Search and Retrieval
Introducing Search and Retrieval Requests
The GDC API provides endpoints that search and retrieve information stored in the GDC according to the GDC Data Model. The general format of requests to search & retrieval endpoints is described below.
Note: Queries described in this section work for datasets that have been released to the GDC Data Portal. Unreleased data that is in the process of being submitted to GDC cannot be queried using these methods. See Submission to learn how to query unreleased data using GraphQL.
Components of a Request
A typical search and retrieval API request specifies the following parameters:
- a
filtersparameter, that specifies the search terms for the query - several parameters that specify the API response, such as:
format— specifies response format (JSON, TSV, XML)fields— specifies the which data elements should be returned in the response, if availablesize— specifies the the maximum number of results to include in the response- other parameters are described below.
Requests can be executed using HTTP GET or HTTP POST. GET requests are limited by maximum URL length, so the POST method is recommended for large queries.
POST Example
The following is an example of an HTTP POST request to the files endpoint of the GDC API. It looks for Gene Expression Quantification files associated with specific TCGA cases (represented by TCGA barcodes) and retrieves the associated biospecimen metadata in TSV format.
Request
curl --request POST --header "Content-Type: application/json" --data @Payload 'https://api.gdc.cancer.gov/files' > response.tsv
Payload
{
"filters":{
"op":"and",
"content":[
{
"op":"in",
"content":{
"field":"cases.submitter_id",
"value":[
"TCGA-CK-4948",
"TCGA-D1-A17N",
"TCGA-4V-A9QX",
"TCGA-4V-A9QM"
]
}
},
{
"op":"=",
"content":{
"field":"files.data_type",
"value":"Gene Expression Quantification"
}
}
]
},
"format":"tsv",
"fields":"file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id,analysis.workflow_type,cases.project.project_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id",
"size":"1000"
}
Each component of the request is explained below.
GET Example
The above request can be executed as an HTTP GET:
https://api.gdc.cancer.gov/files?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-CK-4948%22%2C%22TCGA-D1-A17N%22%2C%22TCGA-4V-A9QX%22%2C%22TCGA-4V-A9QM%22%5D%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%22Gene%20Expression%20Quantification%22%7D%7D%5D%7D&format=tsv&fields=file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id,analysis.workflow_type,cases.project.project_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id&size=1000
Each component of the request is explained below.
Endpoints
The following search and retrieval endpoints are available in the GDC API:
| Endpoints | Description |
|---|---|
| files | Information about files stored in the GDC |
| cases | Information related to cases, or sample donors |
| history | Information related to file version history |
| projects | Information about projects |
| annotations | Information about annotations to GDC data |
| _mapping | Information about elements that can be used to query other endpoints |
The choice of endpoint determines what is listed in the search results. The files endpoint will generate a list of files, whereas the cases endpoint will generate a list of cases. Each of the above endpoints, other than _mapping, can query and return any of the related fields in the GDC Data Model. So the cases endpoint can be queried for file fields (e.g. to look for cases that have certain types of experimental data), and the files endpoint can be queried for clinical metadata associated with a case (e.g. to look for files from cases diagnosed with a specific cancer type).
Project Endpoint
The projects endpoint provides access to project records, the highest level of data organization in the GDC.
Example
This example is a query for projects contained in the GDC. It uses the from, size, sort, and pretty parameters, and returns the first two projects sorted by project id.
curl 'https://api.gdc.cancer.gov/projects?from=0&size=2&sort=project_id:asc&pretty=true'
{
"data": {
"hits": [
{
"id": "APOLLO-LUAD",
"primary_site": [
"Bronchus and lung"
],
"dbgap_accession_number": "phs003011",
"project_id": "APOLLO-LUAD",
"disease_type": [
"Adenomas and Adenocarcinomas"
],
"name": "APOLLO1: Proteogenomic characterization of lung adenocarcinoma",
"releasable": false,
"state": "open",
"released": true
},
{
"id": "BEATAML1.0-COHORT",
"primary_site": [
"Hematopoietic and reticuloendothelial systems"
],
"dbgap_accession_number": "phs001657",
"project_id": "BEATAML1.0-COHORT",
"disease_type": [
"Myelodysplastic Syndromes",
"Leukemias, NOS",
"Unknown",
"Myeloid Leukemias",
"Plasma Cell Tumors",
"Chronic Myeloproliferative Disorders"
],
"name": "Functional Genomic Landscape of Acute Myeloid Leukemia",
"releasable": true,
"state": "open",
"released": true
}
],
"pagination": {
"count": 2,
"total": 78,
"size": 2,
"from": 0,
"sort": "None",
"page": 1,
"pages": 39
}
},
"warnings": {}
}
Retrieval of project metadata using project_id
The project endpoint supports a simple query format that retrieves the metadata of a single project using its project_id:
curl 'https://api.gdc.cancer.gov/projects/TARGET-NBL?expand=summary,summary.experimental_strategies,summary.data_categories&pretty=true'
{
"data": {
"summary": {
"file_count": 5705,
"data_categories": [
{
"file_count": 943,
"case_count": 278,
"data_category": "Sequencing Reads"
},
{
"file_count": 3080,
"case_count": 220,
"data_category": "Simple Nucleotide Variation"
},
{
"file_count": 3,
"case_count": 1119,
"data_category": "Clinical"
},
{
"file_count": 705,
"case_count": 225,
"data_category": "DNA Methylation"
},
{
"file_count": 2,
"case_count": 1132,
"data_category": "Biospecimen"
},
{
"file_count": 324,
"case_count": 155,
"data_category": "Transcriptome Profiling"
},
{
"file_count": 648,
"case_count": 155,
"data_category": "Structural Variation"
}
],
"experimental_strategies": [
{
"file_count": 1458,
"case_count": 155,
"experimental_strategy": "RNA-Seq"
},
{
"file_count": 15,
"case_count": 8,
"experimental_strategy": "WGS"
},
{
"file_count": 3522,
"case_count": 222,
"experimental_strategy": "WXS"
},
{
"file_count": 705,
"case_count": 225,
"experimental_strategy": "Methylation Array"
}
],
"case_count": 1132,
"file_size": 16968781125824
},
"primary_site": [
"Stomach",
"Bones, joints and articular cartilage of limbs",
"Heart, mediastinum, and pleura",
"Peripheral nerves and autonomic nervous system",
"Uterus, NOS",
"Bones, joints and articular cartilage of other and unspecified sites",
"Other endocrine glands and related structures",
"Renal pelvis",
"Retroperitoneum and peritoneum",
"Liver and intrahepatic bile ducts",
"Meninges",
"Connective, subcutaneous and other soft tissues",
"Adrenal gland",
"Unknown",
"Spinal cord, cranial nerves, and other parts of central nervous system",
"Skin",
"Other and ill-defined sites",
"Kidney",
"Lymph nodes",
"Hematopoietic and reticuloendothelial systems"
],
"dbgap_accession_number": "phs000467",
"project_id": "TARGET-NBL",
"disease_type": [
"Neuroepitheliomatous Neoplasms",
"Not Applicable"
],
"name": "Neuroblastoma",
"releasable": true,
"state": "open",
"released": true
},
"warnings": {}
}
Files Endpoint
The GDC Files Endpoint https://api.gdc.cancer.gov/files enables search and retrieval of information relating to files stored in the GDC, including file properties such as file_name, md5sum, data_format, and others.
Example
This example is a query for files contained in the GDC. It uses the from, size, sort, and pretty parameters, and returns only the first two files, sorted by file size, from smallest to largest.
curl 'https://api.gdc.cancer.gov/files?from=0&size=2&sort=file_size:asc&pretty=true'
{
"data": {
"hits": [
{
"id": "0ab5e358-b1ff-4433-8959-c37c5890d9aa",
"data_format": "BEDPE",
"access": "controlled",
"file_name": "090e2828-079c-48e6-97cb-735c763da8d3.wgs.BRASS.rerun_structural_variation.bedpe.gz",
"submitter_id": "247c3c9a-58b9-4b70-bda8-cb197acb5609",
"data_category": "Somatic Structural Variation",
"acl": [
"phs001287"
],
"type": "structural_variation",
"file_size": 20,
"created_datetime": "2022-04-08T20:27:04.633842-05:00",
"updated_datetime": "2022-07-07T11:02:27.204310-05:00",
"file_id": "0ab5e358-b1ff-4433-8959-c37c5890d9aa",
"data_type": "Structural Rearrangement",
"state": "released",
"experimental_strategy": "WGS",
"version": "1",
"data_release": "34.0 - 37.0"
},
{
"id": "a8bc2405-b57d-48bb-b241-18b3e28caa56",
"data_format": "BEDPE",
"access": "controlled",
"file_name": "eae76f14-8aa7-427f-a90c-4e0ed095e0c2.wgs.BRASS.rerun_structural_variation.bedpe.gz",
"submitter_id": "618cd251-ddcb-4a7e-9a6d-efb132b0bd7a",
"data_category": "Somatic Structural Variation",
"acl": [
"phs001287"
],
"type": "structural_variation",
"file_size": 20,
"created_datetime": "2022-04-08T20:43:16.505747-05:00",
"updated_datetime": "2022-07-07T11:00:43.345766-05:00",
"file_id": "a8bc2405-b57d-48bb-b241-18b3e28caa56",
"data_type": "Structural Rearrangement",
"state": "released",
"experimental_strategy": "WGS",
"version": "1",
"data_release": "34.0 - 37.0"
}
],
"pagination": {
"count": 2,
"total": 931947,
"size": 2,
"from": 0,
"sort": "None",
"page": 1,
"pages": 465974
}
},
"warnings": {}
}
Retrieval of file metadata using individual UUIDs:
The /files endpoint supports a simple query format that retrieves the metadata of a single file using its UUID. Note that the /files endpoint is inactive when querying for earlier file versions. In that case, the /history or /files/versions endpoints should be used instead.
curl 'https://api.gdc.cancer.gov/files/20f45e04-3c10-4f11-b57b-719880eab69e?pretty=true'
{
"data": {
"data_format": "VCF",
"access": "controlled",
"file_name": "TCGA_BRCA.8d9cb5ae-e568-41fc-8b53-14467c2623dc.wxs.MuTect2.somatic_annotation.vcf.gz",
"submitter_id": "675f31dd-70e5-4a72-8139-423b14b31564",
"data_category": "Simple Nucleotide Variation",
"acl": [
"phs000178"
],
"type": "annotated_somatic_mutation",
"file_size": 6894331,
"created_datetime": "2022-02-07T08:48:39.178606-06:00",
"updated_datetime": "2022-02-09T12:11:12.781445-06:00",
"file_id": "20f45e04-3c10-4f11-b57b-719880eab69e",
"data_type": "Annotated Somatic Mutation",
"state": "released",
"experimental_strategy": "WXS",
"version": "2",
"data_release": "32.0 - 37.0"
},
"warnings": {}
}
Note: The
file_sizefield associated with each file is reported in bytes.
Example of retrieving file version information:
The https://api.gdc.cancer.gov/files/versions endpoint enables search and retrieval of version information about a file. A file may be versioned if a file is updated by the GDC (e.g. using a new alignment algorithm or fixing a file that contained an error). Version refers to the instance of a particular file. Inputs can either be a list of UUIDs as shown in example 1 or a download manifest as shown in example 2. Output includes information about the current and latest version for any given file. While /files also returns information about a file version this endpoint will only work for the most recent version of a file whereas /files/versions will work for all previous and current versions of a file. In both examples below the output format can be modified by adding the format=tsv parameter.
curl 'https://api.gdc.cancer.gov/files/versions/1dd28069-5777-4ff9-bd2b-d1ba68e88b06,2a03abac-f1a2-49a9-a57c-7543739dd862?pretty=true'
[
{
"id": "1dd28069-5777-4ff9-bd2b-d1ba68e88b06",
"filename": "1dd28069-5777-4ff9-bd2b-d1ba68e88b06.vcf.gz",
"version": "1",
"md5": "c2f9b196e154906a70c7ec46492a859d",
"size": 332092,
"state": "validated",
"release": "12.0",
"latest_id": "76b3f4d8-c6b7-4662-ac42-1d27d4684281",
"latest_filename": "def1cc5b-55f0-4372-a3ff-df3ea93cf3e7.wxs.somaticsniper.raw_somatic_mutation.vcf.gz",
"latest_version": "2",
"latest_size": 357706,
"latest_state": "validated",
"latest_release": [
"32.0",
"33.0",
"33.1",
"34.0",
"35.0",
"36.0",
"37.0"
]
},
{
"id": "2a03abac-f1a2-49a9-a57c-7543739dd862",
"filename": "a5d86cde-32ca-4ed6-b1a5-5a47575f2ac6_gdc_realn_rehead.bam",
"version": "1",
"md5": "48686fcd84ac713d44261ca9e26b89fb",
"size": 6653119038,
"state": "validated",
"release": "12.0",
"latest_id": "de0ce84d-c286-405c-a556-39dac14c7c74",
"latest_filename": "d45c33cc-88e2-4de5-a578-f7e31a6c0738.rna_seq.genomic.gdc_realn.bam",
"latest_version": "2",
"latest_size": 6223445806,
"latest_state": "validated",
"latest_release": [
"32.0",
"33.0",
"33.1",
"34.0",
"35.0",
"36.0",
"37.0"
]
}
]
curl --request POST --header "Content-Type: text/tsv" https://api.gdc.cancer.gov/files/versions/manifest?pretty=true --data-binary @gdc_manifest_20180809_154816.txt
[
{
"id": "0b20e27c-9a09-4f15-923f-d5b4f185dc22",
"filename": "nationwidechildrens.org_clinical.TCGA-13-1500.xml",
"version": "1",
"md5": "597aa4df24c4d544b6c25cbd8b25a33e",
"size": 44857,
"state": "validated",
"release": "12.0",
"latest_id": "0b20e27c-9a09-4f15-923f-d5b4f185dc22",
"latest_filename": "nationwidechildrens.org_clinical.TCGA-13-1500.xml",
"latest_version": "1",
"latest_md5": "597aa4df24c4d544b6c25cbd8b25a33e",
"latest_size": 44857,
"latest_state": "validated",
"latest_release": [
"12.0",
"13.0",
"14.0",
"15.0",
"16.0",
"17.0",
"18.0",
"19.0",
"20.0",
"21.0",
"22.0",
"23.0",
"24.0",
"25.0",
"26.0",
"27.0",
"28.0",
"29.0",
"30.0",
"31.0",
"32.0",
"33.0",
"33.1",
"34.0",
"35.0",
"36.0",
"37.0"
]
},
{
"id": "3edc7084-013c-4493-8507-c00b0e9962d8",
"filename": "BUCKS_p_TCGA_272_273_N_GenomeWideSNP_6_G05_1320676.grch38.seg.v2.txt",
"version": "1",
"md5": "35a18d990a05eedfaf96e753bee0b96d",
"size": 27620,
"state": "validated",
"release": "12.0",
"latest_id": "3edc7084-013c-4493-8507-c00b0e9962d8",
"latest_filename": "BUCKS_p_TCGA_272_273_N_GenomeWideSNP_6_G05_1320676.grch38.seg.v2.txt",
"latest_version": "1",
"latest_md5": "35a18d990a05eedfaf96e753bee0b96d",
"latest_size": 27620,
"latest_state": "validated",
"latest_release": [
"12.0",
"13.0",
"14.0",
"15.0",
"16.0",
"17.0",
"18.0",
"19.0",
"20.0",
"21.0",
"22.0",
"23.0",
"24.0",
"25.0",
"26.0",
"27.0",
"28.0",
"29.0",
"30.0",
"31.0",
"32.0",
"33.0",
"33.1",
"34.0",
"35.0",
"36.0",
"37.0"
]
},
{
"id": "a22f5e32-b16e-458f-a412-7e438056ece6",
"filename": "a22f5e32-b16e-458f-a412-7e438056ece6.vep.vcf.gz",
"version": "1",
"md5": "68b2433b31679bbbc6681919a1b81762",
"size": 2346,
"state": "validated",
"release": "12.0",
"latest_id": "55491171-6170-45cb-af9d-d99345b289e5",
"latest_filename": "4b89bb97-41f6-43c4-a481-287556f7bb4a.targeted_sequencing.annotated_somatic_mutation.vcf.gz",
"latest_version": "2",
"latest_size": 2618,
"latest_state": "validated",
"latest_release": [
"32.0",
"33.0",
"33.1",
"34.0",
"35.0",
"36.0",
"37.0"
]
}
]
Cases Endpoint
The GDC Cases Endpoint https://api.gdc.cancer.gov/cases enables search and retrieval of information related to a specific case.
The cases endpoint is designed to retrieve the metadata associated with one or more cases, including all nested biospecimen entities. Filters can be applied to retrieve information for entire cases, but not for lower-level biospecimen entities. For example, a sample within a case cannot be used to query for aliquots that are associated only with that sample. All aliquots associated with the case would be retrieved.
Example
This example is a query for files contained in GDC. It returns case where submitter id is TCGA-BH-A0EA, using the pretty and filters parameters and the following filtering operators:
{"op":"and","content":[{"op":"in","content":{"field":"submitter_id","value":["TCGA-BH-A0EA"]}}]}
Command:
curl 'https://api.gdc.cancer.gov/cases?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22submitter_id%22%2C%22value%22%3A%5B%22TCGA-BH-A0EA%22%5D%7D%7D%5D%7D%0A%0A&pretty=true'
{
"data": {
"hits": [
{
"id": "1f601832-eee3-48fb-acf5-80c4a454f26e",
"slide_ids": [
"a0826f0d-986a-491b-8c6f-b34f8929f3ee",
"90154ea1-6b76-4445-870e-d531d6fa1239",
"1dd1cab5-5a81-428a-8153-91e8c4cf9905"
],
"submitter_slide_ids": [
"TCGA-BH-A0EA-01Z-00-DX1",
"TCGA-BH-A0EA-01A-01-MSA",
"TCGA-BH-A0EA-01A-01-TSA"
],
"disease_type": "Ductal and Lobular Neoplasms",
"analyte_ids": [
"f19f408a-815f-43d9-8032-e9482b796371",
"fe678556-acf4-4bde-a95e-860bb0150a95",
"69ddc092-88a0-4839-a2bb-9f1c9e760409",
"66ed0f86-5ca5-4dec-ba76-7ee4dcf31831",
"30cb470f-66d4-4085-8c30-83a42e8453d4"
],
"submitter_id": "TCGA-BH-A0EA",
"submitter_analyte_ids": [
"TCGA-BH-A0EA-10A-01D",
"TCGA-BH-A0EA-01A-11D",
"TCGA-BH-A0EA-01A-11R",
"TCGA-BH-A0EA-10A-01W",
"TCGA-BH-A0EA-01A-11W"
],
"aliquot_ids": [
"cde982b7-3b0a-49eb-8710-a599cb0e44c1",
"b1a3739d-d554-4202-b96f-f25a444e2042",
"eef9dce1-6ba6-432b-bbe2-53c7dbe64fe7",
"97c64d6a-7dce-4d0f-9cb3-b3e4eb4719c5",
"262715e1-835c-4f16-8ee7-6900e26f7cf5",
"cfbd5476-e83a-401d-9f9a-639c73a0e35b",
"bcb7fc6d-60a0-48b7-aa81-14c0dda72d76",
"561b8777-801a-49ed-a306-e7dafeb044b6",
"edad5bd3-efe0-4c5f-b05c-2c0c2951c45a",
"42d050e4-e8ee-4442-b9c0-0ee14706b138",
"2beb34c4-d493-4a73-b21e-de77d43251ff",
"ca71ca96-cbb7-4eab-9487-251dda34e107"
],
"submitter_aliquot_ids": [
"TCGA-BH-A0EA-10A-01W-A12U-09",
"TCGA-BH-A0EA-01A-11D-A111-01",
"TCGA-BH-A0EA-01A-11D-A314-09",
"TCGA-BH-A0EA-01A-11D-A10X-02",
"TCGA-BH-A0EA-10A-01D-A10Z-02",
"TCGA-BH-A0EA-10A-01D-A110-09",
"TCGA-BH-A0EA-01A-11D-A10Y-09",
"TCGA-BH-A0EA-10A-01D-A113-01",
"TCGA-BH-A0EA-01A-11D-A112-05",
"TCGA-BH-A0EA-01A-11R-A115-07",
"TCGA-BH-A0EA-01A-11W-A12T-09",
"TCGA-BH-A0EA-01A-11R-A114-13"
],
"created_datetime": null,
"diagnosis_ids": [
"84654ad5-2a2c-5c3b-8340-ecac6a5550fe"
],
"sample_ids": [
"55864d86-dab8-47bb-a3e3-8cfb198b06c1",
"9a6c71a6-82cd-42b1-a93f-f569370848d6",
"7f791228-dd77-4ab0-8227-d784a4c7fea1"
],
"submitter_sample_ids": [
"TCGA-BH-A0EA-01A",
"TCGA-BH-A0EA-01Z",
"TCGA-BH-A0EA-10A"
],
"primary_site": "Breast",
"submitter_diagnosis_ids": [
"TCGA-BH-A0EA_diagnosis"
],
"updated_datetime": "2019-08-06T14:15:54.128069-05:00",
"case_id": "1f601832-eee3-48fb-acf5-80c4a454f26e",
"state": "released",
"portion_ids": [
"cb6086d1-3416-4310-b109-e8fa6e8b72d4",
"8629bf5a-cdaf-4f6a-90bb-27dd4a7565c5",
"ae4f5816-f97a-4605-9b05-9ab820467dee"
],
"submitter_portion_ids": [
"TCGA-BH-A0EA-10A-01",
"TCGA-BH-A0EA-01A-21-A13C-20",
"TCGA-BH-A0EA-01A-11"
]
}
],
"pagination": {
"count": 1,
"total": 1,
"size": 10,
"from": 0,
"sort": "",
"page": 1,
"pages": 1
}
},
"warnings": {}
}
Retrieval of case metadata using individual UUIDs:
The cases endpoint supports a simple query format that retrieves the metadata of a single case using its UUID:
curl 'https://api.gdc.cancer.gov/cases/1f601832-eee3-48fb-acf5-80c4a454f26e?pretty=true&expand=diagnoses'
"data": {
"slide_ids": [
"90154ea1-6b76-4445-870e-d531d6fa1239",
"1dd1cab5-5a81-428a-8153-91e8c4cf9905",
"a0826f0d-986a-491b-8c6f-b34f8929f3ee"
],
"submitter_slide_ids": [
"TCGA-BH-A0EA-01A-01-MSA",
"TCGA-BH-A0EA-01A-01-TSA",
"TCGA-BH-A0EA-01Z-00-DX1"
],
"disease_type": "Ductal and Lobular Neoplasms",
"analyte_ids": [
"fe678556-acf4-4bde-a95e-860bb0150a95",
"66ed0f86-5ca5-4dec-ba76-7ee4dcf31831",
"30cb470f-66d4-4085-8c30-83a42e8453d4",
"69ddc092-88a0-4839-a2bb-9f1c9e760409",
"f19f408a-815f-43d9-8032-e9482b796371"
],
"submitter_id": "TCGA-BH-A0EA",
"submitter_analyte_ids": [
"TCGA-BH-A0EA-01A-11D",
"TCGA-BH-A0EA-01A-11R",
"TCGA-BH-A0EA-10A-01W",
"TCGA-BH-A0EA-01A-11W",
"TCGA-BH-A0EA-10A-01D"
],
"aliquot_ids": [
"eef9dce1-6ba6-432b-bbe2-53c7dbe64fe7",
"2beb34c4-d493-4a73-b21e-de77d43251ff",
"b1a3739d-d554-4202-b96f-f25a444e2042",
"262715e1-835c-4f16-8ee7-6900e26f7cf5",
"cfbd5476-e83a-401d-9f9a-639c73a0e35b",
"edad5bd3-efe0-4c5f-b05c-2c0c2951c45a",
"bcb7fc6d-60a0-48b7-aa81-14c0dda72d76",
"42d050e4-e8ee-4442-b9c0-0ee14706b138",
"97c64d6a-7dce-4d0f-9cb3-b3e4eb4719c5",
"561b8777-801a-49ed-a306-e7dafeb044b6",
"ca71ca96-cbb7-4eab-9487-251dda34e107",
"cde982b7-3b0a-49eb-8710-a599cb0e44c1"
],
"submitter_aliquot_ids": [
"TCGA-BH-A0EA-01A-11R-A115-07",
"TCGA-BH-A0EA-01A-11D-A112-05",
"TCGA-BH-A0EA-10A-01W-A12U-09",
"TCGA-BH-A0EA-01A-11D-A10X-02",
"TCGA-BH-A0EA-10A-01D-A113-01",
"TCGA-BH-A0EA-10A-01D-A110-09",
"TCGA-BH-A0EA-01A-11D-A314-09",
"TCGA-BH-A0EA-01A-11D-A10Y-09",
"TCGA-BH-A0EA-01A-11D-A111-01",
"TCGA-BH-A0EA-10A-01D-A10Z-02",
"TCGA-BH-A0EA-01A-11R-A114-13",
"TCGA-BH-A0EA-01A-11W-A12T-09"
],
"diagnoses": [
{
"synchronous_malignancy": "Not Reported",
"ajcc_pathologic_stage": "Stage IIA",
"days_to_diagnosis": 0,
"created_datetime": null,
"last_known_disease_status": "not reported",
"tissue_or_organ_of_origin": "Breast, NOS",
"days_to_last_follow_up": null,
"age_at_diagnosis": 26548,
"primary_diagnosis": "Infiltrating duct carcinoma, NOS",
"updated_datetime": "2019-08-08T16:25:42.215495-05:00",
"prior_malignancy": "yes",
"year_of_diagnosis": 2008,
"state": "released",
"prior_treatment": "No",
"days_to_last_known_disease_status": null,
"ajcc_staging_system_edition": "6th",
"ajcc_pathologic_t": "T1c",
"days_to_recurrence": null,
"morphology": "8500/3",
"ajcc_pathologic_n": "N1a",
"ajcc_pathologic_m": "M0",
"submitter_id": "TCGA-BH-A0EA_diagnosis",
"classification_of_tumor": "not reported",
"diagnosis_id": "84654ad5-2a2c-5c3b-8340-ecac6a5550fe",
"icd_10_code": "C50.9",
"site_of_resection_or_biopsy": "Breast, NOS",
"tumor_grade": "Not Reported",
"progression_or_recurrence": "not reported"
}
],
"created_datetime": null,
"diagnosis_ids": [
"84654ad5-2a2c-5c3b-8340-ecac6a5550fe"
],
"sample_ids": [
"55864d86-dab8-47bb-a3e3-8cfb198b06c1",
"7f791228-dd77-4ab0-8227-d784a4c7fea1",
"9a6c71a6-82cd-42b1-a93f-f569370848d6"
],
"submitter_sample_ids": [
"TCGA-BH-A0EA-01A",
"TCGA-BH-A0EA-01Z",
"TCGA-BH-A0EA-10A"
],
"primary_site": "Breast",
"submitter_diagnosis_ids": [
"TCGA-BH-A0EA_diagnosis"
],
"updated_datetime": "2019-08-06T14:15:54.128069-05:00",
"case_id": "1f601832-eee3-48fb-acf5-80c4a454f26e",
"state": "released",
"portion_ids": [
"1ef8b20e-43e5-49d7-ac9a-03ce14f58daa",
"cb6086d1-3416-4310-b109-e8fa6e8b72d4",
"8629bf5a-cdaf-4f6a-90bb-27dd4a7565c5",
"ae4f5816-f97a-4605-9b05-9ab820467dee"
],
"submitter_portion_ids": [
"TCGA-BH-A0EA-01A-21-A13C-20",
"TCGA-BH-A0EA-10A-01",
"TCGA-BH-A0EA-01A-21",
"TCGA-BH-A0EA-01A-11"
]
},
"warnings": {}
}
Annotations Endpoint
The GDC Annotation Endpoint https://api.gdc.cancer.gov/annotations enables search and retrieval of annotations stored in the GDC.
Example
This example is a query for any annotations directly associated with the following GDC entities:
- the case with UUID e0d36cc0-652c-4224-bb10-09d15c7bd8f1
- the sample with UUID 25ebc29a-7598-4ae4-ba7f-618d448882cc
- the aliquot with UUID fe660d7c-2746-4b50-ab93-b2ed99960553
The query uses the filters parameter to specify entity UUIDs. Code samples below include the bare and percent-encoded filter JSON.
{
"op":"in",
"content":{
"field":"entity_id",
"value":[
"e0d36cc0-652c-4224-bb10-09d15c7bd8f1",
"25ebc29a-7598-4ae4-ba7f-618d448882cc",
"fe660d7c-2746-4b50-ab93-b2ed99960553"
]
}
}
%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22entity_id%22%2C%22value%22%3A%5B%22e0d36cc0-652c-4224-bb10-09d15c7bd8f1%22%2C%2225ebc29a-7598-4ae4-ba7f-618d448882cc%22%2C%22fe660d7c-2746-4b50-ab93-b2ed99960553%22%5D%7D%7D
curl 'https://api.gdc.cancer.gov/annotations?filters=%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22entity_id%22%2C%22value%22%3A%5B%22e0d36cc0-652c-4224-bb10-09d15c7bd8f1%22%2C%2225ebc29a-7598-4ae4-ba7f-618d448882cc%22%2C%22fe660d7c-2746-4b50-ab93-b2ed99960553%22%5D%7D%7D&pretty=true'
{
"data": {
"hits": [
{
"category": "Item flagged DNU",
"status": "Approved",
"entity_id": "fe660d7c-2746-4b50-ab93-b2ed99960553",
"classification": "CenterNotification",
"entity_type": "aliquot",
"created_datetime": "2015-09-28T00:00:00",
"annotation_id": "5ddadefe-8b57-5ce2-b8b2-918d63d99a59",
"notes": "The aliquot failed Broad pipeline QC and not all files are suitable for use. Consult the SDRF file to determine which files are usable.",
"updated_datetime": "2017-03-09T13:20:38.962182-06:00",
"submitter_id": "29087",
"state": "submitted",
"case_id": "41b59716-116f-4942-8b63-409870a87e26",
"case_submitter_id": "TCGA-DK-A3IM",
"entity_submitter_id": "TCGA-DK-A3IM-10A-01D-A20B-01",
"id": "5ddadefe-8b57-5ce2-b8b2-918d63d99a59"
},
{
"category": "Item is noncanonical",
"status": "Approved",
"entity_id": "25ebc29a-7598-4ae4-ba7f-618d448882cc",
"classification": "Notification",
"entity_type": "sample",
"created_datetime": "2012-07-12T00:00:00",
"annotation_id": "d6500f94-618f-5334-a810-ade76b887ec9",
"notes": "No Matching Normal",
"updated_datetime": "2017-03-09T13:47:18.182075-06:00",
"submitter_id": "8009",
"state": "submitted",
"case_id": "bd114e05-5a97-41e2-a0d5-5d39a1e9d461",
"case_submitter_id": "TCGA-08-0514",
"entity_submitter_id": "TCGA-08-0514-01A",
"id": "d6500f94-618f-5334-a810-ade76b887ec9"
},
{
"category": "Prior malignancy",
"status": "Approved",
"entity_id": "e0d36cc0-652c-4224-bb10-09d15c7bd8f1",
"classification": "Notification",
"entity_type": "case",
"created_datetime": "2013-03-12T00:00:00",
"annotation_id": "33336cdf-2cf0-5af2-bb52-fecd3427f180",
"notes": "Patient had a prior lymphoma. Unknown radiation or systemic chemotherapy.",
"updated_datetime": "2017-03-09T12:11:31.786013-06:00",
"submitter_id": "15630",
"state": "submitted",
"case_id": "e0d36cc0-652c-4224-bb10-09d15c7bd8f1",
"case_submitter_id": "TCGA-FS-A1ZF",
"entity_submitter_id": "TCGA-FS-A1ZF",
"id": "33336cdf-2cf0-5af2-bb52-fecd3427f180"
}
],
"pagination": {
"count": 3,
"sort": "",
"from": 0,
"page": 1,
"total": 3,
"pages": 1,
"size": 10
}
},
"warnings": {}
}
History Endpoint
The GDC History Endpoint https://api.gdc.cancer.gov/history enables search and retrieval of version and release information about a file. This endpoint will return the entire provenance of all versions of a file. A file may be versioned if a file is updated by the GDC (e.g. using a new alignment algorithm or fixing a file that contained an error). Version refers to the instance of a particular file. Release refers to which data release a file was part of. A file may be a part of many different data releases with no change in version number or content.
Example
This example is a query for versioning information associated with the follow with file 1dd28069-5777-4ff9-bd2b-d1ba68e88b06.
curl 'https://api.gdc.cancer.gov/history/1dd28069-5777-4ff9-bd2b-d1ba68e88b06'
[{"uuid": "1dd28069-5777-4ff9-bd2b-d1ba68e88b06", "version": "1", "file_change": "superseded", "release_date": "2018-08-23", "data_release": "12.0"}, {"uuid": "76b3f4d8-c6b7-4662-ac42-1d27d4684281", "version": "2", "file_change": "released", "release_date": "2022-03-29", "data_release": "32.0"}]
_mapping Endpoint
Each search and retrieval endpoint is equipped with a _mapping endpoint that provides information about available fields. For example, files/_mapping endpoint provides information about fields and field groups available at the files endpoint: https://api.gdc.cancer.gov/files/_mapping.
The high-level structure of a response to a _mapping query is as follows:
"_mapping": {}
, "defaults": []
, "expand": []
, "fields": []
, "multi": []
, "nested": []
Each part of the response is described below:
| Part | Description |
|---|---|
_mapping |
All available fields and their descriptions. The endpoint-agnostic field names provided here are compatible with the filters parameter but are not always compatible with the fields parameter |
defaults |
The default set of fields included in the API response when the fields parameter is not used in the request |
expand |
Field group names for use with the expand parameter |
fields |
All available fields in an endpoint-specific format that is compatible with both the filters and fields parameters |
multi |
GDC internal use |
nested |
Nested fields |
Example
curl 'https://api.gdc.cancer.gov/projects/_mapping'
This output was put thought a json format application for easier viewability.
{
...
"_mapping": {
"projects.disease_type": {
"doc_type": "projects",
"field": "disease_type",
"type": "id"
},
"projects.name": {
"doc_type": "projects",
"field": "name",
"type": "id"
}
}
...
}
Similar information can be obtained using the fields parameter; fields queries provide additional information in the response, such as the name of the Elastic Search document (doc_type), the field name and the type of value. A list of supported types (such as string, long, float, ...) can be obtained from Elastic Search Documentation.
Request Parameters
The GDC API supports the following search & retrieval request parameters:
| Parameter | Default | Description |
|---|---|---|
| filters | null | Specifies search parameters |
| format | JSON | Specifies the API response format: JSON, XML, or TSV |
| pretty | false | Returns response with indentations and line breaks in a human-readable format |
| fields | null | Specifies which fields to include in the response |
| expand | null | Returns multiple related fields |
| size | 10 | Specifies the number of results to return |
| from | 0 | Specifies the first record to return from a set of search results |
| sort | null | Specifies sorting for the search results |
| facets | null | Provides all existing values for a given field and the number of records having this value. |
Filters: Specifying the Query
The filters parameter enables passing of complex search queries to the GDC API. The parameter carries a query in the form of a JSON object.
Query Format
A filters query consists of an operator (or a nested set of operators) with a set of field and value operands.
The following filters query operators are supported by the GDC API:
| Operator | Description | Number of Operands | Logic example |
|---|---|---|---|
| = | equals (string or number) | one | gender = "female" |
| != | does not equal (string or number) | one | project_id != "TARGET-AML" |
| < | less than (number) | one | age at diagnosis < 90y |
| <= | less than or equal (number) | one | age at diagnosis <= 17 |
| > | greater than (number) | one | age at diagnosis > 50 |
| >= | greater than or equal (number) | one | age at diagnosis >= 18 |
| is | is (missing) | one | gender is missing |
| not | not (missing) | one | race not missing |
| in | matches a string or number in (a list) | multiple | primary_site in [Brain, Lung] |
| exclude | does not match any strings or values in (a list) | multiple | experimental_strategy exclude [WXS, WGS, "Genotyping array"] |
| and | (operation1) and (operation2) | multiple | {primary_site in [Brain, Lung]} and |
| or | (operation1) or (operation2) | multiple | {project_id != "TARGET-AML"} or |
The field operand specifies a field that corresponds to a property defined in the GDC Data Dictionary. A list of supported fields is provided in Appendix A; the list can also be accessed programmatically at the _mapping endpoint.
The value operand specifies the search terms. Users can get a list of available values for a specific property by making a call to the appropriate API endpoint using the facets parameter, e.g. https://api.gdc.cancer.gov/v0/cases?facets=demographic.gender&size=0&pretty=true. See Facets for details.
A simple query with a single operator looks like this:
{
"op":"=",
"content":{
"field":"cases.demographic.gender",
"value":[
"male"
]
}
}
A more complex query with multiple operators looks like this:
{
"op":"and",
"content":[
{
"op":"in",
"content":{
"field":"cases.submitter_id",
"value":[
"TCGA-CK-4948",
"TCGA-D1-A17N",
"TCGA-4V-A9QX",
"TCGA-4V-A9QM"
]
}
},
{
"op":"=",
"content":{
"field":"files.data_type",
"value":"Gene Expression Quantification"
}
}
]
}
Example: HTTP GET Request
This example requests male cases using HTTP GET.
The JSON object to be passed to the GDC API looks like:
{
"op": "=",
"content": {
"field": "cases.demographic.gender",
"value": [
"male"
]
}
}
URL-encoding the above JSON object using Percent-(URL)-encoding tool results in the following string:
%7B%0D%0A++++%22op%22%3A+%22%3D%22%2C%0D%0A++++%22content%22%3A+%7B%0D%0A++++++++%22field%22%3A+%22cases.demographic.gender%22%2C%0D%0A++++++++%22value%22%3A+%5B%0D%0A++++++++++++%22male%22%0D%0A++++++++%5D%0D%0A++++%7D%0D%0A%7D
The above string can now be passed to the GDC API using the filters parameter:
curl 'https://api.gdc.cancer.gov/cases?filters=%7b%22op%22%3a+%22%3d%22%2c%0d%0a++++++%22content%22%3a+%7b%0d%0a++++++++++%22field%22%3a+%22cases.demographic.gender%22%2c%0d%0a++++++++++%22value%22%3a+%5b%22male%22%5d%0d%0a++++++%7d%0d%0a%7d&pretty=true'
import requests
import json
cases_endpt = 'https://api.gdc.cancer.gov/cases'
filt = {"op":"=",
"content":{
"field": "cases.demographic.gender",
"value": ["male"]
}
}
params = {'filters':json.dumps(filt), 'sort':'demographic.gender:asc'}
# requests URL-encodes automatically
response = requests.get(cases_endpt, params = params)
print(json.dumps(response.json(), indent=2))
{
"data": {
"hits": [
{
"id": "03974dc9-0162-4de8-9897-09f88693681a",
"lost_to_followup": null,
"days_to_lost_to_followup": null,
"disease_type": "Nevi and Melanomas",
"analyte_ids": [
"9747b614-624b-410a-8b94-854a16cd143a",
"c8974764-4836-4a34-aeb8-52b491f78d0e",
"bcea1ed5-b9cb-4a92-ad80-598d8a223fb3"
],
"submitter_id": "HCM-BROD-0334-C43",
"submitter_analyte_ids": [
"HCM-BROD-0334-C43-10A-01D",
"HCM-BROD-0334-C43-85M-01D",
"HCM-BROD-0334-C43-85M-01R"
],
"days_to_consent": null,
"aliquot_ids": [
"dcd74e48-12f3-4a86-a829-c7e055c215b7",
"ea182abf-041d-474a-bc53-f6fdd05cd999",
"33f3ba0a-c902-4288-9fa7-5696d959e51d"
],
"submitter_aliquot_ids": [
"HCM-BROD-0334-C43-85M-01R-A79O-41",
"HCM-BROD-0334-C43-10A-01D-A79L-36",
"HCM-BROD-0334-C43-85M-01D-A79L-36"
],
"created_datetime": "2020-05-21T08:55:40.814734-05:00",
"diagnosis_ids": [
"3d666f1b-58c2-451f-8ebf-87b5caa02aaf",
"fedc3533-85f7-4fc6-b996-a1f596e021df"
],
"sample_ids": [
"cd88baf4-b6eb-4df5-9b42-d55f3aad739c",
"eb79f8b4-1cc3-4a32-ad51-cfea8cf150f0"
],
"consent_type": null,
"submitter_sample_ids": [
"HCM-BROD-0334-C43-10A",
"HCM-BROD-0334-C43-85M"
],
"primary_site": "Skin",
"submitter_diagnosis_ids": [
"HCM-BROD-0334-C43_diagnosis2",
"HCM-BROD-0334-C43_diagnosis"
],
"updated_datetime": "2021-03-03T15:15:08.075155-06:00",
"case_id": "03974dc9-0162-4de8-9897-09f88693681a",
"index_date": "Diagnosis",
"state": "released",
"portion_ids": [
"bd0bc175-5b54-47c1-96fc-c6d8afc0c115"
],
"submitter_portion_ids": [
"HCM-BROD-0334-C43-10A-01"
]
},
{
"id": "03bfeb7c-cecf-4691-8263-33cdfe391ea9",
"lost_to_followup": null,
"days_to_lost_to_followup": null,
"disease_type": "Adenomas and Adenocarcinomas",
"analyte_ids": [
"db8132c3-47a8-49ec-9b78-bc7d18debf67",
"f74bf217-dae2-4554-92e4-8707068ea7a7",
"01764f17-2a97-442e-a08b-8a21303b4770",
"c9884c81-3c8f-4ad9-a962-42c7459a2276",
"d4f1a9f8-f748-4f45-aa06-da4d760c4fab"
],
"submitter_id": "HCM-BROD-0124-C25",
"submitter_analyte_ids": [
"HCM-BROD-0124-C25-85A-01D",
"HCM-BROD-0124-C25-01A-01D",
"HCM-BROD-0124-C25-10A-01D",
"HCM-BROD-0124-C25-85A-01R",
"HCM-BROD-0124-C25-01A-01R"
],
"aliquot_ids": [
"fe8e2565-749a-470a-b843-7afbe95ded81",
"092656af-b279-46b8-9ccf-b1eabfbd1d6f",
"677edb2c-fac3-4878-a28d-cf4e0d7873d7",
"8bb9fff4-24f8-426e-9f2a-4cb30a4ac5c2",
"f1c6f71d-b125-47bb-91ad-90d7cbff0012"
],
"submitter_aliquot_ids": [
"HCM-BROD-0124-C25-01A-01D-A78W-36",
"HCM-BROD-0124-C25-85A-01D-A786-36",
"HCM-BROD-0124-C25-01A-01R-A78X-41",
"HCM-BROD-0124-C25-10A-01D-A78W-36",
"HCM-BROD-0124-C25-85A-01R-A787-41"
],
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"ae4eb402-7c13-46f0-bdf8-361c7fdc9430",
"b720a33e-c858-47f4-9e51-e58748004e96",
"fdf06863-7d14-4f79-ad2c-b46d443d235c",
"a4f88ff3-7c9e-4edc-808f-aa01378ec68d",
"cca66f05-89e0-48a7-8948-53e556fee5be",
"e658c087-c37d-47ac-9472-3b6b6eed7188",
"6be6aff1-9694-4c7f-8f43-f0f902b95849",
"39f9ce44-944c-49b8-b215-05b117d5e62d"
],
"submitter_id": "HCM-BROD-0199-C71",
"submitter_analyte_ids": [
"HCM-BROD-0199-C71-85A-01D",
"HCM-BROD-0199-C71-01A-11D",
"HCM-BROD-0199-C71-85S-01R",
"HCM-BROD-0199-C71-85A-01R",
"HCM-BROD-0199-C71-02A-11R",
"HCM-BROD-0199-C71-02A-11D",
"HCM-BROD-0199-C71-01A-11R",
"HCM-BROD-0199-C71-10A-01D",
"HCM-BROD-0199-C71-85R-01D"
],
"aliquot_ids": [
"9f18daaa-cd67-436e-85a1-1e9b3e1e2135",
"eff144c4-4e2a-497d-998a-5ae6bccf2576",
"7ec23cac-61f4-4f8f-afa7-ed8a3ca1493f",
"6ea15978-902f-45ba-b148-cc4247341882",
"529f3cbf-f65d-4a60-a562-b3fcfbd7d4c9",
"22542d68-476b-47fd-91da-03db887756d6",
"7f4e7f6b-33b0-49da-95bd-88643d5e14ff",
"fc0121b9-5de8-4af6-90db-b36dd8207ebf",
"c9dd10db-bf23-4bb2-a6db-fec1b45549c8"
],
"submitter_aliquot_ids": [
"HCM-BROD-0199-C71-85R-01D-A80U-36",
"HCM-BROD-0199-C71-02A-11R-A80V-41",
"HCM-BROD-0199-C71-02A-11D-A80U-36",
"HCM-BROD-0199-C71-01A-11D-A786-36",
"HCM-BROD-0199-C71-10A-01D-A786-36",
"HCM-BROD-0199-C71-01A-11R-A787-41",
"HCM-BROD-0199-C71-85A-01D-A786-36",
"HCM-BROD-0199-C71-85S-01R-A80V-41",
"HCM-BROD-0199-C71-85A-01R-A787-41"
],
"created_datetime": "2019-04-04T15:00:32.807421-05:00",
"diagnosis_ids": [
"df0230e6-d07c-4814-9aee-5be560d1ce58",
"2d72ecab-4038-4ef7-b921-79b88ad62722"
],
"sample_ids": [
"b5919dd1-039e-4ab4-b6d5-37b9d483893f",
"769c5e1b-89e3-431c-9420-31de5efe5a22",
"5e0faf77-f1b3-4b1a-8b6a-8066270eddb4",
"ee0e94ad-b5b0-4ad6-912c-c4010f1a1d26",
"600a5b42-f871-47a2-8124-68184edf10bd",
"a1dbbc0c-173c-4455-a780-8682dd2e258a"
],
"submitter_sample_ids": [
"HCM-BROD-0199-C71-85R",
"HCM-BROD-0199-C71-02A",
"HCM-BROD-0199-C71-85S",
"HCM-BROD-0199-C71-85A",
"HCM-BROD-0199-C71-10A",
"HCM-BROD-0199-C71-01A"
],
"primary_site": "Brain",
"submitter_diagnosis_ids": [
"HCM-BROD-0199-C71_diagnosis",
"HCM-BROD-0199-C71_diagnosis2"
],
"updated_datetime": "2021-01-06T22:55:10.531130-06:00",
"case_id": "149a8565-e0c5-4474-a693-d44f1b445c0c",
"index_date": "Diagnosis",
"state": "released",
"portion_ids": [
"9dccf7ac-58a0-4c9e-9fb6-4ead8c37d48b",
"5afaa056-b09e-4328-ae5b-feb70faa3595",
"77827fa6-18a9-4e1a-b49f-800cec351fa8"
],
"submitter_portion_ids": [
"HCM-BROD-0199-C71-10A-01",
"HCM-BROD-0199-C71-02A-11",
"HCM-BROD-0199-C71-01A-11"
]
},
{
"id": "19b1e69a-355a-4dd7-9c56-d701f6c2c5a0",
"lost_to_followup": null,
"days_to_lost_to_followup": null,
"disease_type": "Adenomas and Adenocarcinomas",
"analyte_ids": [
"181d5e6e-026d-4983-97e8-f4d9e28a0cfe",
"293683aa-f2ef-4d14-8ec7-681c870d3b71",
"c1f6530c-004c-4b10-bae5-a571542aabd2",
"2140e379-dd8b-4440-a626-bb0e01f8fc00",
"4d337e44-6468-43b8-bf2f-4301750dab99"
],
"submitter_id": "HCM-SANG-0299-C15",
"submitter_analyte_ids": [
"HCM-SANG-0299-C15-10B-01D",
"HCM-SANG-0299-C15-85X-01R",
"HCM-SANG-0299-C15-85A-01R",
"HCM-SANG-0299-C15-85X-01D",
"HCM-SANG-0299-C15-85A-01D"
],
"aliquot_ids": [
"37fee31c-8669-4057-ae95-424586fa2a05",
"d17fd7af-fd14-4cb7-a6c1-c23339589288",
"65b7ffa3-0f1f-4918-a75f-2343720fe40c",
"a331201c-3aef-4eec-83d5-d38f4211c1b1",
"3ef40a4d-21cd-4be4-8c57-cba30c8e0778",
"b8af2a87-5b55-4c73-88f1-90ce5e1d05f5",
"a1988273-c9f8-4cd1-b1a6-5daa2c7a3e51",
"b535f87b-0a61-49bd-828b-bb5e3c11f2f7",
"3bb67aa8-5155-425e-9afc-9aca5120b0f0",
"fa20b306-a835-46d8-ab03-f8ea0b585381",
"65ec4e30-e782-4b6f-b985-33e9c7e72a0a"
],
"submitter_aliquot_ids": [
"HCM-SANG-0299-C15-85B-01D-A80T-32-aliquot",
"HCM-SANG-0299-C15-10A-01D-A80T-32-aliquot",
"HCM-SANG-0299-C15-85A-01R-A78V-41",
"HCM-SANG-0299-C15-85A-01D-A78U-36",
"HCM-SANG-0299-C15-85A-01R-A80W-32-aliquot",
"HCM-SANG-0299-C15-85X-01D-A78U-36",
"HCM-SANG-0299-C15-85X-01R-A78V-41",
"HCM-SANG-0299-C15-85A-01D-A80T-32-aliquot",
"HCM-SANG-0299-C15-01A-01D-A80T-32-aliquot",
"HCM-SANG-0299-C15-85B-01R-A80W-32-aliquot",
"HCM-SANG-0299-C15-10B-01D-A78U-36"
],
"created_datetime": "2019-10-14T10:46:36.257369-05:00",
"diagnosis_ids": [
"7c6aa4ce-6661-4491-a827-c0a8045743a6",
"c1a6f70f-b871-4b4e-a292-aef67c2d4776"
],
"sample_ids": [
"c56f3f94-deda-4d21-8f8e-658108995dfa",
"ce46b9f4-5244-432d-aa87-026e0a27d71a",
"cf134dfb-5126-4bee-bcab-39d584335a21",
"34e0d6ee-97f5-420f-9b34-4784098125f7",
"ac8476c1-53bf-43b5-8695-db441ed1a720",
"9000b366-a14b-44bc-a782-484e09765b2d",
"8541bc01-57e6-4bf7-a42e-da1c8e790633",
"277d7ed9-4e6a-429b-8f4e-438ff0d2ba7a",
"d12d9184-5317-4730-af2e-a8428456a2a7"
],
"submitter_sample_ids": [
"HCM-SANG-0299-C15-85X",
"HCM-SANG-0299-C15-85B-01D-A80T-32",
"HCM-SANG-0299-C15-85A-01R-A80W-32",
"HCM-SANG-0299-C15-10B",
"HCM-SANG-0299-C15-01A-01D-A80T-32",
"HCM-SANG-0299-C15-85A",
"HCM-SANG-0299-C15-85A-01D-A80T-32",
"HCM-SANG-0299-C15-85B-01R-A80W-32",
"HCM-SANG-0299-C15-10A-01D-A80T-32"
],
"primary_site": "Esophagus",
"submitter_diagnosis_ids": [
"HCM-SANG-0299-C15_diagnosis2",
"HCM-SANG-0299-C15_diagnosis"
],
"updated_datetime": "2023-02-22T07:39:25.979291-06:00",
"case_id": "19b1e69a-355a-4dd7-9c56-d701f6c2c5a0",
"index_date": "Sample Procurement",
"state": "released",
"portion_ids": [
"b8192c57-9cda-4dca-a590-1e13beadf2a0"
],
"submitter_portion_ids": [
"HCM-SANG-0299-C15-10B-01"
]
},
{
"id": "19f1d344-4c14-4733-abbd-c2db6737e210",
"lost_to_followup": null,
"days_to_lost_to_followup": null,
"disease_type": "Ductal and Lobular Neoplasms",
"analyte_ids": [
"a21d5f05-af57-41bf-ab60-32d2c869611b",
"696f4b03-5f0d-4eaa-975d-a9feb64dae07",
"c8d4fb23-c55d-4bb6-bd3d-fc1f159d7a33",
"5db09eb8-fecc-433f-aa34-a12a7c9333dd",
"51598aba-be8e-42a0-bf6c-aca34776fc1f"
],
"submitter_id": "HCM-CSHL-0081-C25",
"submitter_analyte_ids": [
"HCM-CSHL-0081-C25-11A-11D",
"HCM-CSHL-0081-C25-85A-01R",
"HCM-CSHL-0081-C25-85B-01D",
"HCM-CSHL-0081-C25-01A-11R",
"HCM-CSHL-0081-C25-01A-11D"
],
"aliquot_ids": [
"0a65e1bd-6af3-44ba-924c-193eb8e099d6",
"61112c39-c838-4f84-89c7-a33bfe5dea88",
"25cd08c3-09a9-406d-8ec3-ab4946224cf1",
"973d4fa3-4fa7-4ff9-8176-cc51c53b7079",
"9aa21acf-1e24-4b7a-a3c1-73354bdd81b6"
],
"submitter_aliquot_ids": [
"HCM-CSHL-0081-C25-11A-11D-A78M-36",
"HCM-CSHL-0081-C25-01A-11R-A78N-41",
"HCM-CSHL-0081-C25-85B-01D-A78M-36",
"HCM-CSHL-0081-C25-01A-11D-A78M-36",
"HCM-CSHL-0081-C25-85A-01R-A78N-41"
],
"created_datetime": "2019-09-19T08:58:31.776805-05:00",
"diagnosis_ids": [
"c1cca3a7-e0ac-40a1-9db7-6902b48d3c62"
],
"sample_ids": [
"d9f23187-9a29-426a-9ead-4bb3a2ce6cf9",
"3709004e-b04d-4473-aa29-8dd84176d17d",
"adcc54e3-074b-4ca6-b179-0a5df8efeb36",
"05478d15-885a-4c44-a46a-81bbe6c9ee11"
],
"submitter_sample_ids": [
"HCM-CSHL-0081-C25-85B",
"HCM-CSHL-0081-C25-01A",
"HCM-CSHL-0081-C25-85A",
"HCM-CSHL-0081-C25-11A"
],
"primary_site": "Pancreas",
"submitter_diagnosis_ids": [
"HCM-CSHL-0081-C25_diagnosis"
],
"updated_datetime": "2023-02-22T07:39:25.979291-06:00",
"case_id": "19f1d344-4c14-4733-abbd-c2db6737e210",
"index_date": "Diagnosis",
"state": "released",
"portion_ids": [
"d9588542-d7ef-413e-900c-3f816b583525",
"b77573f1-e6a3-43c1-a56d-a207c39e18c4"
],
"submitter_portion_ids": [
"HCM-CSHL-0081-C25-01A-11",
"HCM-CSHL-0081-C25-11A-11"
]
}
],
"pagination": {
"count": 10,
"total": 40232,
"size": 10,
"from": 0,
"sort": "",
"page": 1,
"pages": 4024
}
},
"warnings": {}
}
Example: HTTP POST Request
This example demonstrates how to obtain metadata in TSV format for a set of files using their UUIDs (e.g. UUIDs obtained from a download manifest file generated by the GDC Data Portal).
The first step is to construct a JSON query object, including filters, fields, format, and size parameters. The object is then submitted as HTTP POST payload to the GDC API using curl, in order to retrieve a TSV file with the requested metadata.
{
"filters":{
"op":"in",
"content":{
"field":"files.file_id",
"value":[
"0001801b-54b0-4551-8d7a-d66fb59429bf",
"002c67f2-ff52-4246-9d65-a3f69df6789e",
"003143c8-bbbf-46b9-a96f-f58530f4bb82",
"0043d981-3c6b-463f-b512-ab1d076d3e62",
"004e2a2c-1acc-4873-9379-ef1aa12283b6",
"005239a8-2e63-4ff1-9cd4-714f81837a61",
"006b8839-31e5-4697-b912-8e3f4124dd15",
"006ce9a8-cf38-462e-bb99-7f08499244ab",
"007ce9b5-3268-441e-9ffd-b40d1127a319",
"0084a614-780b-42ec-b85f-7a1b83128cd3",
"00a5e471-a79f-4d56-8a4c-4847ac037400",
"00ab2b5a-b59e-4ec9-b297-76f74ff1d3fb",
"00c5f14e-a398-4076-95d1-25f320ee3a37",
"00c74a8b-10aa-40cc-991e-3365ea1f3fce",
"00df5a50-bce3-4edf-a078-641e54800dcb"
]
}
},
"format":"TSV",
"fields":"file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id",
"size":"100"
}
curl --request POST --header "Content-Type: application/json" --data @Payload.txt 'https://api.gdc.cancer.gov/files' > File_metadata.txt
cases_0_submitter_id cases_0_case_id data_type cases_0_samples_0_sample_type cases_0_samples_0_tissue_type file_name cases_0_samples_0_submitter_id cases_0_samples_0_portions_0_analytes_0_aliquots_0_aliquot_id cases_0_samples_0_sample_id file_id data_category cases_0_samples_0_tumor_descriptor cases_0_samples_0_portions_0_analytes_0_aliquots_0_submitter_id
TCGA-B0-5094 8aaa4e25-5c12-4ace-96dc-91aaa0c4457c Aligned Reads Solid Tissue Normal C345.TCGA-B0-5094-11A-01D-1421-08.5_gdc_realn.bam TCGA-B0-5094-11A b4e4630a-b38c-4b62-b0e8-d73f0e3b4e47 7519d7a8-c3ee-417b-9cfc-111bc5ad0637 0001801b-54b0-4551-8d7a-d66fb59429bf Raw Sequencing Data TCGA-B0-5094-11A-01D-1421-08
TCGA-B0-5117 ae55b2d3-62a1-419e-9f9a-5ddfac356db4 Aligned Reads Solid Tissue Normal C345.TCGA-B0-5117-11A-01D-1421-08.5_gdc_realn.bam TCGA-B0-5117-11A 45c68b6b-0bed-424d-9a77-4f87bbaa3649 b1116541-bece-4df3-b3dd-cec50aeb277b 003143c8-bbbf-46b9-a96f-f58530f4bb82 Raw Sequencing Data TCGA-B0-5117-11A-01D-1421-08
TCGA-G7-6790 e7a1cbe2-793c-4747-8412-8be794f2382b Aligned Reads Blood Derived Normal C489.TCGA-G7-6790-10A-01D-1962-08.2_gdc_realn.bam TCGA-G7-6790-10A 66cbb40f-14b3-40c0-a332-e8a8e21bca11 4be83d0f-8b09-4e9e-8318-358371d34332 004e2a2c-1acc-4873-9379-ef1aa12283b6 Raw Sequencing Data TCGA-G7-6790-10A-01D-1962-08
TCGA-B9-A69E a4225cb2-7b4b-4122-b6b9-629c26e3ea56 Aligned Reads Blood Derived Normal TCGA-B9-A69E-10A-01D-A31X-10_Illumina_gdc_realn.bam TCGA-B9-A69E-10A f4799bdc-b207-4053-9a4b-5a26ebf8ab91 5d6d6cd4-6a7b-499d-936a-1be9bf74b07f 0084a614-780b-42ec-b85f-7a1b83128cd3 Raw Sequencing Data TCGA-B9-A69E-10A-01D-A31X-10
TCGA-EE-A2GU 24faa36a-268d-4a13-b3ae-eacd431a2bcc Aligned Reads Blood Derived Normal C828.TCGA-EE-A2GU-10A-01D-A198-08.2_gdc_realn.bam TCGA-EE-A2GU-10A c3feacc2-5a26-4bb2-a312-8b2ee53ccad1 cc4a5ed8-376a-4842-a25d-ffb07d8e1ca0 00c74a8b-10aa-40cc-991e-3365ea1f3fce Raw Sequencing Data TCGA-EE-A2GU-10A-01D-A198-08
TCGA-CE-A484 e62a728d-390f-428a-bea1-fc8c9814fb11 Aligned Reads Blood Derived Normal C499.TCGA-CE-A484-10A-01D-A23U-08.3_gdc_realn.bam TCGA-CE-A484-10A 641a0220-6eec-434a-b606-e256113b65da 27a8008e-044a-4966-b518-cc6905e292ca 00df5a50-bce3-4edf-a078-641e54800dcb Raw Sequencing Data TCGA-CE-A484-10A-01D-A23U-08
TCGA-DA-A1IB 8fc9cc74-f388-49f0-b957-debb62638634 Aligned Reads Blood Derived Normal C828.TCGA-DA-A1IB-10A-01D-A198-08.2_gdc_realn.bam TCGA-DA-A1IB-10A 30919a1a-df9f-4604-835e-f66ac7bcacdf 432952c5-6505-4220-a581-f65270a45281 00ab2b5a-b59e-4ec9-b297-76f74ff1d3fb Raw Sequencing Data TCGA-DA-A1IB-10A-01D-A198-08
TCGA-AX-A2HG 7a2cf5ce-8317-4fff-946e-b9937afab815 Aligned Reads Blood Derived Normal 6c2a8ea343da8d6cc0fd2043492f16df_gdc_realn.bam TCGA-AX-A2HG-10A 8c34ffe2-9012-4b4a-b610-a42a9c6a9780 ef4b80ec-b453-48ec-8ad8-ccac83e1e4db 00c5f14e-a398-4076-95d1-25f320ee3a37 Raw Sequencing Data TCGA-AX-A2HG-10A-01D-A17D-09
TCGA-EC-A24G b5c1e511-baf2-45b3-9919-110e8941e3c2 Aligned Reads Blood Derived Normal 671333b193812fc2bd2744053b383459_gdc_realn.bam TCGA-EC-A24G-10A 2a8cb8fe-b64f-453e-8139-7ede12f3fc51 61cf2e54-1b8d-40a0-9c73-a7449cbd570a 00a5e471-a79f-4d56-8a4c-4847ac037400 Raw Sequencing Data TCGA-EC-A24G-10A-01D-A16D-09
TCGA-B5-A0K0 29c8f468-5ac1-4d6c-8376-e36e6d246926 Aligned Reads Blood Derived Normal TCGA-B5-A0K0-10A-01W-A062-09_IlluminaGA-DNASeq_exome_gdc_realn.bam TCGA-B5-A0K0-10A 02e65074-ffda-4795-b8f5-1bfd20bd1019 1df69e2e-f392-465f-8e61-4671ba2fcd35 007ce9b5-3268-441e-9ffd-b40d1127a319 Raw Sequencing Data TCGA-B5-A0K0-10A-01W-A062-09
TCGA-C8-A27B f0d8a1fe-e313-44f1-99cc-b965cbeeff0e Aligned Reads Blood Derived Normal 3c99d98ea8eb6acbf819e67fc77623d9_gdc_realn.bam TCGA-C8-A27B-10A 922226ba-6244-4953-ad42-f4daa474c288 31139082-7978-45aa-9d8f-ac4789ac5cec 006b8839-31e5-4697-b912-8e3f4124dd15 Raw Sequencing Data TCGA-C8-A27B-10A-01D-A167-09
TCGA-E9-A295 fec0da58-1047-44d2-b6d1-c18cceed43dc Aligned Reads Blood Derived Normal fd4421a6bbf3efd4e3d5c17fdd610314_gdc_realn.bam TCGA-E9-A295-10A cd761feb-9a20-4495-8943-c6243532a5cf e74183e1-f0b4-412a-8dac-a62d404add78 002c67f2-ff52-4246-9d65-a3f69df6789e Raw Sequencing Data TCGA-E9-A295-10A-01D-A16D-09
TCGA-EB-A44O c787c4da-c564-44f1-89eb-dd9da107acb1 Aligned Reads Blood Derived Normal C828.TCGA-EB-A44O-10A-01D-A25O-08.3_gdc_realn.bam TCGA-EB-A44O-10A c723584a-c404-4c88-bfea-e40f5dbba542 5b738547-1825-4684-81bd-864bf2eb43ef 006ce9a8-cf38-462e-bb99-7f08499244ab Raw Sequencing Data TCGA-EB-A44O-10A-01D-A25O-08
TCGA-A2-A3XX 53886143-c1c6-40e9-88e6-e4e5e0271fc8 Aligned Reads Blood Derived Normal b40998d4778f18ed80d6dd8bff0eb761_gdc_realn.bam TCGA-A2-A3XX-10A e96d5811-4736-40dd-966d-e0e172aeb0af c6eb6218-ad71-40a6-88b7-a4f1a015b816 0043d981-3c6b-463f-b512-ab1d076d3e62 Raw Sequencing Data TCGA-A2-A3XX-10A-01D-A23C-09
TCGA-EB-A3XB a9255dcb-b236-4777-ac43-555e3a5386c3 Aligned Reads Blood Derived Normal C828.TCGA-EB-A3XB-10B-01D-A23B-08.1_gdc_realn.bam TCGA-EB-A3XB-10B 9f4ffc2f-d006-4d86-b3b1-b25020481893 0e1d4c7c-204d-4765-b090-68ed4cd83835 005239a8-2e63-4ff1-9cd4-714f81837a61 Raw Sequencing Data TCGA-EB-A3XB-10B-01D-A23B-08
Format
Specifies the format of the API response: JSON (default), TSV or XML.
Examples
curl 'https://api.gdc.cancer.gov/cases?fields=submitter_id&size=5&format=TSV'
import requests
cases_endpt = 'https://api.gdc.cancer.gov/cases'
params = {'fields':'submitter_id',
'format':'TSV'}
response = requests.get(cases_endpt, params = params)
print(response.content)
id submitter_id
0286c31b-a704-4d7d-99e3-0bc4e8975b8b HCM-CSHL-0084-C25
02f6d684-b6b5-419a-b0e1-b74d0a384a30 HCM-BROD-0408-C71
03974dc9-0162-4de8-9897-09f88693681a HCM-BROD-0334-C43
03bfeb7c-cecf-4691-8263-33cdfe391ea9 HCM-BROD-0124-C25
04cbceab-f945-482b-956b-840756a17a4a HCM-BROD-0421-C71
curl 'https://api.gdc.cancer.gov/cases?fields=submitter_id&size=5&format=XML&pretty=true'
import requests
cases_endpt = 'https://api.gdc.cancer.gov/cases'
params = {'fields':'submitter_id',
'format':'XML',
'pretty':'true'}
response = requests.get(cases_endpt, params = params)
print(response.content)
<?xml version="1.0" ?>
<response>
<data>
<hits>
<item>
<id>0286c31b-a704-4d7d-99e3-0bc4e8975b8b</id>
<submitter_id>HCM-CSHL-0084-C25</submitter_id>
</item>
<item>
<id>02f6d684-b6b5-419a-b0e1-b74d0a384a30</id>
<submitter_id>HCM-BROD-0408-C71</submitter_id>
</item>
<item>
<id>03974dc9-0162-4de8-9897-09f88693681a</id>
<submitter_id>HCM-BROD-0334-C43</submitter_id>
</item>
<item>
<id>03bfeb7c-cecf-4691-8263-33cdfe391ea9</id>
<submitter_id>HCM-BROD-0124-C25</submitter_id>
</item>
<item>
<id>04cbceab-f945-482b-956b-840756a17a4a</id>
<submitter_id>HCM-BROD-0421-C71</submitter_id>
</item>
</hits>
<pagination>
<count>5</count>
<total>86962</total>
<size>5</size>
<from>0</from>
<sort/>
<page>1</page>
<pages>17393</pages>
</pagination>
</data>
<warnings/>
</response>
Pretty
Returns when the pretty parameter is set to true, the API response is formatted with additional whitespace to improve legibility.
Example
curl 'https://api.gdc.cancer.gov/cases?fields=submitter_id&sort=submitter_id:asc&size=5'
{"data": {"hits": [{"id": "be37f1f7-2f98-4f74-bc04-6dd2ae2afcad", "submitter_id": "01BR001"}, {"id": "e6915db0-7c89-484d-8f9f-15cca68b82fc", "submitter_id": "01BR008"}, {"id": "16614d46-172b-479c-992b-e80a8e9a2c59", "submitter_id": "01BR009"}, {"id": "567fc9e3-17a6-42b1-a896-5e9a9507d1d8", "submitter_id": "01BR010"}, {"id": "54e89878-a1bc-4f5a-9d68-4842a469586e", "submitter_id": "01BR015"}], "pagination": {"count": 5, "total": 86962, "size": 5, "from": 0, "sort": "None", "page": 1, "pages": 17393}}, "warnings": {}}
curl 'https://api.gdc.cancer.gov/cases?fields=submitter_id&sort=submitter_id:asc&size=5&pretty=true'
{
"data": {
"hits": [
{
"id": "be37f1f7-2f98-4f74-bc04-6dd2ae2afcad",
"submitter_id": "01BR001"
},
{
"id": "e6915db0-7c89-484d-8f9f-15cca68b82fc",
"submitter_id": "01BR008"
},
{
"id": "16614d46-172b-479c-992b-e80a8e9a2c59",
"submitter_id": "01BR009"
},
{
"id": "567fc9e3-17a6-42b1-a896-5e9a9507d1d8",
"submitter_id": "01BR010"
},
{
"id": "54e89878-a1bc-4f5a-9d68-4842a469586e",
"submitter_id": "01BR015"
}
],
"pagination": {
"count": 5,
"total": 86962,
"size": 5,
"from": 0,
"sort": "None",
"page": 1,
"pages": 17393
}
},
"warnings": {}
}
Fields
This query parameter specifies which fields are to be included in the API response. The fields in the API response will be unordered. A listing of available fields for each endpoint is provided in Appendix A.
Example
The following example requests case submitter ID, file UUID, file name and file size from the files endpoint.
curl 'https://api.gdc.cancer.gov/files?fields=cases.submitter_id,file_id,file_name,file_size&pretty=true'
import requests
import json
files_endpt = 'https://api.gdc.cancer.gov/files'
params = {'fields':'cases.submitter_id,file_id,file_name,file_size'}
response = requests.get(files_endpt, params = params)
print(json.dumps(response.json(), indent=2))
{
"data": {
"hits": [
{
"id": "d570eccc-3c1c-4c4f-ae04-96be71fbe016",
"cases": [
{
"submitter_id": "TCGA-AN-A0FL"
}
],
"file_name": "TCGA-AN-A0FL-01Z-00-DX1.20A041C6-A306-4599-A7D1-65032A252AA9.svs",
"file_id": "d570eccc-3c1c-4c4f-ae04-96be71fbe016",
"file_size": 1055798681
},
{
"id": "0f8d8202-a1ca-4ea1-98b2-c20a6b08479a",
"cases": [
{
"submitter_id": "TCGA-AN-A0FL"
}
],
"file_name": "nationwidechildrens.org_ssf.TCGA-AN-A0FL.xml",
"file_id": "0f8d8202-a1ca-4ea1-98b2-c20a6b08479a",
"file_size": 15519
},
{
"id": "b76f87b3-99c5-4297-b2df-8cbea8ecaf61",
"cases": [
{
"submitter_id": "TCGA-BH-A18F"
}
],
"file_name": "7c4e4c2a-a0b1-424f-97d8-359825674429.wxs.aliquot_ensemble_masked.maf.gz",
"file_id": "b76f87b3-99c5-4297-b2df-8cbea8ecaf61",
"file_size": 21571
},
{
"id": "be6d269d-4305-4643-b98e-af703a067761",
"cases": [
{
"submitter_id": "TCGA-BH-A18F"
}
],
"file_name": "HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_E11_741424.CEL",
"file_id": "be6d269d-4305-4643-b98e-af703a067761",
"file_size": 69084893
},
{
"id": "fed73119-1d5e-4f7e-9713-183d1916422b",
"cases": [
{
"submitter_id": "TCGA-BH-A18F"
}
],
"file_name": "3b928f83-14a7-4bd6-a9b0-744b414d4495.wxs.varscan2.raw_somatic_mutation.vcf.gz",
"file_id": "fed73119-1d5e-4f7e-9713-183d1916422b",
"file_size": 35903
},
{
"id": "6877b045-91f1-4030-82ff-b90507e11e17",
"cases": [
{
"submitter_id": "TCGA-BH-A18F"
}
],
"file_name": "5057e3cb-25cd-4a67-8d31-6ac8508ba3c7.methylation_array.sesame.level3betas.txt",
"file_id": "6877b045-91f1-4030-82ff-b90507e11e17",
"file_size": 770500
},
{
"id": "07e8cdc7-d228-4752-ad19-800abd507277",
"cases": [
{
"submitter_id": "TCGA-BH-A0BM"
}
],
"file_name": "TCGA-BRCA.28dcad29-448e-4bcb-911d-556c6f4a5573.star_fusion.rna_fusion.tsv",
"file_id": "07e8cdc7-d228-4752-ad19-800abd507277",
"file_size": 234
},
{
"id": "fef57b45-ede1-49b0-b60d-957a55a15e0e",
"cases": [
{
"submitter_id": "TCGA-BH-A0BM"
}
],
"file_name": "nationwidechildrens.org_biospecimen.TCGA-BH-A0BM.xml",
"file_id": "fef57b45-ede1-49b0-b60d-957a55a15e0e",
"file_size": 127218
},
{
"id": "81a1b323-88b6-4837-bccf-ac84a79828b6",
"cases": [
{
"submitter_id": "TCGA-BH-A0BM"
}
],
"file_name": "TCGA-BRCA.4570b87f-8116-48bf-86d3-b993536c88db.gene_level_copy_number.v36.tsv",
"file_id": "81a1b323-88b6-4837-bccf-ac84a79828b6",
"file_size": 3446816
},
{
"id": "c6bf94a6-9940-4155-86b4-bbb10875dbdb",
"cases": [
{
"submitter_id": "TCGA-BH-A18F"
}
],
"file_name": "TCGA-BRCA.88cae21a-4890-4fdd-a678-c4864620942c.star_fusion.rna_fusion.bedpe",
"file_id": "c6bf94a6-9940-4155-86b4-bbb10875dbdb",
"file_size": 229
}
],
"pagination": {
"count": 10,
"total": 931947,
"size": 10,
"from": 0,
"sort": "",
"page": 1,
"pages": 93195
}
},
"warnings": {}
}
Expand
The expand parameter provides a shortcut to request multiple related fields (field groups) in the response. Instead of specifying each field using the fields parameter, users can specify a field group name using the expand parameter to request all fields in the group. Available field groups are listed in Appendix A; the list can also be accessed programmatically at the _mapping endpoint. The fields and expand parameters can be used together to request custom combinations of field groups and individual fields.
Example
curl 'https://api.gdc.cancer.gov/files/573ee7e9-b8bd-419e-808b-a027c4311731?expand=cases.samples&pretty=true'
{
"data": {
"proportion_reads_mapped": 0.9648433596149857,
"access": "controlled",
"proportion_base_mismatch": 0.004117986,
"contamination_error": 0,
"acl": [
"phs000178"
],
"type": "aligned_reads",
"platform": "Illumina",
"created_datetime": "2022-05-12T14:42:10.014925-05:00",
"updated_datetime": "2022-11-01T11:52:54.136033-05:00",
"pairs_on_diff_chr": 1170013,
"state": "released",
"data_format": "BAM",
"total_reads": 379313036,
"proportion_coverage_30x": 0.000109,
"cases": [
{
"samples": [
{
"sample_type_id": "10",
"tumor_descriptor": "Not Reported",
"sample_id": "4e128a37-be58-477a-a01f-448179360b7c",
"sample_type": "Blood Derived Normal",
"tumor_code": null,
"created_datetime": null,
"time_between_excision_and_freezing": null,
"composition": "Not Reported",
"updated_datetime": "2022-04-28T22:05:09.013808-05:00",
"days_to_collection": 6755,
"state": "released",
"initial_weight": null,
"preservation_method": null,
"intermediate_dimension": null,
"time_between_clamping_and_freezing": null,
"freezing_method": null,
"pathology_report_uuid": null,
"submitter_id": "TCGA-B6-A0RI-10A",
"tumor_code_id": null,
"shortest_dimension": null,
"oct_embedded": "false",
"days_to_sample_procurement": null,
"longest_dimension": null,
"current_weight": null,
"is_ffpe": false,
"tissue_type": "Not Reported"
}
]
}
],
"file_name": "c9478f7d-bfe3-4e80-8161-39b3d440fa16_wgs_gdc_realn.bam",
"mean_coverage": 5.452655,
"proportion_reads_duplicated": 0.009253781617987946,
"submitter_id": "a4e380e5-420e-49af-986d-e721601065fb",
"data_category": "Sequencing Reads",
"proportion_coverage_10x": 0.07674,
"file_size": 42958286722,
"contamination": 0,
"average_base_quality": 32,
"file_id": "573ee7e9-b8bd-419e-808b-a027c4311731",
"data_type": "Aligned Reads",
"average_insert_size": 207,
"average_read_length": 51,
"experimental_strategy": "WGS",
"version": "1",
"data_release": "36.0 - 37.0"
},
"warnings": {}
}
Size and From
GDC API provides a pagination feature that limits the number of results returned by the API. It is implemented using size and from query parameters.
The size query parameter specifies the maximum number of results to return. Default size is 10. If the number of query results is greater than size, only some of the results will be returned.
The from query parameter specifies the first record to return out of the set of results. For example, if there are 20 cases returned from the cases endpoint, then setting from to 11 will return results 12 to 20. The from parameter can be used in conjunction with the size parameter to return a specific subset of results.
Example
curl 'https://api.gdc.cancer.gov/files?fields=file_name&from=0&size=2&pretty=true'
import requests
import json
files_endpt = 'https://api.gdc.cancer.gov/files'
params = {'fields':'file_name',
'from':0, 'size':2}
response = requests.get(files_endpt, params = params)
print(json.dumps(response.json(), indent=2))
{
"data": {
"hits": [
{
"id": "d570eccc-3c1c-4c4f-ae04-96be71fbe016",
"file_name": "TCGA-AN-A0FL-01Z-00-DX1.20A041C6-A306-4599-A7D1-65032A252AA9.svs"
},
{
"id": "0f8d8202-a1ca-4ea1-98b2-c20a6b08479a",
"file_name": "nationwidechildrens.org_ssf.TCGA-AN-A0FL.xml"
}
],
"pagination": {
"count": 2,
"total": 931947,
"size": 2,
"from": 0,
"sort": "",
"page": 1,
"pages": 465974
}
},
"warnings": {}
}
curl 'https://api.gdc.cancer.gov/files?fields=file_name&from=101&size=5&pretty=true'
import requests
import json
files_endpt = 'https://api.gdc.cancer.gov/files'
params = {'fields':'file_name',
'from':101, 'size':5}
response = requests.get(files_endpt, params = params)
print(json.dumps(response.json(), indent=2))
{
"data": {
"hits": [
{
"id": "297933f5-1316-4cb6-b53f-9dbfa7f3d7ed",
"file_name": "TCGA-B6-A0RH-01A-02-TSB.ea83f31e-defb-4436-8a58-5b66b18d13b5.svs"
},
{
"id": "2f31e897-b3e8-49f1-a400-ccf9f00f294a",
"file_name": "URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_F01_735050.grch38.seg.v2.txt"
},
{
"id": "ebd6cf90-4f6b-4193-887a-22fdb5645fbc",
"file_name": "TCGA-BRCA.5994c06d-ee9b-4ead-b3d1-2e1f286f7d6d.ascat2.allelic_specific.seg.txt"
},
{
"id": "aebd6b5a-e676-4357-93df-523b31b55ea0",
"file_name": "TCGA-BRCA.c737131c-636f-4e1b-89b8-bb2d6ddd8164.star_fusion.rna_fusion.bedpe"
},
{
"id": "aa83a7e7-e9cc-4330-a7be-ca750cffb74c",
"file_name": "URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_F01_735050.birdseed.data.txt"
}
],
"pagination": {
"count": 5,
"total": 931947,
"size": 5,
"from": 101,
"sort": "",
"page": 21,
"pages": 186390
}
},
"warnings": {}
}
Sort
The sort query parameter sorts the results by a specific field, and with the sort direction specified using the :asc (ascending) or :desc (descending) prefix, e.g. sort=field:desc. A list of all valid field names is available in Appendix A; the list can also be accessed programmatically at the _mapping endpoint.
Example
Sort cases by submitter_id in ascending order:
curl 'https://api.gdc.cancer.gov/cases?fields=submitter_id&sort=submitter_id:asc&pretty=true'
import requests
import json
cases_endpt = 'https://api.gdc.cancer.gov/cases'
params = {'fields':'submitter_id',
'sort':'submitter_id:asc'}
response = requests.get(cases_endpt, params = params)
print(json.dumps(response.json(), indent=2))
{
"data": {
"hits": [
{
"id": "be37f1f7-2f98-4f74-bc04-6dd2ae2afcad",
"submitter_id": "01BR001"
},
{
"id": "e6915db0-7c89-484d-8f9f-15cca68b82fc",
"submitter_id": "01BR008"
},
{
"id": "16614d46-172b-479c-992b-e80a8e9a2c59",
"submitter_id": "01BR009"
},
{
"id": "567fc9e3-17a6-42b1-a896-5e9a9507d1d8",
"submitter_id": "01BR010"
},
{
"id": "54e89878-a1bc-4f5a-9d68-4842a469586e",
"submitter_id": "01BR015"
},
{
"id": "a1c7b7b9-b8c8-48c3-9420-55497f9318fd",
"submitter_id": "01BR017"
},
{
"id": "ce3c8b98-e275-4cfd-a379-940d675a564b",
"submitter_id": "01BR018"
},
{
"id": "e4ce89ef-bcaa-418a-8a6b-3602793b9bbf",
"submitter_id": "01BR020"
},
{
"id": "19d3c861-8a5f-49a2-acc0-b55b25465c35",
"submitter_id": "01BR023"
},
{
"id": "afae8dce-294a-4108-bb28-376f804ae5c4",
"submitter_id": "01BR025"
}
],
"pagination": {
"count": 10,
"total": 86962,
"size": 10,
"from": 0,
"sort": "None",
"page": 1,
"pages": 8697
}
},
"warnings": {}
}
Facets
The facets parameter provides aggregate information for a specified field. It provides all values that exist for that field, and the number of entities (cases, projects, files, or annotations) that this value. The primary intended use of this parameter is for displaying aggregate information in the GDC Data Portal.
The facets parameter can be used in conjunction with the filters parameter to get aggregate information for a set of search results. The following limitations apply when using facets and filters together:
- The
filtersobject's top level operator must beand, and the internal filters must be limited to:=,!=,in,exclude,is, andnot. - The information provided by
facetsfor a given field will disregard any filters applied to that same field.
Example
This is an example of a request for a count of projects in each program.
curl 'https://api.gdc.cancer.gov/projects?facets=program.name&from=0&size=0&sort=program.name:asc&pretty=true'
import requests
import json
projects_endpt = 'https://api.gdc.cancer.gov/projects'
params = {'facets':'program.name',
'from':0, 'size':0,
'sort':'program.name:asc'}
response = requests.get(projects_endpt, params = params)
print(json.dumps(response.json(), indent=2))
{
"data": {
"hits": [],
"aggregations": {
"program.name": {
"buckets": [
{
"doc_count": 33,
"key": "TCGA"
},
{
"doc_count": 10,
"key": "MATCH"
},
{
"doc_count": 9,
"key": "TARGET"
},
{
"doc_count": 4,
"key": "CGCI"
},
{
"doc_count": 3,
"key": "CMI"
},
{
"doc_count": 2,
"key": "BEATAML1.0"
},
{
"doc_count": 2,
"key": "CPTAC"
},
{
"doc_count": 2,
"key": "MP2PRT"
},
{
"doc_count": 1,
"key": "APOLLO"
},
{
"doc_count": 1,
"key": "CDDP_EAGLE"
},
{
"doc_count": 1,
"key": "CTSP"
},
{
"doc_count": 1,
"key": "EXCEPTIONAL_RESPONDERS"
},
{
"doc_count": 1,
"key": "FM"
},
{
"doc_count": 1,
"key": "HCMI"
},
{
"doc_count": 1,
"key": "MMRF"
},
{
"doc_count": 1,
"key": "NCICCR"
},
{
"doc_count": 1,
"key": "OHSU"
},
{
"doc_count": 1,
"key": "ORGANOID"
},
{
"doc_count": 1,
"key": "REBC"
},
{
"doc_count": 1,
"key": "TRIO"
},
{
"doc_count": 1,
"key": "VAREPOP"
},
{
"doc_count": 1,
"key": "WCDT"
}
]
}
},
"pagination": {
"count": 0,
"total": 79,
"size": 0,
"from": 0,
"sort": "None",
"page": 1,
"pages": 79
}
},
"warnings": {}
}
Example
In this sample POST request, both filters and facets parameters are used. Note that facets ignores the primary_site filter.
{
"filters":{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.primary_site",
"value":"Kidney"
}
},
{
"op":"=",
"content":{
"field":"project.program.name",
"value":"TCGA"
}
}
]
},
"size":"0",
"facets":"project.primary_site",
"pretty":"true"
}
curl --request POST --header "Content-Type: application/json" --data @Payload 'https://api.gdc.cancer.gov/v0/cases'
{
"data": {
"hits": [],
"aggregations": {
"project.primary_site": {
"buckets": [
{
"doc_count": 1202,
"key": "kidney"
},
{
"doc_count": 1191,
"key": "brain"
},
{
"doc_count": 1176,
"key": "bronchus and lung"
},
{
"doc_count": 1156,
"key": "breast"
},
{
"doc_count": 952,
"key": "colon"
},
{
"doc_count": 947,
"key": "stomach"
},
{
"doc_count": 878,
"key": "uterus, nos"
},
{
"doc_count": 869,
"key": "ovary"
},
{
"doc_count": 821,
"key": "corpus uteri"
},
{
"doc_count": 789,
"key": "other and unspecified parts of tongue"
},
{
"doc_count": 670,
"key": "connective, subcutaneous and other soft tissues"
},
{
"doc_count": 633,
"key": "rectosigmoid junction"
},
{
"doc_count": 586,
"key": "bones, joints and articular cartilage of other and unspecified sites"
},
{
"doc_count": 565,
"key": "thyroid gland"
},
{
"doc_count": 528,
"key": "base of tongue"
},
{
"doc_count": 528,
"key": "floor of mouth"
},
{
"doc_count": 528,
"key": "gum"
},
{
"doc_count": 528,
"key": "hypopharynx"
},
{
"doc_count": 528,
"key": "larynx"
},
{
"doc_count": 528,
"key": "lip"
},
{
"doc_count": 528,
"key": "oropharynx"
},
{
"doc_count": 528,
"key": "other and ill-defined sites in lip, oral cavity and pharynx"
},
{
"doc_count": 528,
"key": "other and unspecified parts of mouth"
},
{
"doc_count": 528,
"key": "palate"
},
{
"doc_count": 528,
"key": "tonsil"
},
{
"doc_count": 500,
"key": "prostate gland"
},
{
"doc_count": 498,
"key": "retroperitoneum and peritoneum"
},
{
"doc_count": 470,
"key": "skin"
},
{
"doc_count": 448,
"key": "heart, mediastinum, and pleura"
},
{
"doc_count": 428,
"key": "liver and intrahepatic bile ducts"
},
{
"doc_count": 412,
"key": "bladder"
},
{
"doc_count": 307,
"key": "cervix uteri"
},
{
"doc_count": 271,
"key": "adrenal gland"
},
{
"doc_count": 261,
"key": "bones, joints and articular cartilage of limbs"
},
{
"doc_count": 261,
"key": "meninges"
},
{
"doc_count": 261,
"key": "other and unspecified male genital organs"
},
{
"doc_count": 261,
"key": "peripheral nerves and autonomic nervous system"
},
{
"doc_count": 258,
"key": "hematopoietic and reticuloendothelial systems"
},
{
"doc_count": 208,
"key": "testis"
},
{
"doc_count": 185,
"key": "esophagus"
},
{
"doc_count": 185,
"key": "pancreas"
},
{
"doc_count": 179,
"key": "other and ill-defined sites"
},
{
"doc_count": 179,
"key": "other endocrine glands and related structures"
},
{
"doc_count": 179,
"key": "spinal cord, cranial nerves, and other parts of central nervous system"
},
{
"doc_count": 172,
"key": "rectum"
},
{
"doc_count": 172,
"key": "unknown"
},
{
"doc_count": 124,
"key": "thymus"
},
{
"doc_count": 80,
"key": "eye and adnexa"
},
{
"doc_count": 58,
"key": "lymph nodes"
},
{
"doc_count": 58,
"key": "other and unspecified major salivary glands"
},
{
"doc_count": 58,
"key": "small intestine"
},
{
"doc_count": 51,
"key": "gallbladder"
},
{
"doc_count": 51,
"key": "other and unspecified parts of biliary tract"
}
]
}
},
"pagination": {
"count": 0,
"total": 1202,
"size": 0,
"from": 0,
"sort": "",
"page": 1,
"pages": 1202
}
},
"warnings": {}
}
Alternative Request Format
The GDC API also supports POST requests with Content-Type: application/x-www-form-urlencoded (curl default), which require payloads in the following format:
filters=%7B%0A%20%20%20%20%22op%22%3A%22in%22%2C%0A%20%20%20%20%22content%22%3A%7B%0A%20%20%20%20%20%20%20%20%22field%22%3A%22files.file_id%22%2C%0A%20%20%20%20%20%20%20%20%22value%22%3A%5B%0A%20%20%20%20%20%20%20%20%20%20%20%20%220001801b-54b0-4551-8d7a-d66fb59429bf%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22002c67f2-ff52-4246-9d65-a3f69df6789e%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22003143c8-bbbf-46b9-a96f-f58530f4bb82%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%220043d981-3c6b-463f-b512-ab1d076d3e62%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22004e2a2c-1acc-4873-9379-ef1aa12283b6%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22005239a8-2e63-4ff1-9cd4-714f81837a61%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22006b8839-31e5-4697-b912-8e3f4124dd15%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22006ce9a8-cf38-462e-bb99-7f08499244ab%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22007ce9b5-3268-441e-9ffd-b40d1127a319%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%220084a614-780b-42ec-b85f-7a1b83128cd3%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%2200a5e471-a79f-4d56-8a4c-4847ac037400%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%2200ab2b5a-b59e-4ec9-b297-76f74ff1d3fb%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%2200c5f14e-a398-4076-95d1-25f320ee3a37%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%2200c74a8b-10aa-40cc-991e-3365ea1f3fce%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%2200df5a50-bce3-4edf-a078-641e54800dcb%22%0A%20%20%20%20%20%20%20%20%5D%0A%20%20%20%20%7D%0A%7D&fields=file_id,file_name,cases.submitter_id,cases.case_id,data_category,data_type,cases.samples.tumor_descriptor,cases.samples.tissue_type,cases.samples.sample_type,cases.samples.submitter_id,cases.samples.sample_id&format=tsv&size=100
Using Wildcards
The GDC API supports the use of the wildcard character, an asterisk (*), in the value fields of a JSON query. For example, if a user wanted to retrieve information about projects with a disease type that ended in "Adenocarcinoma" a query for "disease_type": "*Adenocarcinoma" would be appropriate. See below:
{
"size":"20000",
"pretty":"TRUE",
"fields":"submitter_id,disease_type",
"format":"TSV",
"filters":{
"op":"=",
"content":{
"field":"disease_type",
"value":"*Adenocarcinoma"
}
}
}
Quicksearch Endpoint
The GDC Portal has a quicksearch functionality that allows for a project, case, or file to be queried from a search box. This function calls the /v0/all endpoint, which retrieves the top cases, files, projects, genes, mutations, and annotations that match to the query. The quicksearch can also be used programmatically through the API. For example, a search term of 'TCGA' would produce the following query:
curl "https://api.gdc.cancer.gov/v0/all?query=TCGA&size=5"
{"data":{"query":{"hits":[{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUFDQw==","name":"Adrenocortical Carcinoma","primary_site":["Adrenal gland"],"project_id":"TCGA-ACC","project_quicksearch":"Adrenocortical Carcinoma"},{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJQ0g=","name":"Kidney Chromophobe","primary_site":["Kidney"],"project_id":"TCGA-KICH","project_quicksearch":"Kidney Chromophobe"},{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUxJSEM=","name":"Liver Hepatocellular Carcinoma","primary_site":["Liver and intrahepatic bile ducts"],"project_id":"TCGA-LIHC","project_quicksearch":"Liver Hepatocellular Carcinoma"},{"disease_type":["Myeloid Leukemias"],"id":"UHJvamVjdDpUQ0dBLUxBTUw=","name":"Acute Myeloid Leukemia","primary_site":["Hematopoietic and reticuloendothelial systems"],"project_id":"TCGA-LAML","project_quicksearch":"Acute Myeloid Leukemia"},{"disease_type":["Adenomas and Adenocarcinomas"],"id":"UHJvamVjdDpUQ0dBLUtJUlA=","name":"Kidney Renal Papillary Cell Carcinoma","primary_site":["Kidney"],"project_id":"TCGA-KIRP","project_quicksearch":"Kidney Renal Papillary Cell Carcinoma"}],"total":183550}}}
This endpoint can be used to quickly retrieve information about a file. For example, if a user wanted to know the UUID for nationwidechildrens.org_biospecimen.TCGA-EL-A4K1.xml, the following query could be used to quickly retrieve it programmatically:
curl "https://api.gdc.cancer.gov/v0/all?query=nationwidechildrens.org_biospecimen.TCGA-EL-A4K1.xml&size=5"
{"data":{"query":{"hits":[{"file_id":"a74abfec-db78-4ed4-9e4b-604b66e30e30","file_name":"nationwidechildrens.org_biospecimen.TCGA-EL-A4K1.xml","id":"RmlsZTphNzRhYmZlYy1kYjc4LTRlZDQtOWU0Yi02MDRiNjZlMzBlMzA=","submitter_id":"nationwidechildrens.org_biospecimen.TCGA-EL-A4K1.xml"}],"total":1}}}
Additional Examples
More examples of API functionality described in this section are provided in Additional Examples.