Class: Individual

An individual (or subject) typically corresponds to an individual human or another organism. FHIR mapping: Patient (https://www.hl7.org/fhir/patient.html).

URI: phenopackets:Individual

erDiagram Individual { stringList alternateIds string dateOfBirth string id KaryotypicSex karyotypicSex Sex sex } VitalStatus { Status status integer survivalTimeInDays } TimeElement { string timestamp } OntologyClass { string id string label } 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"

Slots

Name	Cardinality and Range	Description	Inheritance
alternateIds	0..* String	An optional list of alternative identifiers for this individual	direct
dateOfBirth	0..1 String	The date of birth of the individual as an ISO8601 UTC timestamp - rounded dow...	direct
gender	0..1 OntologyClass	Self-identified gender	direct
id	0..1 String	An identifier for the individual	direct
karyotypicSex	0..1 KaryotypicSex	The karyotypic sex of the individual	direct
sex	0..1 Sex	The phenotypic sex of the individual ARGO mapping sample_registration::gender...	direct
taxonomy	0..1 OntologyClass	NCBI taxonomic identifier NCBITaxon e	direct
timeAtLastEncounter	0..1 TimeElement	An TimeElement object describing the age of the individual at the last time o...	direct
vitalStatus	0..1 VitalStatus	Vital status of the individual	direct

Usages

used by	used in	type	used
Phenopacket	subject	range	Individual

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Individual
description: 'An individual (or subject) typically corresponds to an individual human
  or another organism. FHIR mapping: Patient (https://www.hl7.org/fhir/patient.html).'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  alternateIds:
    name: alternateIds
    annotations:
      rank:
        tag: rank
        value: 2
    description: An optional list of alternative identifiers for this individual.
      This field is provided for the convenience of users who may have multiple mappings
      to an individual which they need to track.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    domain_of:
    - GeneDescriptor
    - Individual
    range: string
  dateOfBirth:
    name: dateOfBirth
    annotations:
      rank:
        tag: rank
        value: 3
    description: The date of birth of the individual as an ISO8601 UTC timestamp -
      rounded down to the closest known year/month/day/hour/minute e.g. "2018-03-01T00:00:00Z"
      for someone born on an unknown day in March 2018 or "2018-01-01T00:00:00Z" for
      someone born on an unknown day in 2018 or empty if unknown/ not stated.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Individual
    range: string
  gender:
    name: gender
    annotations:
      rank:
        tag: rank
        value: 8
    description: Self-identified gender
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Individual
    range: OntologyClass
    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 for the individual. This must be unique within the
      record. ARGO mapping donor::submitter_donor_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:donor.submitter_donor_id
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  karyotypicSex:
    name: karyotypicSex
    annotations:
      rank:
        tag: rank
        value: 7
    description: The karyotypic sex of the individual
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Individual
    range: KaryotypicSex
  sex:
    name: sex
    annotations:
      rank:
        tag: rank
        value: 6
    description: The phenotypic sex of the individual ARGO mapping sample_registration::gender
      (this is complicated as ARGO only have male/female/other which maps to the phenopacket
      Sex field)
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.gender
    rank: 1000
    domain_of:
    - Individual
    - Person
    range: Sex
  taxonomy:
    name: taxonomy
    annotations:
      rank:
        tag: rank
        value: 9
    description: NCBI taxonomic identifier NCBITaxon e.g. NCBITaxon:9606 or NCBITaxon:1337
      For resources where there may be more than one organism being studied it is
      advisable to indicate the taxonomic identifier of that organism, to its most
      specific level
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Biosample
    - Individual
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  timeAtLastEncounter:
    name: timeAtLastEncounter
    annotations:
      rank:
        tag: rank
        value: 4
    description: An TimeElement object describing the age of the individual at the
      last time of collection. The Age object allows the encoding of the age either
      as ISO8601 duration or time interval (preferred), or as ontology term object.
      See http://build.fhir.org/datatypes
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Individual
    range: TimeElement
    inlined: true
    inlined_as_list: true
  vitalStatus:
    name: vitalStatus
    annotations:
      rank:
        tag: rank
        value: 5
    description: Vital status of the individual. If not present it is assumed that
      the individual is alive. If present it will default to 'false' i.e. the individual
      was alive when the data was collected. ARGO mapping donor::vital_status
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:donor.vital_status
    rank: 1000
    domain_of:
    - Individual
    range: VitalStatus

Induced

name: Individual
description: 'An individual (or subject) typically corresponds to an individual human
  or another organism. FHIR mapping: Patient (https://www.hl7.org/fhir/patient.html).'
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  alternateIds:
    name: alternateIds
    annotations:
      rank:
        tag: rank
        value: 2
    description: An optional list of alternative identifiers for this individual.
      This field is provided for the convenience of users who may have multiple mappings
      to an individual which they need to track.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: alternateIds
    owner: Individual
    domain_of:
    - GeneDescriptor
    - Individual
    range: string
  dateOfBirth:
    name: dateOfBirth
    annotations:
      rank:
        tag: rank
        value: 3
    description: The date of birth of the individual as an ISO8601 UTC timestamp -
      rounded down to the closest known year/month/day/hour/minute e.g. "2018-03-01T00:00:00Z"
      for someone born on an unknown day in March 2018 or "2018-01-01T00:00:00Z" for
      someone born on an unknown day in 2018 or empty if unknown/ not stated.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: dateOfBirth
    owner: Individual
    domain_of:
    - Individual
    range: string
  gender:
    name: gender
    annotations:
      rank:
        tag: rank
        value: 8
    description: Self-identified gender
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: gender
    owner: Individual
    domain_of:
    - Individual
    range: OntologyClass
    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 for the individual. This must be unique within the
      record. ARGO mapping donor::submitter_donor_id
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:donor.submitter_donor_id
    alias: id
    owner: Individual
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  karyotypicSex:
    name: karyotypicSex
    annotations:
      rank:
        tag: rank
        value: 7
    description: The karyotypic sex of the individual
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: karyotypicSex
    owner: Individual
    domain_of:
    - Individual
    range: KaryotypicSex
  sex:
    name: sex
    annotations:
      rank:
        tag: rank
        value: 6
    description: The phenotypic sex of the individual ARGO mapping sample_registration::gender
      (this is complicated as ARGO only have male/female/other which maps to the phenopacket
      Sex field)
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:sample_registration.gender
    rank: 1000
    alias: sex
    owner: Individual
    domain_of:
    - Individual
    - Person
    range: Sex
  taxonomy:
    name: taxonomy
    annotations:
      rank:
        tag: rank
        value: 9
    description: NCBI taxonomic identifier NCBITaxon e.g. NCBITaxon:9606 or NCBITaxon:1337
      For resources where there may be more than one organism being studied it is
      advisable to indicate the taxonomic identifier of that organism, to its most
      specific level
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: taxonomy
    owner: Individual
    domain_of:
    - Biosample
    - Individual
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  timeAtLastEncounter:
    name: timeAtLastEncounter
    annotations:
      rank:
        tag: rank
        value: 4
    description: An TimeElement object describing the age of the individual at the
      last time of collection. The Age object allows the encoding of the age either
      as ISO8601 duration or time interval (preferred), or as ontology term object.
      See http://build.fhir.org/datatypes
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: timeAtLastEncounter
    owner: Individual
    domain_of:
    - Individual
    range: TimeElement
    inlined: true
    inlined_as_list: true
  vitalStatus:
    name: vitalStatus
    annotations:
      rank:
        tag: rank
        value: 5
    description: Vital status of the individual. If not present it is assumed that
      the individual is alive. If present it will default to 'false' i.e. the individual
      was alive when the data was collected. ARGO mapping donor::vital_status
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    exact_mappings:
    - ARGO:donor.vital_status
    rank: 1000
    alias: vitalStatus
    owner: Individual
    domain_of:
    - Individual
    range: VitalStatus