samples().annotations()

Returns TCGA annotations about a specific sample, Takes a sample barcode (of length 16, eg TCGA-01-0628-11A) as a required parameter. User does not need to be authenticated.

Example:

curl https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_tcga_api/v3/samples/TCGA-01-0628-11A/annotations

API explorer example:

Click here to see this endpoint in Google’s API explorer.

Python API Client Example:

from googleapiclient.discovery import build
import httplib2

def get_unauthorized_service():
        api = 'isb_cgc_tcga_api'
        version = 'v3'
        site = 'https://api-dot-isb-cgc.appspot.com'
        discovery_url = '%s/_ah/api/discovery/v1/apis/%s/%s/rest' % (site, api, version)
        return build(api, version, discoveryServiceUrl=discovery_url, http=httplib2.Http())

service = get_unauthorized_service()
data = service.samples().annotations(sample_barcode='TCGA-01-0628-11A').execute()

Request

HTTP request:

GET https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_tcga_api/v3/samples/{sample_barcode}/annotations

Parameters

Parameter name	Value	Description
entity_type	string	Optional.
sample_barcode	string	Required.

Response

If successful, this method returns a response body with the following structure:

{
  "count": integer,
  "items": [
    {
      "aliquot_barcode": string,
      "annotation_gdc_id": string,
      "annotation_submitter_id": string,
      "case_barcode": string,
      "case_gdc_id": string,
      "category": string,
      "classification": string,
      "endpoint_type": string,
      "entity_barcode": string,
      "entity_gdc_id": string,
      "entity_type": string,
      "notes": string,
      "program_name": string,
      "project_short_name": string,
      "sample_barcode": string,
      "status": string
    }
  ]
}

Parameter name	Value	Description
count	integer	Number of annotations returned.
items[]	list	List of annotation items.
items[].aliquot_barcode	string	Aliquot barcode.
items[].annotation_gdc_id	string	Id assigned by the GDC to the annotation
items[].annotation_submitter_id	string	Id assigned to the annotation by the TCGA
items[].case_barcode	string	Case barcode.
items[].case_gdc_id	string	Id assigned by the GDC to the case
items[].category	string	Annotation category name, e.g. ‘Acceptable treatment for TCGA tumor’.
items[].classification	string	Annotation classification, .e.g ‘CenterNotification’, ‘Notification’, ‘Observation’, or ‘Redaction’.
items[].endpoint_type	string	Which type of GDC Annotation API was used, either legacy or current
items[].entity_barcode	string	The TCGA barcode that the annottion is associated with
items[].entity_gdc_id	string	Id assigned by the GDC to the entity
items[].entity_type	string	Entity type, e.g. ‘Case’, ‘Aliquot’, ‘Analyte’, ‘Portion’‘, ‘Slide’, or ‘Sample’.
items[].notes	string	Notes on the annotation
items[].program_name	string	The program name, e.g. ‘TCGA’ (the only program with annotations)
items[].project_short_name	string	The project id, e.g. ‘TCGA-BRCA’, ‘TCGA-OV’.
items[].sample_barcode	string	Sample barcode.
items[].status	string	Status of the annotation, e.g. ‘Approved’, ‘Rescinded’

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