Individual

Status: proposed

Provenance

Authors

Schema source: YAML file

Properties of the Individual class

Property Type Format Description
biocharacteristics array list of Phenotype objects with properly prefixed term ids, describing features of the individual which are not specific to the reported biosample(s); typical examples here are sex, species and "systemic" phenotypes and diseases
created timestamp The creation time of this record, in ISO8601
data_use_conditions Data use conditions applying to data from this individual, as ontology object (e.g. DUO).
description string A free text description of the individual.
external_references array Different representations of the same record, not different records in relation with this individual
geo_provenance This geo_class attribute ideally describes the geographic location of where this individual originates from. This value may reflect either the place of birth or residence, but frequently may correspond to the place the study was performed.
id string The local-unique identifier of this individual (referenced as "individual_id").
info additional variant information, as defined in the example and accompanying documentation TODO this should be its own class
name string A short descriptive "name" for the individual, which may or may not correspond to a "real name". Unstructured text.
organism An NCBI taxonomy term describing the species of the individual. For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to it's most specific level
sex A PATO term describing the biological sex of the individual
updated timestamp The time of the last edit of this record, in ISO8601

Description

An individual is a single organism (here typically a human).

Examples

{
   "biocharacteristics" : [
      {
         "description" : "Patient with Down syndrome",
         "type" : {
            "id" : "HP:0003745",
            "label" : "Genetic anticipation"
         }
      }
   ],
   "created" : "2017-10-25T07:06:03Z",
   "data_use_conditions" : {
      "id" : "DUO:0000004",
      "label" : "no restriction"
   },
   "description" : "patient with lung cancer, male smoker",
   "external_references" : [
      {
         "description" : "Cellosaurus cell line identifier",
         "relation" : "provenance",
         "type" : {
            "id" : "cellosaurus:CVCL_0312",
            "label" : "HOS"
         }
      }
   ],
   "geo_provenance" : {
      "altitude" : 94,
      "city" : "Timisoara",
      "country" : "Romania",
      "label" : "Str Marasesti 5, 300077 Timisoara, Romania",
      "latitude" : 45.75,
      "longitude" : 21.23
   },
   "id" : "AM_BS__NCBISKYCGH-1993",
   "info" : {
      "first_name" : {
         "type" : "string",
         "value" : "Ion"
      },
      "last_name" : {
         "type" : "string",
         "value" : "Tichy"
      }
   },
   "name" : "Ion Tichy, space explorer",
   "organism" : {
      "id" : "NCBITaxon:9606",
      "label" : "Homo sapiens"
   },
   "sex" : {
      "id" : "PATO:0020000",
      "label" : "female genetic sex"
   },
   "updated" : "2017-10-25T07:06:03Z"
}

Notes and examples on the Individual properties

biocharacteristics
'biocharacteristics' : [
  {
    'type' => {
                'label' => 'Genetic anticipation',
                'id' => 'HP:0003745'
              },
    'description' => 'Patient with Down syndrome'
  }
]
created
'created' : "2017-10-25T07:06:03Z"
data_use_conditions
'data_use_conditions' : {
  'id' => 'DUO:0000004',
  'label' => 'no restriction'
}
description
'description' : "patient with lung cancer, male smoker"
external_references
'external_references' : [
  {
    'type' => {
                'id' => 'cellosaurus:CVCL_0312',
                'label' => 'HOS'
              },
    'description' => 'Cellosaurus cell line identifier',
    'relation' => 'provenance'
  }
]
db.individuals.find( { "external_references.type.id" : "pubmed:17440070" } )
geo_provenance
'geo_provenance' : {
  'city' => 'Timisoara',
  'country' => 'Romania',
  'latitude' => '45.75',
  'longitude' => '21.23',
  'altitude' => 94,
  'label' => 'Str Marasesti 5, 300077 Timisoara, Romania'
}
id
'id' : "AM_BS__NCBISKYCGH-1993"
info
'info' : {
  'last_name' => {
                   'type' => 'string',
                   'value' => 'Tichy'
                 },
  'first_name' => {
                    'type' => 'string',
                    'value' => 'Ion'
                  }
}
name
'name' : "Ion Tichy, space explorer"
organism
'organism' : {
  'label' => 'Homo sapiens',
  'id' => 'NCBITaxon:9606'
}
sex
'sex' : {
  'id' => 'PATO:0020000',
  'label' => 'female genetic sex'
}
updated
'updated' : "2022-11-11T09:45:13Z"
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