sample_details

given a sample barcode (of length 16, eg TCGA-B9-7268-01A), this endpoint returns all available “biospecimen” information about this sample, the associated patient barcode, a list of associated aliquots, and a list of “data_details” blocks describing each of the data files associated with this sample

Returns information about a specific sample. Takes a sample barcode as a required parameter. User does not need to be authenticated.

Access control: To call this method, you must have the following roles:

• None

Request

HTTP request

GET https://api-dot-isb-cgc.appspot.com/_ah/api/cohort_api/v1/sample_details

Parameters

Parameter name	Value	Description
Path parameters
sample_barcode	string	Barcode of the sample to get information about. Required.

Response

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

{
  "kind": "cohort_api#cohortsItem",
  "aliquots": [string],
  "biospecimen_data": {
    "ParticipantBarcode": string,
    "Project": string,
    "SampleBarcode": string,
    "Study": string,
    "avg_percent_lymphocyte_infiltration": integer,
    "avg_percent_monocyte_infiltration": integer,
    "avg_percent_necrosis": integer,
    "avg_percent_neutrophil_infiltration": integer,
    "avg_percent_normal_cells": integer,
    "avg_percent_stromal_cells": integer,
    "avg_percent_tumor_cells": integer,
    "avg_percent_tumor_nuclei": integer,
    "batch_number": string,
    "bcr": string,
    "days_to_collection": string,
    "max_percent_lymphocyte_infiltration": string,
    "max_percent_monocyte_infiltration": string,
    "max_percent_necrosis": string,
    "max_percent_neutrophil_infiltration": string,
    "max_percent_normal_cells": string,
    "max_percent_stromal_cells": string,
    "max_percent_tumor_cells": string,
    "max_percent_tumor_nuclei": string,
    "min_percent_lymphocyte_infiltration": string,
    "min_percent_monocyte_infiltration": string,
    "min_percent_necrosis": string,
    "min_percent_neutrophil_infiltration": string,
    "min_percent_normal_cells": string,
    "min_percent_stromal_cells": string,
    "min_percent_tumor_cells": string,
    "min_percent_tumor_nuclei": string
  },
  "data_details": [
    {
    "CloudStoragePath": string,
    "DataCenterName": string,
    "DataCenterType": string,
    "DataFileName": string,
    "DataFileNameKey": string,
    "DataLevel": string,
    "DatafileUploaded": string,
    "Datatype": string,
    "GenomeReference": string,
    "Pipeline": string,
    "Platform": string,
    "Project": string,
    "Repository": string,
    "SDRFFileName": string,
    "SampleBarcode": string,
    "SecurityProtocol": string,
    "platform_full_name": string
    },
  ],
  "data_details_count": string,
  "patient": string
}

Property name	Value	Description
kind	cohort_api#cohortsItem	The resource type.
aliquots[]	list	List of barcodes of aliquots taken from this participant.
biospecimen_data	nested object	Biospecimen data about the sample.
biospecimen_data.ParticipantBarcode	string	Participant barcode.
biospecimen_data.Project	string	Project name, .eg. “TCGA”.
biospecimen_data.SampleBarcode	string	Sample barocde.
biospecimen_data.Study	string	Tumor type abbreviation, e.g. “BRCA”.
biospecimen_data.avg_percent_lymphocyte_infiltration	integer	Average percent lymphocyte infiltration.
biospecimen_data.avg_percent_monocyte_infiltration	integer	Average percent monocyte infiltration.
biospecimen_data.avg_percent_necrosis	integer	Average percent necrosis.
biospecimen_data.avg_percent_neutrophil_infiltration	integer	Average percent neutrophil infiltration.
biospecimen_data.avg_percent_normal_cells	integer	Average percent normal cells.
biospecimen_data.avg_percent_stromal_cells	integer	Average percent stromal cells.
biospecimen_data.avg_percent_tumor_cells	integer	Average percent tumor cells.
biospecimen_data.avg_percent_tumor_nuclei	integer	Average percent tumor nuclei.
biospecimen_data.batch_number	string	Batch number in which the sample was processed.
biospecimen_data.bcr	string	Biospecimen core resource, e.g. “Nationwide Children’s Hospital”, “Washington University”.
biospecimen_data.days_to_collection	string	Days to collection.
biospecimen_data.max_percent_lymphocyte_infiltration	string	Maximum percent lymphocyte infiltration.
biospecimen_data.max_percent_monocyte_infiltration	string	Maximum percent monocyte infiltration
biospecimen_data.max_percent_necrosis	string	Maximum percent necrosis.
biospecimen_data.max_percent_neutrophil_infiltration	string	Maximum percent neutrophil infiltration.
biospecimen_data.max_percent_normal_cells	string	Maximum percent normal cells.
biospecimen_data.max_percent_stromal_cells	string	Maximum percent stromal cells.
biospecimen_data.max_percent_tumor_cells	string	Maximum percent tumor cells.
biospecimen_data.max_percent_tumor_nuclei	string	Maximum percent tumor nuclei.
biospecimen_data.min_percent_lymphocyte_infiltration	string	Minimum percent lymphocyte infiltration.
biospecimen_data.min_percent_monocyte_infiltration	string	Minimum percent monocyte infiltration.
biospecimen_data.min_percent_necrosis	string	Minimum percent necrosis.
biospecimen_data.min_percent_neutrophil_infiltration	string	Minimum percent neutrophil infiltration.
biospecimen_data.min_percent_normal_cells	string	Minimum percent normal cells.
biospecimen_data.min_percent_stromal_cells	string	Minimum percent stromal cells.
biospecimen_data.min_percent_tumor_cells	string	Minimum percent tumor cells.
biospecimen_data.min_percent_tumor_nuclei	string	Minimum percent tumor nuclei.
data_details[]	list	List of information about each data file associated with the sample barcode.
data_details[].CloudStoragePath	string	Path to file, if it exists.
data_details[].DataCenterName	string	Short name of the contributing data center, e.g. “bcgsc.ca”.
data_details[].DataCenterType	string	Abbreviation of the type of contributing data center, e.g. “cgcc”.
data_details[].DataFileName	string	Name of the datafile stored on the DCC file system.
data_details[].DataFileNameKey	string	Key into the ISB-CGC GCS bucket for this file.
data_details[].DatafileUploaded	string	Whether the file fit requirements to be uploaded into the project.
data_details[].DataLevel	string	Level of the type of data, depending on where it is stored in the DCC directory structure. Data levels are defined by TCGA DCC.
data_details[].Datatype	string	Data type, e.g. “Complete Clinical Set, CNV (SNP Array)”, “DNA Methylation”, “Expression-Protein”, “Fragment Analysis Results”, “miRNASeq”, “Protected Mutations”, “RNASeq”, “RNASeqV2”, “Somatic Mutations”, “TotalRNASeqV2”.
data_details[].GenomeReference	string	Allows a center to associate results with a specific genome build that was used as the basis for analysis, e.g. “hg19 (GRCh37)”
data_details[].Pipeline	string	A combination of the center and the platform that can distinguish between two ways of performing the sequencing or assay for the same platform, e.g. “bcgsc.ca__miRNASeq”.
data_details[].Platform	string	A platform (within the scope of TCGA) is a vendor-specific technology for assaying or sequencing that could possibly be customized by a GSC or CGCC, e.g. “IlluminaHiSeq_miRNASeq”.
data_details[].platform_full_name	string	The full name of the sequencing platform used, e.g. “Illumina HiSeq 2000”, “Ion Torrent PGM”, “AB SOLiD System 2.0”.
data_details[].Project	string	The study for which the data was generated, e.g. “TCGA”.
data_details[].Repository	string	A storage location where files are deposited and made available, e.g. “DCC”, “CGHub”.
data_details[].SDRFFileName	string	Name of SDRF file stored on the DCC file system, e.g. “bcgsc.ca_KIRC.IlluminaHiSeq_miRNASeq.sdrf.txt”
data_details[].SampleBarcode	string	Sample barcode.
data_details[].SecurityProtocol	string	An indication of the security protocol necessary to fulfill in order to access the data from the file, e.g. “”DBGap Protected Access”, “DBGap Open Access”
data_details_count	string	Length of data_details list.
patient	string	Participant barcode.

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