GA4GH individual

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

The schema definitions are done in the YAML file.

Individual

Properties of the Individual class

Property	Type	Format	Description
id	string		The local-unique identifier of this individual (referenced as "individual_id").
name	string		A short descriptive "name" for the individual, which may or may not correspond to a "real name". Unstructured text.
description	string		A free text description of the individual.
data_use_conditions			Data use conditions applying to data from this individual, as ontology object (e.g. DUO).
organism			An NCBI taxonomy term describing the species of the individual.
sex			A PATO term describing the biological sex 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.
biocharacteristics	array		list of Phenotype_class 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
info			additional variant information, as defined in the example and accompanying documentation TODO this should be its own class
created	timestamp		The creation time of this record, in ISO8601
updated	timestamp		The time of the last edit of this record, in ISO8601

Extended notes and examples on the Individual properties

---

id

The local-unique identifier of this individual (referenced as “individual_id”).

Example

'id' : "AM_BS__NCBISKYCGH-1993"

---

name

A short descriptive “name” for the individual, which may or may not correspond to a “real name”. Unstructured text.

Example

'name' : "Ion Tichy, space explorer"

---

description

A free text description of the individual.

Example

'description' : "patient with lung cancer, male smoker"

---

data_use_conditions

Data use conditions applying to data from this individual, as ontology object (e.g. DUO).

Example

'data_use_conditions' : "undef"

---

organism

An NCBI taxonomy term describing the species of the individual.

Example

'organism' : [
  {
    'class' : {
                 'id' : 'NCBITaxon:9606',
                 'label' : 'Homo sapiens'
               },
    'description' : 'Jean-Luc Picard'
  }
]

---

sex

A PATO term describing the biological sex of the individual

Example

'sex' : [
  {
    'description' : 'girl',
    'class' : {
                 'id' : 'PATO:0020000',
                 'label' : 'female genetic sex'
               }
  }
]

---

external_references

Different representations of the same record, not different records in relation with this individual

Example

'external_references' : [
  {
    'type' : {
                'label' : 'HOS',
                'id' : 'cellosaurus:CVCL_0312'
              },
    'relation' : 'provenance',
    'description' : 'Cellosaurus cell line identifier'
  }
]

Queries:

The query will return all individuals which have been reported in experiments in this publication.

db.individuals.find( { "external_references.type.id" : "pubmed:17440070" } )

---

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.

Example

'geo_provenance' : {
  'city' : 'Timisoara',
  'country' : 'Romania',
  'longitude' : 21.23,
  'altitude' : 94,
  'latitude' : 45.75,
  'label' : 'Str Marasesti 5, 300077 Timisoara, Romania'
}

---

biocharacteristics

list of Phenotype_class 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

Example

'biocharacteristics' : [
  {
    'description' : 'Patient with Down syndrome',
    'type' : {
                'id' : 'HP:0003745',
                'label' : 'Genetic anticipation'
              }
  }
]

Queries:

the query will return all individuals who have been properly labeled as human

db.individual.find( { "biocharacteristics.type.id" : "NCBITaxon:9606" } )

this call to the distinct funcion will return all HPO annotated classes

db.biosamples.distinct( { "biocharacteristics.type.id", "biocharacteristics.type.id" : { $regex : /HP\:/i } } )

---

info

additional variant information, as defined in the example and accompanying documentation TODO this should be its own class

Example

'info' : {
  'first_name' : {
                    'type' : 'string',
                    'value' : 'Ion'
                  },
  'last_name' : {
                   'type' : 'string',
                   'value' : 'Tichy'
                 }
}

---

created

The creation time of this record, in ISO8601

Example

'created' : "2017-10-25T07:06:03Z"

---

updated

The time of the last edit of this record, in ISO8601

Example

'updated' : "2022-11-11T09:45:13Z"