{"__v":0,"_id":"5845ae4b9f6fbb1b0043085d","category":{"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","_id":"58458b4fba4f1c0f009692bb","__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","user":"5613e4f8fdd08f2b00437620","version":{"__v":37,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","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"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-12-05T18:13:31.202Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":41,"body":"Follow the steps below to use the CGC API to access the data resulting from SPARQL queries.\n\n##Step 1: Obtain file IDs\nIssue a SPARQL query to obtain file IDs, as shown below.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\nprefix tcga: <https://www.sbgenomics.com/ontologies/2014/11/tcga#>\\n \\nselect distinct ?case ?sample ?file_name ?id ?file_index ?xs_label ?subtype_label\\nwhere\\n{\\n ?case a tcga:Case .\\n ?case tcga:hasDiseaseType ?disease_type .\\n ?disease_type rdfs:label \\\"Lung Adenocarcinoma\\\" .\\n  \\n ?case tcga:hasHistologicalDiagnosis ?hd .\\n ?hd rdfs:label \\\"Lung Adenocarcinoma Mixed Subtype\\\" .\\n  \\n ?case tcga:hasFollowUp ?follow_up .\\n ?follow_up tcga:hasDaysToLastFollowUp ?days_to_last_follow_up .\\n filter(?days_to_last_follow_up>550)\\n   \\n ?follow_up tcga:hasVitalStatus ?vital_status .\\n ?vital_status rdfs:label ?vital_status_label .\\n filter(?vital_status_label=\\\"Alive\\\")\\n  \\n ?case tcga:hasDrugTherapy ?drug_therapy .\\n ?drug_therapy tcga:hasPharmaceuticalTherapyType ?pt_type .\\n ?pt_type rdfs:label ?pt_type_label .\\n filter(?pt_type_label=\\\"Chemotherapy\\\")\\n   \\n ?case tcga:hasSample ?sample .\\n ?sample tcga:hasSampleType ?st .\\n ?st rdfs:label ?st_label\\n filter(?st_label=\\\"Primary Tumor\\\")\\n      \\n ?sample tcga:hasFile ?file .\\n ?file rdfs:label ?file_name .\\n  \\n ?file tcga:hasFileId ?id .\\n \\n ?file tcga:hasIndex ?file_index .\\n   \\n ?file tcga:hasExperimentalStrategy ?xs.\\n ?xs rdfs:label ?xs_label .\\n filter(?xs_label=\\\"WXS\\\")\\n   \\n ?file tcga:hasDataSubtype ?subtype .\\n ?subtype rdfs:label ?subtype_label\\n \\n}\",\n      \"language\": \"text\"\n    }\n  ]\n}\n[/block]\n##Step 2: Make a CGC API request to copy a file\n\nUse the values for `id` and `file_index` obtained from the SPARQL query above to make the CGC API request to [copy a file](copy-files-between-projects-1). `file_index` contains the IDs of associated index files (*.BAI) which are required for analysis alongside of BAM files on the CGC. If `file_index` displays as `none`, there are no associated index files.\n\nFor instance, if you obtained the file IDs 564a3581e3b0289zk2c68351 and 564a378bc7b093360b6080d4, use them in your API request as shown below.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"POST /v2/action/files/copy HTTP/1.1\\nHost: cgc-api.sbgenomics.com\\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96\",\n      \"language\": \"http\",\n      \"name\": \"Copy a file\"\n    }\n  ]\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"project\\\": \\\"RFranklin/my-project\\\",\\n  \\\"file_ids\\\": [\\\"564a3581e3b0289zk2c68351\\\", \\\"564a378bc7b093360b6080d4\\\"]\\n}\",\n      \"language\": \"json\",\n      \"name\": \"Request body\"\n    }\n  ]\n}\n[/block]\nThis returns the following response:\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"5655df71e4b08c5d86970945\\\": {\\n    \\\"status\\\": \\\"OK\\\",\\n    \\\"new_file_id\\\": \\\"568cf5f4e4b0307bc0462062\\\",\\n    \\\"new_file_name\\\": \\\"ResultCount_MERGING_1_NIC1254A17.hg19_rCRSchrm.fa.realign.mdups.recal.MERGED.ID.vcf\\\"\\n  },\\n  \\\"564a378bc7b093360b6080d4\\\": {\\n    \\\"status\\\": \\\"OK\\\",\\n    \\\"new_file_id\\\": \\\"578cf5f4e4d0307ec0463064\\\",\\n    \\\"new_file_name\\\": \\\"TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a_Breast_tumor.realign.mdups.recal.MERGED.ID.vcf\\\"\\n  },\\n}\",\n      \"language\": \"json\",\n      \"name\": \"Response body\"\n    }\n  ]\n}\n[/block]","excerpt":"<a href=\"access-data-from-datasets\" style=\"color:#132c56\">ACCESS DATA FROM DATASETS</a> > Access data from SPARQL","slug":"access-data-from-sparql","type":"basic","title":"Access data from SPARQL"}

Access data from SPARQL

<a href="access-data-from-datasets" style="color:#132c56">ACCESS DATA FROM DATASETS</a> > Access data from SPARQL

Follow the steps below to use the CGC API to access the data resulting from SPARQL queries. ##Step 1: Obtain file IDs Issue a SPARQL query to obtain file IDs, as shown below. [block:code] { "codes": [ { "code": "prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nprefix tcga: <https://www.sbgenomics.com/ontologies/2014/11/tcga#>\n \nselect distinct ?case ?sample ?file_name ?id ?file_index ?xs_label ?subtype_label\nwhere\n{\n ?case a tcga:Case .\n ?case tcga:hasDiseaseType ?disease_type .\n ?disease_type rdfs:label \"Lung Adenocarcinoma\" .\n \n ?case tcga:hasHistologicalDiagnosis ?hd .\n ?hd rdfs:label \"Lung Adenocarcinoma Mixed Subtype\" .\n \n ?case tcga:hasFollowUp ?follow_up .\n ?follow_up tcga:hasDaysToLastFollowUp ?days_to_last_follow_up .\n filter(?days_to_last_follow_up>550)\n \n ?follow_up tcga:hasVitalStatus ?vital_status .\n ?vital_status rdfs:label ?vital_status_label .\n filter(?vital_status_label=\"Alive\")\n \n ?case tcga:hasDrugTherapy ?drug_therapy .\n ?drug_therapy tcga:hasPharmaceuticalTherapyType ?pt_type .\n ?pt_type rdfs:label ?pt_type_label .\n filter(?pt_type_label=\"Chemotherapy\")\n \n ?case tcga:hasSample ?sample .\n ?sample tcga:hasSampleType ?st .\n ?st rdfs:label ?st_label\n filter(?st_label=\"Primary Tumor\")\n \n ?sample tcga:hasFile ?file .\n ?file rdfs:label ?file_name .\n \n ?file tcga:hasFileId ?id .\n \n ?file tcga:hasIndex ?file_index .\n \n ?file tcga:hasExperimentalStrategy ?xs.\n ?xs rdfs:label ?xs_label .\n filter(?xs_label=\"WXS\")\n \n ?file tcga:hasDataSubtype ?subtype .\n ?subtype rdfs:label ?subtype_label\n \n}", "language": "text" } ] } [/block] ##Step 2: Make a CGC API request to copy a file Use the values for `id` and `file_index` obtained from the SPARQL query above to make the CGC API request to [copy a file](copy-files-between-projects-1). `file_index` contains the IDs of associated index files (*.BAI) which are required for analysis alongside of BAM files on the CGC. If `file_index` displays as `none`, there are no associated index files. For instance, if you obtained the file IDs 564a3581e3b0289zk2c68351 and 564a378bc7b093360b6080d4, use them in your API request as shown below. [block:code] { "codes": [ { "code": "POST /v2/action/files/copy HTTP/1.1\nHost: cgc-api.sbgenomics.com\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96", "language": "http", "name": "Copy a file" } ] } [/block] [block:code] { "codes": [ { "code": "{\n \"project\": \"RFranklin/my-project\",\n \"file_ids\": [\"564a3581e3b0289zk2c68351\", \"564a378bc7b093360b6080d4\"]\n}", "language": "json", "name": "Request body" } ] } [/block] This returns the following response: [block:code] { "codes": [ { "code": "{\n \"5655df71e4b08c5d86970945\": {\n \"status\": \"OK\",\n \"new_file_id\": \"568cf5f4e4b0307bc0462062\",\n \"new_file_name\": \"ResultCount_MERGING_1_NIC1254A17.hg19_rCRSchrm.fa.realign.mdups.recal.MERGED.ID.vcf\"\n },\n \"564a378bc7b093360b6080d4\": {\n \"status\": \"OK\",\n \"new_file_id\": \"578cf5f4e4d0307ec0463064\",\n \"new_file_name\": \"TCGA-A7-A0CE-01A-11D-A148-05_4ff7626b-4c2f-40fd-9df1-10c1a488402a_Breast_tumor.realign.mdups.recal.MERGED.ID.vcf\"\n },\n}", "language": "json", "name": "Response body" } ] } [/block]