direct | |
| role | 0..1 String |
direct | |
| conforms_to | 0..1 String |
Reference to a mechanism module that this pathophysiology node is an organ-sp... | 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 |
Names of subtypes (foreign keys to this disease's `has_subtypes[] | 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 | |
| genetic_context | 0..1 GeneticContext |
The genetic context under which this qualification applies | direct |
| pdb_structures | * ProteinStructure |
Experimental or predicted 3D protein structures relevant to this treatment's ... | direct |
| mechanism_confidence | 0..1 MechanismConfidenceEnum |
Level of confidence in this pathophysiology mechanism | 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
- molecular_functions
- locations
- examples
- role
- conforms_to
- synonyms
- consequence
- consequences
- gene
- pathways
- downstream
- genes
- subtypes
- cellular_components
- protein_complexes
- chemical_entities
- gene_products
- triggers
- assays
- mechanisms
- notes
- frequency
- genetic_context
- pdb_structures
- mechanism_confidence
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:
- ExperimentalModel
- ClinicalTrial
- ComputationalModel
- ModelVariable
- SeverityTier
- DifferentialDiagnosis
- Subtype
- ExternalAssertion
- 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
- DietaryModification
- GeneticContext
- Dataset
- ExperimentalModel
- ClinicalTrial
- ComputationalModel
- ModelVariable
- DifferentialDiagnosis
- Subtype
- CausalEdge
- TreatmentMechanismTarget
- ModelMechanismLink
- ProteinStructure
- ExternalAssertion
- 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:
- ExperimentalModel
- 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
- ExperimentalModel
- ClinicalTrial
- ComputationalModel
- DifferentialDiagnosis
- Subtype
- CausalEdge
- TreatmentMechanismTarget
- ModelMechanismLink
- ExternalAssertion
- 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
molecular_functions:
name: molecular_functions
examples:
- value: '[{preferred_term: Kinase Activity}]'
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
alias: molecular_functions
owner: Pathophysiology
domain_of:
- Pathophysiology
range: MolecularFunctionDescriptor
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
conforms_to:
name: conforms_to
description: 'Reference to a mechanism module that this pathophysiology node is
an organ-specific instance of. Value is a path relative to kb/modules/ (e.g.,
"fibrotic_response") plus an optional node name after a hash (e.g., "fibrotic_response#Mesenchymal
Cell Activation"). Used for cross-disorder consistency checking: if a node declares
conformance, it should include the expected cell types, biological processes,
and causal edges defined in the referenced module node.'
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
alias: conforms_to
owner: Pathophysiology
domain_of:
- Pathophysiology
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
description: Names of subtypes (foreign keys to this disease's `has_subtypes[].name`)
associated with a phenotype, biochemical finding, pathophysiology node, or other
subtyped entry. Use this multivalued form when an item is characteristic of
more than one subtype with overlapping features. For single-subtype associations,
the scalar `subtype` slot may still be used.
examples:
- value: '[''DENV-1'', ''DENV-2'', ''DENV-3'', ''DENV-4'']'
- value: '[''Type 1'', ''Type 2'']'
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
alias: subtypes
owner: Pathophysiology
domain_of:
- Pathophysiology
- Phenotype
- Biochemical
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
- ExperimentalModel
- ClinicalTrial
- ComputationalModel
- ModelVariable
- DifferentialDiagnosis
- ExternalAssertion
- TrackedIssue
- 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
genetic_context:
name: genetic_context
description: The genetic context under which this qualification applies. May specify
genes, mutation types, zygosity, complementation groups, or complex genotypes.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
alias: genetic_context
owner: Pathophysiology
domain_of:
- PhenotypeContext
- Pathophysiology
range: GeneticContext
inlined: true
pdb_structures:
name: pdb_structures
description: Experimental or predicted 3D protein structures relevant to this
treatment's mechanism of action. Typically co-crystal structures of the drug
bound to its target protein, or AlphaFold predictions of the drug target.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
alias: pdb_structures
owner: Pathophysiology
domain_of:
- Pathophysiology
- Treatment
range: ProteinStructure
multivalued: true
inlined: true
inlined_as_list: true
mechanism_confidence:
name: mechanism_confidence
description: Level of confidence in this pathophysiology mechanism. If not specified,
the mechanism is assumed to be established.
from_schema: https://w3id.org/monarch-initiative/dismech
rank: 1000
alias: mechanism_confidence
owner: Pathophysiology
domain_of:
- Pathophysiology
range: MechanismConfidenceEnum