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: .. code-block:: javascript { "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. | +------------------------------------------------------------+---------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+