Example query 5: Complex example for filtering TCGA data

QUERY DATASETS > About the Datasets API > Query via the Datasets API > 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

POST /datasets/tcga/v0/query HTTP/1.1 Host: cgc-datasets-api.sbgenomics.com X-SBG-Auth-Token: 3210a98c1db9304ea9d9273156740f74
{ "entity": "cases", "hasSample": { "hasSampleType": "Primary Tumor", "hasPortion": { "hasPortionNumber":11 } }, "hasNewTumorEvent": { "hasNewTumorAnatomicSite": ["Liver", "Pancrease"], "hasNewTumorEventType":{ "filter": { "contains":"Recurrence" } } } }

Response body

This request returns the response below. Note that it contains 79 cases objects: one for each case matching the query above.

{ "_embedded": { "cases": [ { "label": "0304D251-123A-456B-B175-C94C2F5B1B81", "id": "0304D251-123A-456B-B175-C94C2F5B1B81", "_links": { "self": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0304D251-123A-456B-B175-C94C2F5B1B81" } } }, { "label": "001867AA-36D0-463F-7890-DEC7043B4F2E", "id": "001867AA-36D0-463F-7890-DEC7043B4F2E", "_links": { "self": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/001867AA-36D0-463F-7890-DEC7043B4F2E" } } }, { "label": "03DF105E-123A-4577-BFDB-9634758D778E", "id": "03DF105E-123A-4577-BFDB-9634758D778E", "_links": { "self": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/03DF105E-123A-4577-BFDB-9634758D778E" } } }, <snip> ] }, "count": 79 }

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.

GET /datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81 HTTP/1.1 Host: cgc-datasets-api.sbgenomics.com X-SBG-Auth-Token: 3210a98c1db9304ea9d9273156740f74
{ "hasNewTumorEventAfterInitialTreatment": "YES", "hasPriorDiagnosis": "No", "hasPathologicT": "T1", "hasIcdO3Site": "C22.0", "hasDaysToLastFollowUp": 2405, "hasInvestigation": "TCGA-LIHC", "hasGender": "MALE", "hasYearOfDiagnosis": 2007, "hasID": "TCGA-DD-AAVP", "hasProgram": "TCGA", "hasAgeAtDiagnosis": 48, "hasEthnicity": "NOT HISPANIC OR LATINO", "hasPathologicN": "N0", "hasPathologicStage": "Stage I", "hasPrimarySite": "Liver", "hasVitalStatus": "Alive", "_links": { "hasNewTumorEvent": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0304D251-123A-456B-B175-C94C2F5B1B81/new_tumor_events" }, "self": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0304D251-123A-456B-B175-C94C2F5B1B81" }, "hasSample": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0304D251-123A-456B-B175-C94C2F5B1B81/samples" }, "hasFile": { "href": "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0304D251-123A-456B-B175-C94C2F5B1B81/files" } }, "hasBatchNumber": "425", "label": "0304D251-123A-456B-B175-C94C2F5B1B81", "hasHistologicalDiagnosis": "Hepatocellular Carcinoma", "hasRace": "ASIAN", "hasIcdO3Histology": "8170/3", "hasTumorStatus": "TUMOR FREE", "id": "0304D251-123A-456B-B175-C94C2F5B1B81", "hasIcd10": "C22.0", "hasPerformanceStatusScoreECOG": "0", "hasDiseaseType": "Liver Hepatocellular Carcinoma" }
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