#Get all stduies in PDC
import requests
import json
# The URL for our API calls
url = 'https://pdc.esacinc.com/graphql'
# query to get study summary details
query = '''{
uiStudy {
submitter_id_name
program_name
project_name
disease_type
primary_site
analytical_fraction
experiment_type
cases_count
num_raw
num_mzml
num_prot
num_prot_assem
num_psm
}
}'''
response = requests.post(url, json={'query': query})
if(response.ok):
#If the response was OK then print the returned JSON
jData = json.loads(response.content)
print (json.dumps(jData, indent=4, sort_keys=True))
else:
# If response code is not ok (200), print the resulting http error code with description
response.raise_for_status()
{
"data": {
"uiStudy": [
{
"analytical_fraction": "Phosphoproteome",
"cases_count": 125,
"disease_type": "Breast Invasive Carcinoma",
"experiment_type": "TMT10",
"num_mzml": 221,
"num_prot": 8,
"num_prot_assem": 6,
"num_psm": 442,
"num_raw": 221,
"primary_site": "Breast",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Breast_BI_Phosphoproteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 112,
"disease_type": "Breast Invasive Carcinoma",
"experiment_type": "TMT10",
"num_mzml": 425,
"num_prot": 8,
"num_prot_assem": 5,
"num_psm": 850,
"num_raw": 425,
"primary_site": "Breast",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Breast_BI_Proteome"
},
{
"analytical_fraction": "Phosphoproteome",
"cases_count": 101,
"disease_type": "Colon Adenocarcinoma",
"experiment_type": "TMT10",
"num_mzml": 132,
"num_prot": 2,
"num_prot_assem": 8,
"num_psm": 264,
"num_raw": 132,
"primary_site": "Colon",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Colon_PNNL_Phosphoproteome_Lumos"
},
{
"analytical_fraction": "Proteome",
"cases_count": 101,
"disease_type": "Colon Adenocarcinoma",
"experiment_type": "TMT10",
"num_mzml": 264,
"num_prot": 1,
"num_prot_assem": 3,
"num_psm": 528,
"num_raw": 264,
"primary_site": "Colon",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Colon_PNNL_Proteome_Qeplus"
},
{
"analytical_fraction": "Proteome",
"cases_count": 100,
"disease_type": "Colon Adenocarcinoma",
"experiment_type": "Label Free",
"num_mzml": 600,
"num_prot": 11,
"num_prot_assem": 0,
"num_psm": 1200,
"num_raw": 600,
"primary_site": "Colon",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Colon_VU_Proteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 85,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "TMT10",
"num_mzml": 312,
"num_prot": 12,
"num_prot_assem": 0,
"num_psm": 624,
"num_raw": 312,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Ovarian_JHU_Proteome"
},
{
"analytical_fraction": "Phosphoproteome",
"cases_count": 84,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "TMT10",
"num_mzml": 144,
"num_prot": 13,
"num_prot_assem": 4,
"num_psm": 288,
"num_raw": 144,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Ovarian_PNNL_Phosphoproteome_Lumos"
},
{
"analytical_fraction": "Proteome",
"cases_count": 84,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "TMT10",
"num_mzml": 288,
"num_prot": 12,
"num_prot_assem": 0,
"num_psm": 576,
"num_raw": 288,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Confirmatory",
"submitter_id_name": "Prospective_Ovarian_PNNL_Proteome_Qeplus"
},
{
"analytical_fraction": "Phosphoproteome",
"cases_count": 108,
"disease_type": "Breast Invasive Carcinoma",
"experiment_type": "iTRAQ4",
"num_mzml": 37,
"num_prot": 6,
"num_prot_assem": 4,
"num_psm": 37,
"num_raw": 37,
"primary_site": "Breast",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Breast_Cancer_Phosphoproteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 108,
"disease_type": "Breast Invasive Carcinoma",
"experiment_type": "iTRAQ4",
"num_mzml": 38,
"num_prot": 6,
"num_prot_assem": 3,
"num_psm": 38,
"num_raw": 38,
"primary_site": "Breast",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Breast_Cancer_Proteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 60,
"disease_type": "Colon Adenocarcinoma",
"experiment_type": "Label Free",
"num_mzml": 1425,
"num_prot": 5,
"num_prot_assem": 4,
"num_psm": 2850,
"num_raw": 1425,
"primary_site": "Colon",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Colon_Cancer_Proteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 30,
"disease_type": "Rectum Adenocarcinoma",
"experiment_type": "Label Free",
"num_mzml": 1425,
"num_prot": 5,
"num_prot_assem": 4,
"num_psm": 2850,
"num_raw": 1425,
"primary_site": "Rectum",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Colon_Cancer_Proteome"
},
{
"analytical_fraction": "Glycoproteome",
"cases_count": 122,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "iTRAQ4",
"num_mzml": 132,
"num_prot": 8,
"num_prot_assem": 4,
"num_psm": 264,
"num_raw": 132,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Ovarian_JHU_Glycoproteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 122,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "iTRAQ4",
"num_mzml": 1100,
"num_prot": 8,
"num_prot_assem": 3,
"num_psm": 2200,
"num_raw": 1100,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Ovarian_JHU_Proteome"
},
{
"analytical_fraction": "Phosphoproteome",
"cases_count": 69,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "iTRAQ4",
"num_mzml": 276,
"num_prot": 8,
"num_prot_assem": 4,
"num_psm": 552,
"num_raw": 276,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Ovarian_PNNL_Phosphoproteome_Velos_Qexatvive"
},
{
"analytical_fraction": "Proteome",
"cases_count": 84,
"disease_type": "Ovarian Serous Cystadenocarcinoma",
"experiment_type": "iTRAQ4",
"num_mzml": 672,
"num_prot": 8,
"num_prot_assem": 3,
"num_psm": 1344,
"num_raw": 672,
"primary_site": "Ovary",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Ovarian_PNNL_Proteome"
}
]
}
}
#Get details about a single study
import requests
import json
# The URL for our API calls
url = 'https://pdc.esacinc.com/graphql'
# query to get study summary details
query = '''{
uiStudy(study_submitter_id: "S016-1") {
submitter_id_name
program_name
project_name
disease_type
primary_site
analytical_fraction
experiment_type
cases_count
num_raw
num_mzml
num_prot
num_prot_assem
num_psm
}
}'''
response = requests.post(url, json={'query': query})
if(response.ok):
#If the response was OK then print the returned JSON
jData = json.loads(response.content)
print (json.dumps(jData, indent=4, sort_keys=True))
else:
# If response code is not ok (200), print the resulting http error code with description
response.raise_for_status()
{
"data": {
"uiStudy": [
{
"analytical_fraction": "Proteome",
"cases_count": 60,
"disease_type": "Colon Adenocarcinoma",
"experiment_type": "Label Free",
"num_mzml": 1425,
"num_prot": 5,
"num_prot_assem": 4,
"num_psm": 2850,
"num_raw": 1425,
"primary_site": "Colon",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Colon_Cancer_Proteome"
},
{
"analytical_fraction": "Proteome",
"cases_count": 30,
"disease_type": "Rectum Adenocarcinoma",
"experiment_type": "Label Free",
"num_mzml": 1425,
"num_prot": 5,
"num_prot_assem": 4,
"num_psm": 2850,
"num_raw": 1425,
"primary_site": "Rectum",
"program_name": "Clinical Proteomic Tumor Analysis Consortium",
"project_name": "CPTAC-Retrospective",
"submitter_id_name": "TCGA_Colon_Cancer_Proteome"
}
]
}
}
#Get a specific type of files for a specific study
import requests
import json
# The URL for our API calls
url = 'https://pdc.esacinc.com/graphql'
# query to get study summary details
query = '''{
filesPerStudy (study_submitter_id: "S038-3", file_type: "RAW"){
study_submitter_id
file_name
file_type
md5sum
}
}'''
response = requests.post(url, json={'query': query})
if(response.ok):
#If the response was OK then print the returned JSON
jData = json.loads(response.content)
print (json.dumps(jData, indent=4, sort_keys=True))
else:
# If response code is not ok (200), print the resulting http error code with description
response.raise_for_status()
{
"data": {
"filesPerStudy": [
{
"file_name": "007a03e9-e982-43c7-9f68-54eced2bc30b.raw",
"file_type": "RAW",
"md5sum": "29128f0ea9b57216277635b2702f50c4",
"study_submitter_id": "S038-3"
},
{
"file_name": "0119f87e-4798-4fd1-b40b-8f59a2cd5e7c.raw",
"file_type": "RAW",
"md5sum": "c01ff51ad5c23f78222b6906892b758b",
"study_submitter_id": "S038-3"
},
{
"file_name": "02f7b6c0-4abb-4b78-b113-507b486321d7.raw",
"file_type": "RAW",
"md5sum": "eacdf378490aa0094339957ac4dec21f",
"study_submitter_id": "S038-3"
},
{
"file_name": "03b2f46b-b969-4cb4-922d-d5f0da764b08.raw",
"file_type": "RAW",
"md5sum": "47b188fcaa587ef58f73db4e6669ae43",
"study_submitter_id": "S038-3"
},
{
"file_name": "07af17c4-95d8-44fe-a101-7c09d19c9745.raw",
"file_type": "RAW",
"md5sum": "691bbfcc0eb04ed3d71e796e5448db4a",
"study_submitter_id": "S038-3"
},
{
"file_name": "07ecf90c-ccbe-4ca0-b639-9bb299974195.raw",
"file_type": "RAW",
"md5sum": "acf709e92e298487046e8d40599c5009",
"study_submitter_id": "S038-3"
},
{
"file_name": "0817b9b3-c201-4bd2-afc9-c9244dd19676.raw",
"file_type": "RAW",
"md5sum": "4dc245b6bb05afa0427a567a9786edc6",
"study_submitter_id": "S038-3"
},
{
"file_name": "0a387d33-1175-4a9d-908c-0108404963a0.raw",
"file_type": "RAW",
"md5sum": "ec44f8e60ad4ff6e1cef714ce57b0ff9",
"study_submitter_id": "S038-3"
},
{
"file_name": "0b3b464a-5709-4507-8798-47085660ebf5.raw",
"file_type": "RAW",
"md5sum": "adb63ddc68ed745129c37987f80ce763",
"study_submitter_id": "S038-3"
},
{
"file_name": "0bd92f38-4179-4eba-8dc1-4320a3d4b003.raw",
"file_type": "RAW",
"md5sum": "a346517905caefadcb6cde051c3e397a",
"study_submitter_id": "S038-3"
},
{
"file_name": "0c4cda40-cb9b-46d6-ae89-f73581a0509b.raw",
"file_type": "RAW",
"md5sum": "e227313f8250a10d68f0b2325a8982f3",
"study_submitter_id": "S038-3"
},
{
"file_name": "0cad1f58-7c5e-4f3c-947f-4ba3689c390b.raw",
"file_type": "RAW",
"md5sum": "dcda8dbab1577ba57cc5f7c0f0413138",
"study_submitter_id": "S038-3"
},
{
"file_name": "10ac3dfc-64c3-4e18-9f94-078550b5d3c9.raw",
"file_type": "RAW",
"md5sum": "7a57377993e7476cb15e1736e7c95cf3",
"study_submitter_id": "S038-3"
},
{
"file_name": "1196dd6f-aa0d-4c6f-ab52-9b28fa0df3fb.raw",
"file_type": "RAW",
"md5sum": "efa2420f18bf41178f5001838c9ad465",
"study_submitter_id": "S038-3"
},
{
"file_name": "13a9039d-0a45-4cba-94ac-c465836bb1a0.raw",
"file_type": "RAW",
"md5sum": "41523caa4aa5517a9bfde0f914fe7e1a",
"study_submitter_id": "S038-3"
},
{
"file_name": "176f89e8-0fe9-4745-9a59-36039bb4ef06.raw",
"file_type": "RAW",
"md5sum": "8b91b61a06eef24cb72c9be799bf74ff",
"study_submitter_id": "S038-3"
},
{
"file_name": "1797f3e5-8800-47ed-a6ec-b267b8a1e36f.raw",
"file_type": "RAW",
"md5sum": "0a83f7f4e8cb85a8a2a666dec4ccb877",
"study_submitter_id": "S038-3"
},
{
"file_name": "18f974a4-92f6-4ef1-a289-c9b379bd0f30.raw",
"file_type": "RAW",
"md5sum": "ffbbfc8faec92b51317aded276401ba9",
"study_submitter_id": "S038-3"
},
{
"file_name": "197cfea1-edde-49ba-b511-94b35d77f435.raw",
"file_type": "RAW",
"md5sum": "ee8cc97b541aee1fac479e80869fa7e4",
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},
{
"file_name": "1a5feaac-f3af-49d0-afaa-4b42f3c794b5.raw",
"file_type": "RAW",
"md5sum": "1257bcd5c13050ff0ab3c93f80a4eddd",
"study_submitter_id": "S038-3"
},
{
"file_name": "1aabcc01-4ee0-47df-83fb-9d8aea700a24.raw",
"file_type": "RAW",
"md5sum": "2b6ed659387769a988608d196d2336c5",
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},
{
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},
{
"file_name": "1ba104f1-e888-43af-a765-0bcc96f4c474.raw",
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{
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},
{
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"file_type": "RAW",
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{
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{
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{
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},
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},
{
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{
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{
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{
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{
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{
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"file_type": "RAW",
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{
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"study_submitter_id": "S038-3"
},
{
"file_name": "e642a646-12bc-44d7-a79a-052c4cd5f602.raw",
"file_type": "RAW",
"md5sum": "fd28d697b356eda0ade053279a34e201",
"study_submitter_id": "S038-3"
},
{
"file_name": "e6ffc372-ce66-4ee1-b1ce-0d0e589cd56c.raw",
"file_type": "RAW",
"md5sum": "c9b6fd733faaf5d58f101cea08b5b943",
"study_submitter_id": "S038-3"
},
{
"file_name": "e892082b-8b2d-45ba-bd5e-a39bf2bf7bc2.raw",
"file_type": "RAW",
"md5sum": "1d7c41e391beffa79e538717a5c557fb",
"study_submitter_id": "S038-3"
},
{
"file_name": "e981eef7-cdcb-44dd-abb0-aa159561bf72.raw",
"file_type": "RAW",
"md5sum": "67ac81ccd925a95a71006fb3f5b35c73",
"study_submitter_id": "S038-3"
},
{
"file_name": "eab40dc7-30ed-43bf-92dd-2b36fde8268a.raw",
"file_type": "RAW",
"md5sum": "73a12f71a054df1e99f852491c17a965",
"study_submitter_id": "S038-3"
},
{
"file_name": "eef0c5d0-f636-4343-a44f-1338d30f0bca.raw",
"file_type": "RAW",
"md5sum": "26fe3a24f40150992b2212033a7e7905",
"study_submitter_id": "S038-3"
},
{
"file_name": "f5cc4368-635d-4e56-9592-1621d9d68639.raw",
"file_type": "RAW",
"md5sum": "53df8bf7cf17e5dbd1ff30db235acddc",
"study_submitter_id": "S038-3"
},
{
"file_name": "f7ee7c82-5c1f-4649-a05f-60d4892ead3d.raw",
"file_type": "RAW",
"md5sum": "9882eb51154eb47b1181b14cf136ef3c",
"study_submitter_id": "S038-3"
},
{
"file_name": "f81ce5bb-233a-4e59-8d01-4fa251d1deee.raw",
"file_type": "RAW",
"md5sum": "07d4172f39f6d3381cce55c78a961795",
"study_submitter_id": "S038-3"
},
{
"file_name": "faa2ae56-ea39-4aab-a7c8-2512136f0c4b.raw",
"file_type": "RAW",
"md5sum": "57d7d95055e8b7d8221dfa6ac2fa29b4",
"study_submitter_id": "S038-3"
},
{
"file_name": "fadd2bb6-2148-4981-98f1-4278dbfbbd9a.raw",
"file_type": "RAW",
"md5sum": "fc52ee19ca2b6fdbb08ef67dc21d06cd",
"study_submitter_id": "S038-3"
},
{
"file_name": "fb297373-7c86-4336-b420-d7ea54a7836f.raw",
"file_type": "RAW",
"md5sum": "354a355fff3e33719086bfcddeabefcd",
"study_submitter_id": "S038-3"
},
{
"file_name": "fdaa238c-3bfa-44b8-a216-add9d275d7f0.raw",
"file_type": "RAW",
"md5sum": "7f713fb11db3254cd021754577523901",
"study_submitter_id": "S038-3"
},
{
"file_name": "fe561bd3-2b7d-4c3a-9d4a-71c0f78dc6f6.raw",
"file_type": "RAW",
"md5sum": "4b2a1381789d0303d8ba582c84347e56",
"study_submitter_id": "S038-3"
},
{
"file_name": "feb3f2c6-9928-472b-a105-989cc7c14725.raw",
"file_type": "RAW",
"md5sum": "7e8bb1070fd394b5dbd4474b708e56a0",
"study_submitter_id": "S038-3"
}
]
}
}
#Get details for a case
import requests
import json
# The URL for our API calls
url = 'https://pdc.esacinc.com/graphql'
# query to get study summary details
query = '''{
case(case_submitter_id: "01BR001") {
case_submitter_id
project_submitter_id
gdc_case_id
disease_type
}
}'''
response = requests.post(url, json={'query': query})
if(response.ok):
#If the response was OK then print the returned JSON
jData = json.loads(response.content)
print (json.dumps(jData, indent=4, sort_keys=True))
else:
# If response code is not ok (200), print the resulting http error code with description
response.raise_for_status()
{
"data": {
"case": {
"case_submitter_id": "01BR001",
"disease_type": "Breast Invasive Carcinoma",
"gdc_case_id": "be37f1f7-2f98-4f74-bc04-6dd2ae2afcad",
"project_submitter_id": "CPTAC-2"
}
}
}
#Get metadata about available genomic data for a case
# use the requests/json packages:
import json, requests
# save your query in 'Query' variable:
Query = '{"content":[{"content":{"field":"cases.case_id","value":["60014a6e-6a13-4f92-bbfd-eeeee9632f98"]},"op":"="},{"content":{"field":"data_format","value":["BAM"]},"op":"in"},{"content":{"field":"experimental_strategy","value":["WXS"]},"op":"in"}],"op":"and"}'
# save the fields you want back in 'Fields' variable:
Fields = 'cases.samples.portions.analytes.aliquots.submitter_id,cases.case_id,cases.project.project_id,access,data_type,file_id'
Size = '10000' #this variable limits the number of records returned from API
Payload = {'filters':Query,'format':'json','fields':Fields,'size':Size} # This is the payload sent to the API
r = requests.post('https://api.gdc.cancer.gov/files', json=Payload) # This command sends the payload to the API endpoint
data = json.loads(r.text) # Save the response text in json format using "json.loads" from the "json" python package
print (json.dumps(data, indent=2, sort_keys=True)) # Print the prettified response text with "json.dumps"
{
"data": {
"hits": [
{
"access": "controlled",
"cases": [
{
"case_id": "60014a6e-6a13-4f92-bbfd-eeeee9632f98",
"project": {
"project_id": "TCGA-OV"
},
"samples": [
{
"portions": [
{
"analytes": [
{
"aliquots": [
{
"submitter_id": "TCGA-09-1670-10A-01W-0633-09"
}
]
}
]
}
]
}
]
}
],
"data_type": "Aligned Reads",
"file_id": "e5a3b193-e471-4de3-bc22-425b946cb950",
"id": "e5a3b193-e471-4de3-bc22-425b946cb950"
},
{
"access": "controlled",
"cases": [
{
"case_id": "60014a6e-6a13-4f92-bbfd-eeeee9632f98",
"project": {
"project_id": "TCGA-OV"
},
"samples": [
{
"portions": [
{
"analytes": [
{
"aliquots": [
{
"submitter_id": "TCGA-09-1670-01A-01W-0633-09"
}
]
}
]
}
]
}
]
}
],
"data_type": "Aligned Reads",
"file_id": "dc4a231b-e18e-4fd2-b2bc-265795094fcf",
"id": "dc4a231b-e18e-4fd2-b2bc-265795094fcf"
}
],
"pagination": {
"count": 2,
"from": 0,
"page": 1,
"pages": 1,
"size": 10000,
"sort": "",
"total": 2
}
},
"warnings": {}
}