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Class: AnimalModel

A whole-organism animal model of the disease. This is the home for animal models; non-animal systems (organoids, organ-chips, cell lines, iPSC-derived and primary cultures) belong in experimental_models as ExperimentalModel.

URI: dismech:class/AnimalModel

 classDiagram
    class AnimalModel
    click AnimalModel href "../../classes/AnimalModel/"
      AnimalModel : alleles

      AnimalModel : associated_phenotypes

      AnimalModel : background

      AnimalModel : category

      AnimalModel : description

      AnimalModel : evidence





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



      AnimalModel : genes





        AnimalModel --> "*" GeneDescriptor : genes
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      AnimalModel : genotype

      AnimalModel : modeled_mechanisms





        AnimalModel --> "*" ModelMechanismLink : modeled_mechanisms
        click ModelMechanismLink href "../../classes/ModelMechanismLink/"



      AnimalModel : name

      AnimalModel : notes

      AnimalModel : publication

      AnimalModel : species

Slots

Name Cardinality and Range Description Inheritance
species 0..1
String		 direct
genotype 0..1
String		 direct
background 0..1
String		 direct
genes *
GeneDescriptor		 direct
category 0..1
String		 direct
alleles *
String		 direct
description 0..1
String		 direct
publication 0..1
PMID		 Primary publication describing the model, when one paper is the canonical ref... direct
associated_phenotypes *
String		 direct
modeled_mechanisms *
ModelMechanismLink		 Pathophysiology mechanism nodes this animal model recapitulates, perturbs, me... direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct
name 0..1 recommended
String		 Short stable label for the model, e direct

Usages

used by used in type used
Disease animal_models range AnimalModel

Comments

  • Use modeled_mechanisms to link the model to the pathophysiology nodes it recapitulates, perturbs, measures, or fails to recapitulate, so the model appears in the pathograph rather than as a disconnected list.
  • name is optional but recommended once modeled_mechanisms is populated: it is the stable label used for pathograph nodes and in-page anchors. When absent, renderers fall back to a label derived from genotype and species, which is not stable across edits and collides when one entry file carries two models of the same genotype.
  • Animal-model evidence should carry evidence_source: MODEL_ORGANISM and should not be the sole support for a human phenotype.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: AnimalModel
description: A whole-organism animal model of the disease. This is the home for animal
  models; non-animal systems (organoids, organ-chips, cell lines, iPSC-derived and
  primary cultures) belong in `experimental_models` as ExperimentalModel.
comments:
- Use `modeled_mechanisms` to link the model to the pathophysiology nodes it recapitulates,
  perturbs, measures, or fails to recapitulate, so the model appears in the pathograph
  rather than as a disconnected list.
- '`name` is optional but recommended once `modeled_mechanisms` is populated: it is
  the stable label used for pathograph nodes and in-page anchors. When absent, renderers
  fall back to a label derived from genotype and species, which is not stable across
  edits and collides when one entry file carries two models of the same genotype.'
- 'Animal-model evidence should carry `evidence_source: MODEL_ORGANISM` and should
  not be the sole support for a human phenotype.'
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- species
- genotype
- background
- genes
- category
- alleles
- description
- publication
- associated_phenotypes
- modeled_mechanisms
- evidence
- notes
slot_usage:
  publication:
    name: publication
    description: Primary publication describing the model, when one paper is the canonical
      reference for it. Per-claim citations still go in `evidence`.
  modeled_mechanisms:
    name: modeled_mechanisms
    description: Pathophysiology mechanism nodes this animal model recapitulates,
      perturbs, measures, rescues, or fails to recapitulate.
attributes:
  name:
    name: name
    description: 'Short stable label for the model, e.g. "SOD1-G93A transgenic mouse".
      Used as the pathograph node label and in-page anchor. Optional but recommended
      once `modeled_mechanisms` is populated. Defined as a class-local attribute (not
      the global identifier `name` slot) so it is a plain optional label: 425 of 439
      existing animal models omit it, and AnimalModel is an inlined object that needs
      no identifier.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    domain_of:
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - 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
    recommended: true

Induced

name: AnimalModel
description: A whole-organism animal model of the disease. This is the home for animal
  models; non-animal systems (organoids, organ-chips, cell lines, iPSC-derived and
  primary cultures) belong in `experimental_models` as ExperimentalModel.
comments:
- Use `modeled_mechanisms` to link the model to the pathophysiology nodes it recapitulates,
  perturbs, measures, or fails to recapitulate, so the model appears in the pathograph
  rather than as a disconnected list.
- '`name` is optional but recommended once `modeled_mechanisms` is populated: it is
  the stable label used for pathograph nodes and in-page anchors. When absent, renderers
  fall back to a label derived from genotype and species, which is not stable across
  edits and collides when one entry file carries two models of the same genotype.'
- 'Animal-model evidence should carry `evidence_source: MODEL_ORGANISM` and should
  not be the sole support for a human phenotype.'
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  publication:
    name: publication
    description: Primary publication describing the model, when one paper is the canonical
      reference for it. Per-claim citations still go in `evidence`.
  modeled_mechanisms:
    name: modeled_mechanisms
    description: Pathophysiology mechanism nodes this animal model recapitulates,
      perturbs, measures, rescues, or fails to recapitulate.
attributes:
  name:
    name: name
    description: 'Short stable label for the model, e.g. "SOD1-G93A transgenic mouse".
      Used as the pathograph node label and in-page anchor. Optional but recommended
      once `modeled_mechanisms` is populated. Defined as a class-local attribute (not
      the global identifier `name` slot) so it is a plain optional label: 425 of 439
      existing animal models omit it, and AnimalModel is an inlined object that needs
      no identifier.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    alias: name
    owner: AnimalModel
    domain_of:
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - 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
    recommended: true
  species:
    name: species
    examples:
    - value: Human
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: species
    owner: AnimalModel
    domain_of:
    - AnimalModel
    range: string
  genotype:
    name: genotype
    examples:
    - value: HLA-DQ2
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genotype
    owner: AnimalModel
    domain_of:
    - AnimalModel
    range: string
  background:
    name: background
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: background
    owner: AnimalModel
    domain_of:
    - AnimalModel
    range: string
  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: AnimalModel
    domain_of:
    - GeneticContext
    - Dataset
    - ExperimentalPerturbation
    - Subtype
    - Pathophysiology
    - AnimalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  category:
    name: category
    examples:
    - value: Hematologic
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: category
    owner: AnimalModel
    domain_of:
    - Phenotype
    - Disease
    - AnimalModel
    range: string
  alleles:
    name: alleles
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: alleles
    owner: AnimalModel
    domain_of:
    - AnimalModel
    range: string
    multivalued: true
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: AnimalModel
    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
  publication:
    name: publication
    description: Primary publication describing the model, when one paper is the canonical
      reference for it. Per-claim citations still go in `evidence`.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: publication
    owner: AnimalModel
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - ProteinStructure
    - AnimalModel
    range: PMID
  associated_phenotypes:
    name: associated_phenotypes
    examples:
    - value: '[''Celiac Disease'', ''Type 1 Diabetes'', ''Autoimmune Thyroid Disease'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: associated_phenotypes
    owner: AnimalModel
    domain_of:
    - AnimalModel
    range: string
    multivalued: true
  modeled_mechanisms:
    name: modeled_mechanisms
    description: Pathophysiology mechanism nodes this animal model recapitulates,
      perturbs, measures, rescues, or fails to recapitulate.
    comments:
    - Target names should match pathophysiology entry names in the same disease file
    - Use description to capture the specific assayable or modeled assertion, not
      just the node label
    - Use readouts on each link to record the outcome measures that ground the assertion
    - Applies to experimental (NAM), animal, and computational models alike
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: modeled_mechanisms
    owner: AnimalModel
    domain_of:
    - ExperimentalModel
    - ComputationalModel
    - AnimalModel
    range: ModelMechanismLink
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: AnimalModel
    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
  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: AnimalModel
    domain_of:
    - GeneticContext
    - OnsetDescriptor
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - ReferenceRange
    - SurrogateEndpoint
    - SurrogateEndpointCollection
    - ExternalAssertion
    - TrackedIssue
    - Prevalence
    - GeneCaseFraction
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - Transmission
    - Diagnosis
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - TermMapping
    - MappingConsistency
    - ComorbidityAssociation
    - AssociationSignal
    - AssociationMetric
    - AssociationStatistics
    - MechanisticHypothesis
    - Discussion
    - Grouping
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    range: string