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Class: Genetic

URI: dismech:class/Genetic

 classDiagram
    class Genetic
    click Genetic href "../../classes/Genetic/"
      Genetic : association

      Genetic : evidence





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



      Genetic : examples

      Genetic : features

      Genetic : frequency





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



      Genetic : gene_term





        Genetic --> "0..1" GeneDescriptor : gene_term
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      Genetic : inheritance





        Genetic --> "*" Inheritance : inheritance
        click Inheritance href "../../classes/Inheritance/"



      Genetic : name

      Genetic : notes

      Genetic : presence

      Genetic : relationship_type





        Genetic --> "0..1" GeneDiseaseRelationshipEnum : relationship_type
        click GeneDiseaseRelationshipEnum href "../../enums/GeneDiseaseRelationshipEnum/"



      Genetic : review_notes

      Genetic : subtype

      Genetic : variant_origin





        Genetic --> "0..1" VariantOriginEnum : variant_origin
        click VariantOriginEnum href "../../enums/VariantOriginEnum/"



      Genetic : variants





        Genetic --> "*" Variant : variants
        click Variant href "../../classes/Variant/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
gene_term 0..1
GeneDescriptor		 The HGNC term for this gene direct
presence 0..1
String		 direct
evidence * recommended
EvidenceItem		 direct
association 0..1
String		 Free-text descriptor of how the gene is associated with the disease direct
relationship_type 0..1
GeneDiseaseRelationshipEnum		 Controlled-vocabulary classification of the gene-disease relationship (e direct
variant_origin 0..1
VariantOriginEnum		 The origin of disease-associated variation in this gene (germline, somatic, d... direct
review_notes 0..1
String		 direct
subtype 0..1
String		 direct
frequency 0..1
Any or 
FrequencyEnum or 
FrequencyQuantity		 direct
inheritance *
Inheritance		 direct
variants *
Variant		 direct
features 0..1
String		 direct
notes 0..1
String		 direct
examples *
String		 direct

Usages

used by used in type used
Disease genetic range Genetic

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Genetic
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- gene_term
- presence
- evidence
- association
- relationship_type
- variant_origin
- review_notes
- subtype
- frequency
- inheritance
- variants
- features
- notes
- examples

Induced

name: Genetic
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: Genetic
    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
  gene_term:
    name: gene_term
    description: The HGNC term for this gene
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene_term
    owner: Genetic
    domain_of:
    - Genetic
    range: GeneDescriptor
    inlined: true
  presence:
    name: presence
    examples:
    - value: Positive
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: presence
    owner: Genetic
    domain_of:
    - Biochemical
    - Genetic
    - Environmental
    - Diagnosis
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Genetic
    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
  association:
    name: association
    description: Free-text descriptor of how the gene is associated with the disease.
      For a controlled vocabulary, also set `relationship_type`.
    examples:
    - value: Susceptibility
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: association
    owner: Genetic
    domain_of:
    - Genetic
    range: string
  relationship_type:
    name: relationship_type
    description: Controlled-vocabulary classification of the gene-disease relationship
      (e.g., causative, risk factor, modifier, somatic driver). Use this in addition
      to the free-text `association` slot when possible.
    examples:
    - value: RISK_FACTOR
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: relationship_type
    owner: Genetic
    domain_of:
    - Genetic
    range: GeneDiseaseRelationshipEnum
  variant_origin:
    name: variant_origin
    description: The origin of disease-associated variation in this gene (germline,
      somatic, de novo, or both). Bound to GENO allele origin terms.
    examples:
    - value: SOMATIC
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: variant_origin
    owner: Genetic
    domain_of:
    - Genetic
    range: VariantOriginEnum
  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: Genetic
    domain_of:
    - ClinicalTrial
    - Subtype
    - ProgressionInfo
    - Phenotype
    - Genetic
    - Environmental
    - Disease
    - 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: Genetic
    domain_of:
    - PhenotypeContext
    - Prevalence
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: string
  frequency:
    name: frequency
    examples:
    - value: Occasional
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: frequency
    owner: Genetic
    domain_of:
    - PhenotypeContext
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  inheritance:
    name: inheritance
    examples:
    - value: Autosomal Dominant
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: inheritance
    owner: Genetic
    domain_of:
    - Subtype
    - Genetic
    - Disease
    range: Inheritance
    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: Genetic
    domain_of:
    - Genetic
    - Disease
    range: Variant
    multivalued: true
    inlined: true
    inlined_as_list: true
  features:
    name: features
    examples:
    - value: DNA virus from the Orthopoxvirus genus
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: features
    owner: Genetic
    domain_of:
    - Genetic
    range: string
  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: Genetic
    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
  examples:
    name: examples
    examples:
    - value: '[''Kaposi Sarcoma'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: examples
    owner: Genetic
    domain_of:
    - Pathophysiology
    - Genetic
    - Environmental
    - Stage
    - Treatment
    range: string
    multivalued: true