{"_id":"5845ac4e9f79b51900b076b3","category":{"_id":"58458b4fba4f1c0f009692bb","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":37,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"__v":0,"user":"5613e4f8fdd08f2b00437620","updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-12-05T18:05:02.763Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","examples":{"codes":[]},"method":"post","auth":"required","params":[],"url":""},"isReference":false,"order":38,"body":"Complex queries are well-suited to the Datasets API.\n\nFor instance, use the following query to obtain all cases that have a sample with a Primary tumor sample type of portion number 11, a new tumor anatomic site of the liver or pancreas, and a new tumor event type containing the word \"recurrence\".\n\n##Request\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"POST /datasets/tcga/v0/query HTTP/1.1\\nHost: cgc-datasets-api.sbgenomics.com\\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96\",\n      \"language\": \"http\",\n      \"name\": \"Complex query\"\n    }\n  ]\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n    \\\"entity\\\": \\\"cases\\\",\\n    \\\"hasSample\\\": {\\n        \\\"hasSampleType\\\": \\\"Primary Tumor\\\",\\n        \\\"hasPortion\\\": {\\n            \\\"hasPortionNumber\\\":11\\n            }\\n        },\\n    \\\"hasNewTumorEvent\\\": {\\n        \\\"hasNewTumorAnatomicSite\\\": [\\\"Liver\\\", \\\"Pancrease\\\"],\\n        \\\"hasNewTumorEventType\\\":{\\n            \\\"filter\\\": {\\n                \\\"contains\\\":\\\"Recurrence\\\"\\n            }\\n        }\\n    }\\n}\",\n      \"language\": \"json\",\n      \"name\": \"Request body\"\n    }\n  ]\n}\n[/block]\n##Response body\n\nThis request returns the response below. Note that it contains 79 cases objects: one for each case matching the query above.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"_embedded\\\": {\\n    \\\"cases\\\": [\\n      {\\n        \\\"label\\\": \\\"0004D251-3F70-4395-B175-C94C2F5B1B81\\\",\\n        \\\"id\\\": \\\"0004D251-3F70-4395-B175-C94C2F5B1B81\\\",\\n        \\\"_links\\\": {\\n          \\\"self\\\": {\\n            \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81\\\"\\n          }\\n        }\\n      },\\n      {\\n        \\\"label\\\": \\\"001887AA-36D0-463F-8BCA-DEC7043B4F2E\\\",\\n        \\\"id\\\": \\\"001887AA-36D0-463F-8BCA-DEC7043B4F2E\\\",\\n        \\\"_links\\\": {\\n          \\\"self\\\": {\\n            \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/001887AA-36D0-463F-8BCA-DEC7043B4F2E\\\"\\n          }\\n        }\\n      },\\n      {\\n        \\\"label\\\": \\\"03DF105E-A005-4577-BFDB-9644758D778E\\\",\\n        \\\"id\\\": \\\"03DF105E-A005-4577-BFDB-9644758D778E\\\",\\n        \\\"_links\\\": {\\n          \\\"self\\\": {\\n            \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/03DF105E-A005-4577-BFDB-9644758D778E\\\"\\n          }\\n        }\\n      },\\n    <snip>\\n    ]\\n  },\\n  \\\"count\\\": 79\\n}\",\n      \"language\": \"json\"\n    }\n  ]\n}\n[/block]\nFor each case returned, the response lists:\n  * Its TCGA `label`\n  * Its TCGA `id`\n  * Its `href`: this is a path that can be used to obtain full information about the case. \n\n##Secondary request\nUse a `GET` request to the `href` path obtain this information, as shown below.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"GET /datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81 HTTP/1.1\\nHost: cgc-datasets-api.sbgenomics.com\\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96\",\n      \"language\": \"http\",\n      \"name\": \"Secondary request\"\n    }\n  ]\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"hasNewTumorEventAfterInitialTreatment\\\": \\\"YES\\\",\\n  \\\"hasPriorDiagnosis\\\": \\\"No\\\",\\n  \\\"hasPathologicT\\\": \\\"T1\\\",\\n  \\\"hasIcdO3Site\\\": \\\"C22.0\\\",\\n  \\\"hasDaysToLastFollowUp\\\": 2405,\\n  \\\"hasInvestigation\\\": \\\"TCGA-LIHC\\\",\\n  \\\"hasGender\\\": \\\"MALE\\\",\\n  \\\"hasYearOfDiagnosis\\\": 2007,\\n  \\\"hasID\\\": \\\"TCGA-DD-AAVP\\\",\\n  \\\"hasProgram\\\": \\\"TCGA\\\",\\n  \\\"hasAgeAtDiagnosis\\\": 48,\\n  \\\"hasEthnicity\\\": \\\"NOT HISPANIC OR LATINO\\\",\\n  \\\"hasPathologicN\\\": \\\"N0\\\",\\n  \\\"hasPathologicStage\\\": \\\"Stage I\\\",\\n  \\\"hasPrimarySite\\\": \\\"Liver\\\",\\n  \\\"hasVitalStatus\\\": \\\"Alive\\\",\\n  \\\"_links\\\": {\\n    \\\"hasNewTumorEvent\\\": {\\n      \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81/new_tumor_events\\\"\\n    },\\n    \\\"self\\\": {\\n      \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81\\\"\\n    },\\n    \\\"hasSample\\\": {\\n      \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81/samples\\\"\\n    },\\n    \\\"hasFile\\\": {\\n      \\\"href\\\": \\\"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81/files\\\"\\n    }\\n  },\\n  \\\"hasBatchNumber\\\": \\\"425\\\",\\n  \\\"label\\\": \\\"0004D251-3F70-4395-B175-C94C2F5B1B81\\\",\\n  \\\"hasHistologicalDiagnosis\\\": \\\"Hepatocellular Carcinoma\\\",\\n  \\\"hasRace\\\": \\\"ASIAN\\\",\\n  \\\"hasIcdO3Histology\\\": \\\"8170/3\\\",\\n  \\\"hasTumorStatus\\\": \\\"TUMOR FREE\\\",\\n  \\\"id\\\": \\\"0004D251-3F70-4395-B175-C94C2F5B1B81\\\",\\n  \\\"hasIcd10\\\": \\\"C22.0\\\",\\n  \\\"hasPerformanceStatusScoreECOG\\\": \\\"0\\\",\\n  \\\"hasDiseaseType\\\": \\\"Liver Hepatocellular Carcinoma\\\"\\n}\",\n      \"language\": \"json\",\n      \"name\": \"Response body\"\n    }\n  ]\n}\n[/block]","excerpt":"<a href=\"query-datasets\" style=\"color:#132c56\">QUERY DATASETS</a> > <a href=\"about-the-datasets-api\" style=\"color:#132c56\">About the Datasets API</a> > <a href=\"query-via-the-datasets-api\" style=\"color:#132c56\">Query via the Datasets API</a> > Example query 5: Complex example...","slug":"example-query-5-complex-example-for-filtering-tcga-data","type":"endpoint","title":"Example query 5: Complex example for filtering TCGA data"}

postExample query 5: Complex example for filtering TCGA data

<a href="query-datasets" style="color:#132c56">QUERY DATASETS</a> > <a href="about-the-datasets-api" style="color:#132c56">About the Datasets API</a> > <a href="query-via-the-datasets-api" style="color:#132c56">Query via the Datasets API</a> > Example query 5: Complex example...

Complex queries are well-suited to the Datasets API. For instance, use the following query to obtain all cases that have a sample with a Primary tumor sample type of portion number 11, a new tumor anatomic site of the liver or pancreas, and a new tumor event type containing the word "recurrence". ##Request [block:code] { "codes": [ { "code": "POST /datasets/tcga/v0/query HTTP/1.1\nHost: cgc-datasets-api.sbgenomics.com\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96", "language": "http", "name": "Complex query" } ] } [/block] [block:code] { "codes": [ { "code": "{\n \"entity\": \"cases\",\n \"hasSample\": {\n \"hasSampleType\": \"Primary Tumor\",\n \"hasPortion\": {\n \"hasPortionNumber\":11\n }\n },\n \"hasNewTumorEvent\": {\n \"hasNewTumorAnatomicSite\": [\"Liver\", \"Pancrease\"],\n \"hasNewTumorEventType\":{\n \"filter\": {\n \"contains\":\"Recurrence\"\n }\n }\n }\n}", "language": "json", "name": "Request body" } ] } [/block] ##Response body This request returns the response below. Note that it contains 79 cases objects: one for each case matching the query above. [block:code] { "codes": [ { "code": "{\n \"_embedded\": {\n \"cases\": [\n {\n \"label\": \"0004D251-3F70-4395-B175-C94C2F5B1B81\",\n \"id\": \"0004D251-3F70-4395-B175-C94C2F5B1B81\",\n \"_links\": {\n \"self\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81\"\n }\n }\n },\n {\n \"label\": \"001887AA-36D0-463F-8BCA-DEC7043B4F2E\",\n \"id\": \"001887AA-36D0-463F-8BCA-DEC7043B4F2E\",\n \"_links\": {\n \"self\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/001887AA-36D0-463F-8BCA-DEC7043B4F2E\"\n }\n }\n },\n {\n \"label\": \"03DF105E-A005-4577-BFDB-9644758D778E\",\n \"id\": \"03DF105E-A005-4577-BFDB-9644758D778E\",\n \"_links\": {\n \"self\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/03DF105E-A005-4577-BFDB-9644758D778E\"\n }\n }\n },\n <snip>\n ]\n },\n \"count\": 79\n}", "language": "json" } ] } [/block] For each case returned, the response lists: * Its TCGA `label` * Its TCGA `id` * Its `href`: this is a path that can be used to obtain full information about the case. ##Secondary request Use a `GET` request to the `href` path obtain this information, as shown below. [block:code] { "codes": [ { "code": "GET /datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81 HTTP/1.1\nHost: cgc-datasets-api.sbgenomics.com\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96", "language": "http", "name": "Secondary request" } ] } [/block] [block:code] { "codes": [ { "code": "{\n \"hasNewTumorEventAfterInitialTreatment\": \"YES\",\n \"hasPriorDiagnosis\": \"No\",\n \"hasPathologicT\": \"T1\",\n \"hasIcdO3Site\": \"C22.0\",\n \"hasDaysToLastFollowUp\": 2405,\n \"hasInvestigation\": \"TCGA-LIHC\",\n \"hasGender\": \"MALE\",\n \"hasYearOfDiagnosis\": 2007,\n \"hasID\": \"TCGA-DD-AAVP\",\n \"hasProgram\": \"TCGA\",\n \"hasAgeAtDiagnosis\": 48,\n \"hasEthnicity\": \"NOT HISPANIC OR LATINO\",\n \"hasPathologicN\": \"N0\",\n \"hasPathologicStage\": \"Stage I\",\n \"hasPrimarySite\": \"Liver\",\n \"hasVitalStatus\": \"Alive\",\n \"_links\": {\n \"hasNewTumorEvent\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81/new_tumor_events\"\n },\n \"self\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81\"\n },\n \"hasSample\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81/samples\"\n },\n \"hasFile\": {\n \"href\": \"https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81/files\"\n }\n },\n \"hasBatchNumber\": \"425\",\n \"label\": \"0004D251-3F70-4395-B175-C94C2F5B1B81\",\n \"hasHistologicalDiagnosis\": \"Hepatocellular Carcinoma\",\n \"hasRace\": \"ASIAN\",\n \"hasIcdO3Histology\": \"8170/3\",\n \"hasTumorStatus\": \"TUMOR FREE\",\n \"id\": \"0004D251-3F70-4395-B175-C94C2F5B1B81\",\n \"hasIcd10\": \"C22.0\",\n \"hasPerformanceStatusScoreECOG\": \"0\",\n \"hasDiseaseType\": \"Liver Hepatocellular Carcinoma\"\n}", "language": "json", "name": "Response body" } ] } [/block]