Skip to content

Class: Phenopacket

An anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses. This is a bundle of high-level concepts with no specifically defined relational concepts. It is expected that the resources sharing the phenopackets will define and enforce their own semantics and level of requirements for included fields.

URI: phenopackets:Phenopacket

erDiagram Phenopacket { string id } Individual { stringList alternateIds string dateOfBirth string id KaryotypicSex karyotypicSex Sex sex } VitalStatus { Status status integer survivalTimeInDays } TimeElement { string timestamp } OntologyClass { string id string label } PhenotypicFeature { string description boolean excluded } Evidence { } 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 } MedicalAction { } Treatment { DrugType drugType } TherapeuticRegimen { RegimenStatus regimenStatus } RadiationTherapy { integer dosage integer fractions } Procedure { } Measurement { string description } Value { } ComplexValue { } Interpretation { string id ProgressStatus progressStatus string summary } Diagnosis { } File { string uri } Dictionary { } Disease { boolean excluded } Biosample { string derivedFromId string description string id string individualId } 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" VitalStatus ||--|o OntologyClass : "causeOfDeath" VitalStatus ||--|o TimeElement : "timeOfDeath" TimeElement ||--|o Age : "age" TimeElement ||--|o AgeRange : "ageRange" TimeElement ||--|o GestationalAge : "gestationalAge" TimeElement ||--|o TimeInterval : "interval" TimeElement ||--|o OntologyClass : "ontologyClass" PhenotypicFeature ||--}o Evidence : "evidence" PhenotypicFeature ||--}o OntologyClass : "modifiers" PhenotypicFeature ||--|o TimeElement : "onset" PhenotypicFeature ||--|o TimeElement : "resolution" PhenotypicFeature ||--|o OntologyClass : "severity" PhenotypicFeature ||--|o OntologyClass : "type" Evidence ||--|o OntologyClass : "evidenceCode" Evidence ||--|o ExternalReference : "reference" MetaData ||--}o ExternalReference : "externalReferences" MetaData ||--}o Resource : "resources" MetaData ||--}o Update : "updates" 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" Treatment ||--|o OntologyClass : "agent" Treatment ||--|o Quantity : "cumulativeDose" Treatment ||--}o DoseInterval : "doseIntervals" Treatment ||--|o OntologyClass : "routeOfAdministration" TherapeuticRegimen ||--|o TimeElement : "endTime" TherapeuticRegimen ||--|o ExternalReference : "externalReference" TherapeuticRegimen ||--|o OntologyClass : "ontologyClass" TherapeuticRegimen ||--|o TimeElement : "startTime" RadiationTherapy ||--|| OntologyClass : "bodySite" RadiationTherapy ||--|| OntologyClass : "modality" Procedure ||--|o OntologyClass : "bodySite" Procedure ||--|o OntologyClass : "code" Procedure ||--|o TimeElement : "performed" Measurement ||--|o OntologyClass : "assay" Measurement ||--|o ComplexValue : "complexValue" Measurement ||--|o Procedure : "procedure" Measurement ||--|o TimeElement : "timeObserved" Measurement ||--|o Value : "value" Value ||--|o OntologyClass : "ontologyClass" Value ||--|o Quantity : "quantity" ComplexValue ||--}o TypedQuantity : "typedQuantities" Interpretation ||--|o Diagnosis : "diagnosis" Diagnosis ||--|o OntologyClass : "disease" Diagnosis ||--}o GenomicInterpretation : "genomicInterpretations" 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
biosamples 0..*
Biosample		 Biosample(s) derived from the patient or a collection of biosamples in isolat... direct
diseases 0..*
Disease		 Field for disease identifiers - could be used for listing either diagnosed or... direct
files 0..*
File		 Pointer to the relevant file(s) for the individual direct
id 0..1
String		 An identifier specific for this phenopacket direct
interpretations 0..*
Interpretation		 direct
measurements 0..*
Measurement		 Quantifiable measurements related to the individual direct
medicalActions 0..*
MedicalAction		 direct
metaData 1..1
MetaData		 Structured definitions of the resources and ontologies used within the phenop... direct
phenotypicFeatures 0..*
PhenotypicFeature		 Phenotypic features relating to the subject of the phenopacket direct
subject 0..1
Individual		 The individual representing the focus of this packet - e direct

Usages

used by used in type used
Cohort members range Phenopacket
Family proband range Phenopacket
Family relatives range Phenopacket

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Phenopacket
description: An anonymous phenotypic description of an individual or biosample with
  potential genes of interest and/or diagnoses.  This is a bundle of high-level concepts
  with no specifically defined relational concepts. It is expected that the resources
  sharing the phenopackets will define and enforce their own semantics and level of
  requirements for included fields.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  biosamples:
    name: biosamples
    annotations:
      rank:
        tag: rank
        value: 5
    description: Biosample(s) derived from the patient or a collection of biosamples
      in isolation
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Phenopacket
    range: Biosample
    inlined: true
    inlined_as_list: true
  diseases:
    name: diseases
    annotations:
      rank:
        tag: rank
        value: 7
    description: Field for disease identifiers - could be used for listing either
      diagnosed or suspected conditions. The resources using these fields should define
      what this represents in their context.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Phenopacket
    range: Disease
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 10
    description: Pointer to the relevant file(s) for the individual
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    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: An identifier specific for this phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  interpretations:
    name: interpretations
    annotations:
      rank:
        tag: rank
        value: 6
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Phenopacket
    range: Interpretation
    inlined: true
    inlined_as_list: true
  measurements:
    name: measurements
    annotations:
      rank:
        tag: rank
        value: 4
    description: Quantifiable measurements related to the individual
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Phenopacket
    - Biosample
    range: Measurement
    inlined: true
    inlined_as_list: true
  medicalActions:
    name: medicalActions
    annotations:
      rank:
        tag: rank
        value: 9
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Phenopacket
    range: MedicalAction
    inlined: true
    inlined_as_list: true
  metaData:
    name: metaData
    annotations:
      rank:
        tag: rank
        value: 11
    description: Structured definitions of the resources and ontologies used within
      the phenopacket. REQUIRED
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    range: MetaData
    required: true
  phenotypicFeatures:
    name: phenotypicFeatures
    annotations:
      rank:
        tag: rank
        value: 3
    description: Phenotypic features relating to the subject of the phenopacket
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Phenopacket
    - Biosample
    range: PhenotypicFeature
    inlined: true
    inlined_as_list: true
  subject:
    name: subject
    annotations:
      rank:
        tag: rank
        value: 2
    description: The individual representing the focus of this packet - e.g. the proband
      in rare disease cases or cancer patient
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Phenopacket
    range: Individual
    inlined: true
    inlined_as_list: true
tree_root: true

Induced

name: Phenopacket
description: An anonymous phenotypic description of an individual or biosample with
  potential genes of interest and/or diagnoses.  This is a bundle of high-level concepts
  with no specifically defined relational concepts. It is expected that the resources
  sharing the phenopackets will define and enforce their own semantics and level of
  requirements for included fields.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  biosamples:
    name: biosamples
    annotations:
      rank:
        tag: rank
        value: 5
    description: Biosample(s) derived from the patient or a collection of biosamples
      in isolation
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: biosamples
    owner: Phenopacket
    domain_of:
    - Phenopacket
    range: Biosample
    inlined: true
    inlined_as_list: true
  diseases:
    name: diseases
    annotations:
      rank:
        tag: rank
        value: 7
    description: Field for disease identifiers - could be used for listing either
      diagnosed or suspected conditions. The resources using these fields should define
      what this represents in their context.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: diseases
    owner: Phenopacket
    domain_of:
    - Phenopacket
    range: Disease
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 10
    description: Pointer to the relevant file(s) for the individual
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: files
    owner: Phenopacket
    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: An identifier specific for this phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: id
    owner: Phenopacket
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  interpretations:
    name: interpretations
    annotations:
      rank:
        tag: rank
        value: 6
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: interpretations
    owner: Phenopacket
    domain_of:
    - Phenopacket
    range: Interpretation
    inlined: true
    inlined_as_list: true
  measurements:
    name: measurements
    annotations:
      rank:
        tag: rank
        value: 4
    description: Quantifiable measurements related to the individual
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: measurements
    owner: Phenopacket
    domain_of:
    - Phenopacket
    - Biosample
    range: Measurement
    inlined: true
    inlined_as_list: true
  medicalActions:
    name: medicalActions
    annotations:
      rank:
        tag: rank
        value: 9
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: medicalActions
    owner: Phenopacket
    domain_of:
    - Phenopacket
    range: MedicalAction
    inlined: true
    inlined_as_list: true
  metaData:
    name: metaData
    annotations:
      rank:
        tag: rank
        value: 11
    description: Structured definitions of the resources and ontologies used within
      the phenopacket. REQUIRED
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: metaData
    owner: Phenopacket
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    range: MetaData
    required: true
  phenotypicFeatures:
    name: phenotypicFeatures
    annotations:
      rank:
        tag: rank
        value: 3
    description: Phenotypic features relating to the subject of the phenopacket
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: phenotypicFeatures
    owner: Phenopacket
    domain_of:
    - Phenopacket
    - Biosample
    range: PhenotypicFeature
    inlined: true
    inlined_as_list: true
  subject:
    name: subject
    annotations:
      rank:
        tag: rank
        value: 2
    description: The individual representing the focus of this packet - e.g. the proband
      in rare disease cases or cancer patient
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: subject
    owner: Phenopacket
    domain_of:
    - Phenopacket
    range: Individual
    inlined: true
    inlined_as_list: true
tree_root: true