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Class: GeneDiseaseValidityAssertion

One external classification of how well established a gene-disease relationship is: the tier, who assigned it, and the assertion's identifier. Attribution is required because a tier is only meaningful under the framework that produced it; dismech records such tiers and does not assign them (#10179). just check-gene-validity compares a ClinGen assertion against its cached CGGV: record.

URI: dismech:class/GeneDiseaseValidityAssertion

 classDiagram
    class GeneDiseaseValidityAssertion
    click GeneDiseaseValidityAssertion href "../../classes/GeneDiseaseValidityAssertion/"
      GeneDiseaseValidityAssertion : classified_by





        GeneDiseaseValidityAssertion --> "1" GeneDiseaseValiditySourceEnum : classified_by
        click GeneDiseaseValiditySourceEnum href "../../enums/GeneDiseaseValiditySourceEnum/"



      GeneDiseaseValidityAssertion : evidence





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



      GeneDiseaseValidityAssertion : external_id

      GeneDiseaseValidityAssertion : notes

      GeneDiseaseValidityAssertion : subtype

      GeneDiseaseValidityAssertion : validity_classification





        GeneDiseaseValidityAssertion --> "1" GeneDiseaseValidityClassificationEnum : validity_classification
        click GeneDiseaseValidityClassificationEnum href "../../enums/GeneDiseaseValidityClassificationEnum/"

Slots

Name Cardinality and Range Description Inheritance
validity_classification 1
GeneDiseaseValidityClassificationEnum		 The tier assigned, copied from the source named in classified_by direct
classified_by 1
GeneDiseaseValiditySourceEnum		 The external curation body that assigned the classification direct
external_id 0..1 recommended
String		 The source's identifier for this assertion direct
subtype 0..1
String		 The has_subtypes[] direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
Genetic gene_disease_validity range GeneDiseaseValidityAssertion

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GeneDiseaseValidityAssertion
description: 'One external classification of how well established a gene-disease relationship
  is: the tier, who assigned it, and the assertion''s identifier. Attribution is required
  because a tier is only meaningful under the framework that produced it; dismech
  records such tiers and does not assign them (#10179). `just check-gene-validity`
  compares a ClinGen assertion against its cached `CGGV:` record.'
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- validity_classification
- classified_by
- external_id
- subtype
- evidence
- notes
slot_usage:
  validity_classification:
    name: validity_classification
    required: true
  classified_by:
    name: classified_by
    required: true
  external_id:
    name: external_id
    description: The source's identifier for this assertion. For ClinGen, the `CGGV:assertion_...`
      CURIE, which is also what the evidence item cites; `just check-gene-validity`
      reads the cached record and fails if its classification differs.
    recommended: true
  subtype:
    name: subtype
    description: 'The has_subtypes[].name this classification applies to, when the
      entry''s subtypes are classified separately (ATP7A: Menkes disease and X-linked
      distal SMA).'

Induced

name: GeneDiseaseValidityAssertion
description: 'One external classification of how well established a gene-disease relationship
  is: the tier, who assigned it, and the assertion''s identifier. Attribution is required
  because a tier is only meaningful under the framework that produced it; dismech
  records such tiers and does not assign them (#10179). `just check-gene-validity`
  compares a ClinGen assertion against its cached `CGGV:` record.'
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  validity_classification:
    name: validity_classification
    required: true
  classified_by:
    name: classified_by
    required: true
  external_id:
    name: external_id
    description: The source's identifier for this assertion. For ClinGen, the `CGGV:assertion_...`
      CURIE, which is also what the evidence item cites; `just check-gene-validity`
      reads the cached record and fails if its classification differs.
    recommended: true
  subtype:
    name: subtype
    description: 'The has_subtypes[].name this classification applies to, when the
      entry''s subtypes are classified separately (ATP7A: Menkes disease and X-linked
      distal SMA).'
attributes:
  validity_classification:
    name: validity_classification
    description: The tier assigned, copied from the source named in `classified_by`.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: validity_classification
    owner: GeneDiseaseValidityAssertion
    domain_of:
    - GeneDiseaseValidityAssertion
    range: GeneDiseaseValidityClassificationEnum
    required: true
  classified_by:
    name: classified_by
    description: The external curation body that assigned the classification. Required,
      so a tier is never recorded without saying whose it is.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: classified_by
    owner: GeneDiseaseValidityAssertion
    domain_of:
    - GeneDiseaseValidityAssertion
    range: GeneDiseaseValiditySourceEnum
    required: true
  external_id:
    name: external_id
    description: The source's identifier for this assertion. For ClinGen, the `CGGV:assertion_...`
      CURIE, which is also what the evidence item cites; `just check-gene-validity`
      reads the cached record and fails if its classification differs.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: external_id
    owner: GeneDiseaseValidityAssertion
    domain_of:
    - ExternalAssertion
    - GeneDiseaseValidityAssertion
    range: string
    recommended: true
  subtype:
    name: subtype
    description: 'The has_subtypes[].name this classification applies to, when the
      entry''s subtypes are classified separately (ATP7A: Menkes disease and X-linked
      distal SMA).'
    examples:
    - value: Eyelid Myoclonia with Absences
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: subtype
    owner: GeneDiseaseValidityAssertion
    domain_of:
    - PhenotypeContext
    - Prevalence
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    range: string
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: GeneDiseaseValidityAssertion
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    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: GeneDiseaseValidityAssertion
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - GeneClassification
    - GeneClassificationCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - Transmission
    - Diagnosis
    - VariantPopulationEffect
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string