Callset

Status: proposed

Provenance

Authors

Schema source: YAML file

Properties of the Callset class

Property Type Format Description
biosample_id string The identifier ("biosample.id") of the biosample this variant was reported from. This is a shortcut to using the variant -> callset -> biosample chaining.
created timestamp The creation time of this record, in ISO8601
data_use_conditions ./Ontology_term Data use conditions applying to data from this callset, as ontology object (e.g. DUO).
description string A free text description of the callset.
geo_provenance ./Geo_location This geo_class attribute ideally describes the geographic location of where this callset was analysed.
id string The local-unique identifier of this callset (referenced as "callset_id").
info ./Info additional variant information, as defined in the example and accompanying documentation
updated timestamp The time of the last edit of this record, in ISO8601

Description

The callset object contains information about an experiment performed on material from a single biosample and is a shared identifier for all variants detected in this experiment, attributed to the referenced biosample.

Examples

{
   "biosample_id" : "SAMEA1234",
   "created" : "2017-10-25T07:06:03Z",
   "data_use_conditions" : {
      "id" : "DUO:0000004",
      "label" : "no restriction"
   },
   "description" : "SNP6 array of cancer sample BRCA-0893",
   "geo_provenance" : {
      "city" : "Timisoara",
      "country" : "Romania",
      "label" : "Str Marasesti 5, 300077 Timisoara, Romania",
      "latitude" : 45.75,
      "longitude" : 21.23
   },
   "id" : "GSM264198",
   "info" : "no restriction",
   "updated" : "2017-10-25T07:06:03Z"
}

Notes and examples on the Callset properties

biosample_id
'biosample_id' : "pgx-bs-987647"
created
'created' : "2017-10-25T07:06:03Z"
data_use_conditions
'data_use_conditions' : {
  'id' => 'DUO:0000004',
  'label' => 'no restriction'
}
description
'description' : "SNP6 array of cancer sample BRCA-0893"
geo_provenance
'geo_provenance' : {
  'city' => 'Timisoara',
  'country' => 'Romania',
  'label' => 'Str Marasesti 5, 300077 Timisoara, Romania',
  'latitude' => '45.75',
  'longitude' => '21.23'
}
id
'id' : "GSM264198"
info
'info' : {
  'statusmaps' => {
                    'description' => 'The cnv_maps object is a wrapper for genomic interval mapped status information. In Progenetix and arrayMap, this is used to indictate - for fixed 1MB genome intervals - the status (dup_map => "DUP" or "", del_map => "DEL" or ""), or the maximum / minimum positive / negative value encountered in the segment, as far as it has been called to contain DUP or DEL.
With a standard binning of 1MB, the arrays would contain ~3000 values each (depending on genome edition).
',
                    'ref' => './Info',
                    'value' => {
                                 'binning' => {
                                                'description' => 'interval size in bases for the binning, when creating the cnv_maps',
                                                'format' => 'int64',
                                                'type' => 'number',
                                                'value' => 1000000
                                              },
                                 'dupmap' => {
                                               'description' => 'gain cnv status for the corresponding genome intervals
',
                                               'type' => 'array',
                                               'value' => [
                                                            '',
                                                            '',
                                                            'DUP',
                                                            'DUP',
                                                            'DUP',
                                                            '',
                                                            '',
                                                            '',
                                                            '',
                                                            '',
                                                            ''
                                                          ]
                                             }
                               }
                  }
}
updated
'updated' : "2022-11-11T09:45:13Z"
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