Class: ModelDivergence

One typed way in which a model departs from the mechanism node it is linked to, with the curator's explanation of why that gap applies to this particular claim.

URI: dismech:class/ModelDivergence

 classDiagram
    class ModelDivergence
    click ModelDivergence href "../../classes/ModelDivergence/"
      ModelDivergence : description

      ModelDivergence : divergence_type





        ModelDivergence --> "1" ModelDivergenceTypeEnum : divergence_type
        click ModelDivergenceTypeEnum href "../../enums/ModelDivergenceTypeEnum/"



      ModelDivergence : evidence





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



      ModelDivergence : materiality





        ModelDivergence --> "0..1" ModelDivergenceMaterialityEnum : materiality
        click ModelDivergenceMaterialityEnum href "../../enums/ModelDivergenceMaterialityEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
divergence_type	1 ModelDivergenceTypeEnum	Kind of departure between the model and the mechanism it is linked to	direct
description	1 String	Why this kind of divergence applies to this link, in specific terms -- which ...	direct
materiality	0..1 ModelDivergenceMaterialityEnum	Whether this specific divergence bears on the specific claim the link makes	direct
evidence	* recommended EvidenceItem	Optional citation for the divergence itself, when it is a published finding r...	direct

Usages

used by	used in	type	used
ModelMechanismLink	divergences	range	ModelDivergence

Comments

• The point of the type is queryability -- "which models are limited by calibration provenance rather than by species" is not answerable against a prose limitations string. The point of the required description is that the type alone is never the argument: BOUNDARY_OMISSION says a component is missing, not which one or why it matters here.
• Orthogonal to relationship and fidelity. A link can be RECAPITULATES with several QUALIFYING divergences, or PARTIALLY_RECAPITULATES for a reason that is not a divergence in this taxonomy at all.

See Also

• PMID:32993675
• https://www.asme.org/codes-standards/find-codes-standards/assessing-credibility-of-computational-modeling-through-verification-and-validation-application-to-medical-devices
• https://www.fda.gov/regulatory-information/search-fda-guidance-documents/assessing-credibility-computational-modeling-and-simulation-medical-device-submissions

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ModelDivergence
description: One typed way in which a model departs from the mechanism node it is
  linked to, with the curator's explanation of why that gap applies to this particular
  claim.
comments:
- 'The point of the type is queryability -- "which models are limited by calibration
  provenance rather than by species" is not answerable against a prose `limitations`
  string. The point of the required `description` is that the type alone is never
  the argument: BOUNDARY_OMISSION says a component is missing, not which one or why
  it matters here.'
- Orthogonal to `relationship` and `fidelity`. A link can be RECAPITULATES with several
  QUALIFYING divergences, or PARTIALLY_RECAPITULATES for a reason that is not a divergence
  in this taxonomy at all.
from_schema: https://w3id.org/monarch-initiative/dismech
see_also:
- PMID:32993675
- https://www.asme.org/codes-standards/find-codes-standards/assessing-credibility-of-computational-modeling-through-verification-and-validation-application-to-medical-devices
- https://www.fda.gov/regulatory-information/search-fda-guidance-documents/assessing-credibility-computational-modeling-and-simulation-medical-device-submissions
slots:
- divergence_type
- description
- materiality
- evidence
slot_usage:
  divergence_type:
    name: divergence_type
    required: true
  description:
    name: description
    description: Why this kind of divergence applies to this link, in specific terms
      -- which component is outside the boundary, which quantity is standing in for
      which, which cohort the calibration came from. Never a restatement of the enum
      value.
    required: true
  evidence:
    name: evidence
    description: Optional citation for the divergence itself, when it is a published
      finding rather than a reading of the model's own scope -- a later study displacing
      an assumption the model encodes, for instance.

Induced

name: ModelDivergence
description: One typed way in which a model departs from the mechanism node it is
  linked to, with the curator's explanation of why that gap applies to this particular
  claim.
comments:
- 'The point of the type is queryability -- "which models are limited by calibration
  provenance rather than by species" is not answerable against a prose `limitations`
  string. The point of the required `description` is that the type alone is never
  the argument: BOUNDARY_OMISSION says a component is missing, not which one or why
  it matters here.'
- Orthogonal to `relationship` and `fidelity`. A link can be RECAPITULATES with several
  QUALIFYING divergences, or PARTIALLY_RECAPITULATES for a reason that is not a divergence
  in this taxonomy at all.
from_schema: https://w3id.org/monarch-initiative/dismech
see_also:
- PMID:32993675
- https://www.asme.org/codes-standards/find-codes-standards/assessing-credibility-of-computational-modeling-through-verification-and-validation-application-to-medical-devices
- https://www.fda.gov/regulatory-information/search-fda-guidance-documents/assessing-credibility-computational-modeling-and-simulation-medical-device-submissions
slot_usage:
  divergence_type:
    name: divergence_type
    required: true
  description:
    name: description
    description: Why this kind of divergence applies to this link, in specific terms
      -- which component is outside the boundary, which quantity is standing in for
      which, which cohort the calibration came from. Never a restatement of the enum
      value.
    required: true
  evidence:
    name: evidence
    description: Optional citation for the divergence itself, when it is a published
      finding rather than a reading of the model's own scope -- a later study displacing
      an assumption the model encodes, for instance.
attributes:
  divergence_type:
    name: divergence_type
    description: Kind of departure between the model and the mechanism it is linked
      to
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: divergence_type
    owner: ModelDivergence
    domain_of:
    - ModelDivergence
    range: ModelDivergenceTypeEnum
    required: true
  description:
    name: description
    description: Why this kind of divergence applies to this link, in specific terms
      -- which component is outside the boundary, which quantity is standing in for
      which, which cohort the calibration came from. Never a restatement of the enum
      value.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: ModelDivergence
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string
    required: true
  materiality:
    name: materiality
    description: Whether this specific divergence bears on the specific claim the
      link makes. Per-divergence, where `fidelity` is per-link.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: materiality
    owner: ModelDivergence
    domain_of:
    - ModelDivergence
    range: ModelDivergenceMaterialityEnum
  evidence:
    name: evidence
    description: Optional citation for the divergence itself, when it is a published
      finding rather than a reading of the model's own scope -- a later study displacing
      an assumption the model encodes, for instance.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: ModelDivergence
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - 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