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Class: Dataset

A reference to a publicly available omics or phenotype dataset

URI: dismech:class/Dataset

 classDiagram
    class Dataset
    click Dataset href "../../classes/Dataset/"
      Dataset : accession

      Dataset : conditions

      Dataset : data_type





        Dataset --> "0..1" DatasetTypeEnum : data_type
        click DatasetTypeEnum href "../../enums/DatasetTypeEnum/"



      Dataset : description

      Dataset : evidence





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



      Dataset : exposures





        Dataset --> "*" ExposureDescriptor : exposures
        click ExposureDescriptor href "../../classes/ExposureDescriptor/"



      Dataset : findings





        Dataset --> "*" Finding : findings
        click Finding href "../../classes/Finding/"



      Dataset : genes





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



      Dataset : notes

      Dataset : organism





        Dataset --> "0..1" OrganismDescriptor : organism
        click OrganismDescriptor href "../../classes/OrganismDescriptor/"



      Dataset : platform

      Dataset : publication

      Dataset : sample_count

      Dataset : sample_types





        Dataset --> "*" SampleTypeDescriptor : sample_types
        click SampleTypeDescriptor href "../../classes/SampleTypeDescriptor/"



      Dataset : title

Slots

Name Cardinality and Range Description Inheritance
accession 1
Uriorcurie		 Dataset accession identifier as a CURIE (e direct
title 0..1
String		 Title of the publication direct
description 0..1 recommended
String		 A description of the dataset direct
organism 0..1
OrganismDescriptor		 The organism from which samples were derived direct
data_type 0..1
DatasetTypeEnum		 The type of omics or other data in the dataset direct
sample_types *
SampleTypeDescriptor		 Types of biological samples in the dataset direct
sample_count 0..1
Integer		 Total number of samples in the dataset direct
conditions *
String		 Experimental conditions or disease states represented direct
exposures *
ExposureDescriptor		 Environmental exposures studied in the dataset direct
genes *
GeneDescriptor		 direct
platform 0..1
String		 Sequencing or array platform used direct
publication 0..1
PMID		 Associated publication (PMID) direct
findings *
Finding		 Key findings or claims extracted from this source (publication or dataset) direct
evidence * recommended
EvidenceItem		 direct
notes 0..1
String		 direct

Usages

used by used in type used
Experiment datasets range Dataset
Disease datasets range Dataset

Comments

  • Supports GEO, ArrayExpress, SRA, dbGaP, GTEx, ENCODE, MorPhiC, phenopacket-store, and other repositories

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Dataset
description: A reference to a publicly available omics or phenotype dataset
comments:
- Supports GEO, ArrayExpress, SRA, dbGaP, GTEx, ENCODE, MorPhiC, phenopacket-store,
  and other repositories
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- accession
- title
- description
- organism
- data_type
- sample_types
- sample_count
- conditions
- exposures
- genes
- platform
- publication
- findings
- evidence
- notes
slot_usage:
  description:
    name: description
    description: A description of the dataset. This may typically be redundant with
      the `title` slot, but the description is more human-readable and may be used
      to communicate nuances not captured by the rigid standardization of the title
      slot.
    recommended: true

Induced

name: Dataset
description: A reference to a publicly available omics or phenotype dataset
comments:
- Supports GEO, ArrayExpress, SRA, dbGaP, GTEx, ENCODE, MorPhiC, phenopacket-store,
  and other repositories
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  description:
    name: description
    description: A description of the dataset. This may typically be redundant with
      the `title` slot, but the description is more human-readable and may be used
      to communicate nuances not captured by the rigid standardization of the title
      slot.
    recommended: true
attributes:
  accession:
    name: accession
    implements:
    - linkml:authoritative_reference
    description: Dataset accession identifier as a CURIE (e.g., geo:GSE67472)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: accession
    owner: Dataset
    domain_of:
    - Dataset
    range: uriorcurie
    required: true
  title:
    name: title
    implements:
    - linkml:title
    description: Title of the publication
    comments:
    - 'The `linkml:title` annotation is INERT for linkml-reference-validator detection
      — lrv''s TitleURIs matches only "dcterms:title" / "dc/terms/title". Where this
      slot IS title-checked (on PublicationReference) that happens via lrv''s exact-name
      fallback FallbackSlotNames.TITLE = ("title",), not via this annotation. Kept
      because it is a reasonable semantic mapping, and noted here for the same reason
      the EvidenceItem `reference_title` comment exists: an annotation that looks
      like it enables a check, but does not, misleads readers. The title-normalization
      work that this deferral pointed at has now happened (EvidenceItem.reference_title
      carries `dcterms:title` and is checked), but this slot is still NOT retargeted:
      it is shared by PublicationReference, Dataset and TrackedIssue, so swapping
      the URI would newly expose Dataset.title and TrackedIssue.title to lrv detection.
      PublicationReference.title loses nothing by waiting — it is already checked
      via the exact-name fallback. Retarget only alongside a check of what the other
      two classes would then be asserting.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: title
    owner: Dataset
    domain_of:
    - Dataset
    - PublicationReference
    - TrackedIssue
    range: string
  description:
    name: description
    description: A description of the dataset. This may typically be redundant with
      the `title` slot, but the description is more human-readable and may be used
      to communicate nuances not captured by the rigid standardization of the title
      slot.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Dataset
    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
    recommended: true
  organism:
    name: organism
    description: The organism from which samples were derived
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: organism
    owner: Dataset
    domain_of:
    - Dataset
    - ExperimentalModel
    range: OrganismDescriptor
    inlined: true
  data_type:
    name: data_type
    description: The type of omics or other data in the dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: data_type
    owner: Dataset
    domain_of:
    - Dataset
    range: DatasetTypeEnum
  sample_types:
    name: sample_types
    description: Types of biological samples in the dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: sample_types
    owner: Dataset
    domain_of:
    - Dataset
    range: SampleTypeDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  sample_count:
    name: sample_count
    description: Total number of samples in the dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: sample_count
    owner: Dataset
    domain_of:
    - Dataset
    range: integer
  conditions:
    name: conditions
    description: Experimental conditions or disease states represented
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: conditions
    owner: Dataset
    domain_of:
    - Dataset
    - ExperimentalModel
    range: string
    multivalued: true
  exposures:
    name: exposures
    description: Environmental exposures studied in the dataset
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: exposures
    owner: Dataset
    domain_of:
    - Dataset
    range: ExposureDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: Dataset
    domain_of:
    - GeneticContext
    - Dataset
    - ExperimentalPerturbation
    - Subtype
    - Pathophysiology
    - AnimalModel
    range: GeneDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  platform:
    name: platform
    description: Sequencing or array platform used
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: platform
    owner: Dataset
    domain_of:
    - Dataset
    range: string
  publication:
    name: publication
    description: Associated publication (PMID)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: publication
    owner: Dataset
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - ProteinStructure
    - AnimalModel
    range: PMID
  findings:
    name: findings
    description: Key findings or claims extracted from this source (publication or
      dataset)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: findings
    owner: Dataset
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - PublicationReference
    range: Finding
    multivalued: true
    inlined: true
    inlined_as_list: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Dataset
    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: Dataset
    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