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Class: Family

Phenotype, sample and pedigree data required for a genomic diagnosis. Equivalent to the Genomics England InterpretationRequestRD https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl

URI: phenopackets:Family

erDiagram Family { boolean consanguinousParents string id } Phenopacket { string id } Individual { stringList alternateIds string dateOfBirth string id KaryotypicSex karyotypicSex Sex sex } PhenotypicFeature { string description boolean excluded } MetaData { string created string createdBy string phenopacketSchemaVersion string submittedBy } 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 } Pedigree { } Person { AffectedStatus affectedStatus string familyId string individualId string maternalId string paternalId Sex sex } Family ||--}o File : "files" Family ||--|| MetaData : "metaData" Family ||--|o Pedigree : "pedigree" Family ||--|o Phenopacket : "proband" Family ||--}o Phenopacket : "relatives" 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" 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" 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" Pedigree ||--}o Person : "persons"

Slots

Name Cardinality and Range Description Inheritance
consanguinousParents 0..1
Boolean		 flag to indicate that the parents of the proband are consanguinous direct
files 0..*
File		 Pointer to the relevant file(s) for the family direct
id 0..1
String		 An identifier specific for this family direct
metaData 1..1
MetaData		 Structured definitions of the resources and ontologies used within the phenop... direct
pedigree 0..1
Pedigree		 The pedigree defining the relations between the proband and their relatives direct
proband 0..1
Phenopacket		 The individual representing the focus of this packet - e direct
relatives 0..*
Phenopacket		 Individuals related in some way to the patient direct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Family
description: Phenotype, sample and pedigree data required for a genomic diagnosis.
  Equivalent to the Genomics England InterpretationRequestRD https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  consanguinousParents:
    name: consanguinousParents
    annotations:
      rank:
        tag: rank
        value: 7
    description: flag to indicate that the parents of the proband are consanguinous
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Family
    range: boolean
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 5
    description: Pointer to the relevant file(s) for the family. These should be files
      relating to one or more of the family members e.g a multi-sample VCF. Files
      relating exclusively to individual phenopackets should be contained in the Phenopacket.
    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 family.
    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
  metaData:
    name: metaData
    annotations:
      rank:
        tag: rank
        value: 6
    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
  pedigree:
    name: pedigree
    annotations:
      rank:
        tag: rank
        value: 4
    description: The pedigree defining the relations between the proband and their
      relatives. Pedigree.individual_id should map to the PhenoPacket.Individual.id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Family
    range: Pedigree
  proband:
    name: proband
    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:
    - Family
    range: Phenopacket
    inlined: true
    inlined_as_list: true
  relatives:
    name: relatives
    annotations:
      rank:
        tag: rank
        value: 3
    description: Individuals related in some way to the patient. For instance, the
      individuals may be genetically related or may be members of a cohort. If this
      field is used, then  it is expected that a pedigree will be included for genetically
      related individuals for use cases such as genomic diagnostics. If a phenopacket
      is being used to describe one member of a cohort, then in general one phenopacket
      will be created for each of the individuals in the cohort.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - Family
    range: Phenopacket
    inlined: true
    inlined_as_list: true

Induced

name: Family
description: Phenotype, sample and pedigree data required for a genomic diagnosis.
  Equivalent to the Genomics England InterpretationRequestRD https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  consanguinousParents:
    name: consanguinousParents
    annotations:
      rank:
        tag: rank
        value: 7
    description: flag to indicate that the parents of the proband are consanguinous
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: consanguinousParents
    owner: Family
    domain_of:
    - Family
    range: boolean
  files:
    name: files
    annotations:
      rank:
        tag: rank
        value: 5
    description: Pointer to the relevant file(s) for the family. These should be files
      relating to one or more of the family members e.g a multi-sample VCF. Files
      relating exclusively to individual phenopackets should be contained in the Phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: files
    owner: Family
    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 family.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: id
    owner: Family
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  metaData:
    name: metaData
    annotations:
      rank:
        tag: rank
        value: 6
    description: Structured definitions of the resources and ontologies used within
      the phenopacket. REQUIRED
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: metaData
    owner: Family
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    range: MetaData
    required: true
  pedigree:
    name: pedigree
    annotations:
      rank:
        tag: rank
        value: 4
    description: The pedigree defining the relations between the proband and their
      relatives. Pedigree.individual_id should map to the PhenoPacket.Individual.id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: pedigree
    owner: Family
    domain_of:
    - Family
    range: Pedigree
  proband:
    name: proband
    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: proband
    owner: Family
    domain_of:
    - Family
    range: Phenopacket
    inlined: true
    inlined_as_list: true
  relatives:
    name: relatives
    annotations:
      rank:
        tag: rank
        value: 3
    description: Individuals related in some way to the patient. For instance, the
      individuals may be genetically related or may be members of a cohort. If this
      field is used, then  it is expected that a pedigree will be included for genetically
      related individuals for use cases such as genomic diagnostics. If a phenopacket
      is being used to describe one member of a cohort, then in general one phenopacket
      will be created for each of the individuals in the cohort.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: relatives
    owner: Family
    domain_of:
    - Family
    range: Phenopacket
    inlined: true
    inlined_as_list: true