Callset ga4gh

{S}[B] Status [i]
proposed
Provenance
Used by
Contributors
Source (v0.0.1)

Attributes

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

Properties

Property Type
biosample_id string
created string
data_use_conditions https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
description string
geo_provenance https://schemablocks.org/schemas/ga4gh/v0.0.1/GeoLocation.json [SRC] [HTML]
id string
info object
updated string

biosample_id

The identifier (“biosample.id”) of the biosample this variant was reported from. This attribute provides an alternative to an implicit variant -> callset -> biosample chaining.

biosample_id Value Example
"pgx-bs-987647"

created

The creation time of this record, as ISO8601 string. System-specific implementations may transfer this to a date object.

created Value Example

data_use_conditions

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

data_use_conditions Value Example
{
   "id" : "DUO:0000004",
   "label" : "no restriction"
}

description

A free text description about the callset.

description Value Example
"SNP6 array of cancer sample BRCA-0893"

geo_provenance

This geo_class attribute ideally describes the geographic location of where this callset was analysed.

geo_provenance Value Example
{
   "city" : "Timisoara",
   "country" : "Romania",
   "label" : "Str Marasesti 5, 300077 Timisoara, Romania",
   "latitude" : "45.75",
   "longitude" : "21.23"
}

id

The local-unique identifier of this callset (referenced as “callset_id”).

id Value Example
"GSM264198"

info

Additional information object, in a format defined in examples and accompanying documentation of the specific implementation.

info Value Example
{
   "statusmaps" : {
      "binning" : "1000000",
      "description" : "The cnv_maps object is a wrapper for genomic interval mapped status \ninformation. In Progenetix and arrayMap, this is used to indictate \nfor fixed 1MB genome intervals - the status\n- dupmap => \"DUP\" or \"\"\n- delmap => \"DEL\" or \"\"  \nor the maximum / minimum positive / negative value encountered in \nthe segment, as far as it has been called to contain DUP or DEL.\n",
      "dupmap" : [
         "",
         "",
         "DUP",
         "DUP",
         "DUP",
         "",
         "",
         "",
         "",
         "",
         ""
      ]
   }
}

updated

The update time of this record’s content, as ISO8601 string. System-specific implementations may transfer this to a date object.

updated Value Example

Callset Value Example

{
   "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" : {
      "statusmaps" : {
         "binning" : "1000000",
         "dupmap" : [
            "",
            "",
            "DUP",
            "DUP",
            "DUP",
            "",
            "",
            "",
            "",
            "",
            ""
         ]
      },
      "technology" : "Affymetrix SNP6 genotyping array"
   },
   "updated" : "2017-10-25T07:06:03Z"
}