Class: Genetic

URI: dismech:class/Genetic

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





        Genetic --> "*" GenomicRegion : affected_regions
        click GenomicRegion href "../../classes/GenomicRegion/"



      Genetic : association

      Genetic : case_fractions





        Genetic --> "*" GeneCaseFraction : case_fractions
        click GeneCaseFraction href "../../classes/GeneCaseFraction/"



      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_disease_validity





        Genetic --> "*" GeneDiseaseValidityAssertion : gene_disease_validity
        click GeneDiseaseValidityAssertion href "../../classes/GeneDiseaseValidityAssertion/"



      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 : mhc_term





        Genetic --> "0..1" MHCDescriptor : mhc_term
        click MHCDescriptor href "../../classes/MHCDescriptor/"



      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
mhc_term	0..1 MHCDescriptor	Optional MRO (MHC Restriction Ontology) term for an HLA/MHC allele, serotype,...	direct
affected_regions	* GenomicRegion	Named genomic regions affected by the physical alteration, including regulato...	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 FrequencyEnum or FrequencyQuantity or Any		direct
case_fractions	* GeneCaseFraction	Per-cohort estimates of the fraction of cases of a genetically heterogeneous ...	direct
gene_disease_validity	* GeneDiseaseValidityAssertion	Gene-disease validity classifications made by external curation bodies for th...	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
- mhc_term
- affected_regions
- presence
- evidence
- association
- relationship_type
- variant_origin
- review_notes
- subtype
- frequency
- case_fractions
- gene_disease_validity
- 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:
    - GenomicRegion
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    - Grouping
    - ModuleCollection
    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
  mhc_term:
    name: mhc_term
    description: 'Optional MRO (MHC Restriction Ontology) term for an HLA/MHC allele,
      serotype, haplotype, or presenting protein complex. On a Genetic entry, complements
      `gene_term` (which binds the locus in HGNC, e.g. HLA-DQA1 or HLA-B) with the
      allele, serotype, haplotype, or heterodimer specificity (e.g. `MRO:0000283`
      HLA-DQ2 serotype, `MRO:0001284` HLA-DRB1*03:01 protein complex). On a TreatmentEffectModifier
      with `effect_modifier_type: GENOTYPE`, grounds an HLA-restricted vaccine or
      immunotherapy responder/non-responder stratum.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: mhc_term
    owner: Genetic
    domain_of:
    - Genetic
    - TreatmentEffectModifier
    range: MHCDescriptor
    inlined: true
  affected_regions:
    name: affected_regions
    description: Named genomic regions affected by the physical alteration, including
      regulatory elements or chromosome intervals. Each item describes the named feature,
      which need not span the entire variant. Record only source-supported locations;
      disease-level regions need not have exact patient-specific breakpoints. Evidence
      belongs on the enclosing record. Location landmarks do not assert regulatory
      targeting or causal gene involvement. Existing free-text descriptions remain
      valid.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: affected_regions
    owner: Genetic
    domain_of:
    - GeneticContext
    - Genetic
    - Variant
    range: GenomicRegion
    multivalued: true
    inlined: true
    inlined_as_list: 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
    - 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
  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:
    - GeneticContext
    - 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
    - Pathophysiology
    - 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
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - 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
    - ImagingFinding
    - Genetic
    range: Any
    any_of:
    - range: FrequencyEnum
    - range: FrequencyQuantity
  case_fractions:
    name: case_fractions
    description: Per-cohort estimates of the fraction of cases of a genetically heterogeneous
      disease attributable to this gene (the genetic-spectrum analog of population
      Prevalence records). Multivalued because the share varies by cohort/ancestry.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: case_fractions
    owner: Genetic
    domain_of:
    - Genetic
    range: GeneCaseFraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  gene_disease_validity:
    name: gene_disease_validity
    description: 'Gene-disease validity classifications made by external curation
      bodies for this gene and this entry''s disease. Each records the tier, who assigned
      it, and the identifier of the assertion. Multivalued because one gene-disease
      pair can carry several: ClinGen classifies each mode of inheritance separately,
      an entry''s subtypes can be separate ClinGen diseases, and GenCC submitters
      do not always agree. Leave absent when no external body has classified the pair;
      that is not the same as NO_KNOWN_DISEASE_RELATIONSHIP.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene_disease_validity
    owner: Genetic
    domain_of:
    - Genetic
    range: GeneDiseaseValidityAssertion
    multivalued: true
    inlined: true
    inlined_as_list: true
  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
    - 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
  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