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Class: Cohort

A group of individuals related in some phenotypic or genotypic aspect.

URI: phenopackets:Cohort

erDiagram Cohort { string description string id } MetaData { string created string createdBy string phenopacketSchemaVersion string submittedBy } Update { string comment string timestamp string updatedBy } Resource { string id string iriPrefix string name string namespacePrefix string url string version } ExternalReference { string description string id string reference } Phenopacket { string id } Individual { stringList alternateIds string dateOfBirth string id KaryotypicSex karyotypicSex Sex sex } PhenotypicFeature { string description boolean excluded } MedicalAction { } Measurement { string description } Interpretation { string id ProgressStatus progressStatus string summary } File { string uri } Disease { boolean excluded } Biosample { string derivedFromId string description string id string individualId } Cohort ||--}o File : "files" Cohort ||--}o Phenopacket : "members" Cohort ||--|| MetaData : "metaData" MetaData ||--}o ExternalReference : "externalReferences" MetaData ||--}o Resource : "resources" MetaData ||--}o Update : "updates" Phenopacket ||--}o Biosample : "biosamples" Phenopacket ||--}o Disease : "diseases" Phenopacket ||--}o File : "files" Phenopacket ||--}o Interpretation : "interpretations" Phenopacket ||--}o Measurement : "measurements" Phenopacket ||--}o MedicalAction : "medicalActions" Phenopacket ||--|| MetaData : "metaData" Phenopacket ||--}o PhenotypicFeature : "phenotypicFeatures" Phenopacket ||--|o Individual : "subject" Individual ||--|o OntologyClass : "gender" Individual ||--|o OntologyClass : "taxonomy" Individual ||--|o TimeElement : "timeAtLastEncounter" Individual ||--|o VitalStatus : "vitalStatus" PhenotypicFeature ||--}o Evidence : "evidence" PhenotypicFeature ||--}o OntologyClass : "modifiers" PhenotypicFeature ||--|o TimeElement : "onset" PhenotypicFeature ||--|o TimeElement : "resolution" PhenotypicFeature ||--|o OntologyClass : "severity" PhenotypicFeature ||--|o OntologyClass : "type" MedicalAction ||--}o OntologyClass : "adverseEvents" MedicalAction ||--|o Procedure : "procedure" MedicalAction ||--|o RadiationTherapy : "radiationTherapy" MedicalAction ||--|o OntologyClass : "responseToTreatment" MedicalAction ||--|o TherapeuticRegimen : "therapeuticRegimen" MedicalAction ||--|o Treatment : "treatment" MedicalAction ||--|o OntologyClass : "treatmentIntent" MedicalAction ||--|o OntologyClass : "treatmentTarget" MedicalAction ||--|o OntologyClass : "treatmentTerminationReason" Measurement ||--|o OntologyClass : "assay" Measurement ||--|o ComplexValue : "complexValue" Measurement ||--|o Procedure : "procedure" Measurement ||--|o TimeElement : "timeObserved" Measurement ||--|o Value : "value" Interpretation ||--|o Diagnosis : "diagnosis" File ||--|o Dictionary : "fileAttributes" File ||--|o Dictionary : "individualToFileIdentifiers" Disease ||--}o OntologyClass : "clinicalTnmFinding" Disease ||--}o OntologyClass : "diseaseStage" Disease ||--|o OntologyClass : "laterality" Disease ||--|o TimeElement : "onset" Disease ||--|o OntologyClass : "primarySite" Disease ||--|o TimeElement : "resolution" Disease ||--|o OntologyClass : "term" Biosample ||--}o OntologyClass : "diagnosticMarkers" Biosample ||--}o File : "files" Biosample ||--|o OntologyClass : "histologicalDiagnosis" Biosample ||--|o OntologyClass : "materialSample" Biosample ||--}o Measurement : "measurements" Biosample ||--|o OntologyClass : "pathologicalStage" Biosample ||--}o OntologyClass : "pathologicalTnmFinding" Biosample ||--}o PhenotypicFeature : "phenotypicFeatures" Biosample ||--|o Procedure : "procedure" Biosample ||--|o OntologyClass : "sampleProcessing" Biosample ||--|o OntologyClass : "sampleStorage" Biosample ||--|o OntologyClass : "sampleType" Biosample ||--|o OntologyClass : "sampledTissue" Biosample ||--|o OntologyClass : "taxonomy" Biosample ||--|o TimeElement : "timeOfCollection" Biosample ||--|o OntologyClass : "tumorGrade" Biosample ||--|o OntologyClass : "tumorProgression"

Slots

Name Cardinality and Range Description Inheritance
description 0..1
String		 direct
files 0..*
File		 Pointer to relevant file(s) for the cohort direct
id 0..1
String		 direct
members 0..*
Phenopacket		 direct
metaData 1..1
MetaData		 Structured definitions of the resources and ontologies used within the phenop... direct

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type Mapped Value
self phenopackets:Cohort
native phenopackets:Cohort

LinkML Source

Direct

name: Cohort
description: A group of individuals related in some phenotypic or genotypic aspect.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 4
    description: Pointer to relevant file(s) for the cohort. Files relating exclusively
      to individual phenopackets should be contained in the Phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - Biosample
    range: File
    inlined: true
    inlined_as_list: true
  id:
    name: id
    annotations:
      percent_encoded:
        tag: percent_encoded
        value: true
      rank:
        tag: rank
        value: 1
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  members:
    name: members
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Cohort
    - Member
    range: Phenopacket
    inlined: true
    inlined_as_list: true
  metaData:
    name: metaData
    annotations:
      rank:
        tag: rank
        value: 5
    description: Structured definitions of the resources and ontologies used within
      the phenopacket. REQUIRED
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    range: MetaData
    required: true

Induced

name: Cohort
description: A group of individuals related in some phenotypic or genotypic aspect.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: description
    owner: Cohort
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 4
    description: Pointer to relevant file(s) for the cohort. Files relating exclusively
      to individual phenopackets should be contained in the Phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: files
    owner: Cohort
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - Biosample
    range: File
    inlined: true
    inlined_as_list: true
  id:
    name: id
    annotations:
      percent_encoded:
        tag: percent_encoded
        value: true
      rank:
        tag: rank
        value: 1
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: id
    owner: Cohort
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  members:
    name: members
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: members
    owner: Cohort
    domain_of:
    - Cohort
    - Member
    range: Phenopacket
    inlined: true
    inlined_as_list: true
  metaData:
    name: metaData
    annotations:
      rank:
        tag: rank
        value: 5
    description: Structured definitions of the resources and ontologies used within
      the phenopacket. REQUIRED
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: metaData
    owner: Cohort
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    range: MetaData
    required: true