{"_id":"584592c7ba4f1c0f0096932b","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,"__v":2,"version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"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","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"project":"55faf11ba62ba1170021a9a7","githubsync":"","user":"5613e4f8fdd08f2b00437620","updates":["5a94491ebec35c00121d3359","5b132c96bc90f5000319ee22"],"next":{"pages":[],"description":""},"createdAt":"2016-12-05T16:16:07.155Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"examples":{"codes":[]},"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":30,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"[ 1 ] Dataset name](#dataset-name)\\n[ 2 ] Query name](#query-name)\\n[ 3 ] Queries](#queries)\\n[ 4 ] Save a query](#save-a-query)\\n[ 5 ] The Search Box](#search)\\n[ 6 ] Count](#count)\\n[ 7 ] Clear All](#clear-all)\\n[ 8 ] Copy files to project](#copy-files-to-project) \\n[ 9 ] Table of results: List view](#table-of-results)\\n[ 10 ] Table of results: Details view](#details-view)\\n[ 11 ] Table of results: Analytics view](#distribution-graphs) \\n[ 12 ] Export query results](#export-query-results)\"\n}\n[/block]\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/a315a99-data-browser-features-cgc.jpg\",\n        \"data-browser-features-cgc.jpg\",\n        1296,\n        813,\n        \"#4d4f79\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n<a name=\"dataset-name\"></a>\n\n##[ 1 ] Dataset name\n\nThe name of the dataset you are querying is on the left side of the top navigation bar. In the image above, you are querying the TCGA dataset.\n\nTo clear your canvas and switch to another dataset (e.g. CCLE), simply click on the visible dataset name (e.g. TCGA). This opens a dialog box in which you can select the alternate dataset.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n<a name=\"query-name\"></a>\n\n##[ 2 ] Query name\n\nThe name of your query is also on the left side of the top navigation bar. This defaults to **New query** if your query is unsaved.\n\n<a name=\"create-new-query\"></a>\n\n##[ 3 ] Create new query\n\nClick to delete all previous queries and open a new query canvas.\n\n<a name=\"queries\"></a>\n##[ 4 ] Queries\n\nClick on **Queries** to reveal different actions relating to queries, as shown above.\n\nChoose to open a previously saved query, open an example query provided by the CGC team, or save your current query.\n\nLearn more about:\n\n* [Starting from an example query](doc:data-browser-query-start-from-an-example-query)\n* [Building a query from search terms](doc:data-browser-query-start-by-searching-through-a-dataset)  \n* [Building a query from scratch](doc:data-browser-query-start-from-scratch) \n* [Working from an existing query](doc:data-browser-query-start-from-an-existing-query) \n\n<a name=\"save-a-query\"></a>\n##[ 5 ] Save a query\n\nYou can save any query generated in the Data Browser. Note that empty canvases cannot be saved as queries.\n\nTo save a query:\n1. Click **Queries** on the top right of the Data Browser canvas.\n2. Select **Save** from the drop-down menu.\n3. In the pop-up window that appears, you can name and, if you wish, add a brief description of your query.\n4. Then click **Save as new query**.\n\nAll saved queries can be accessed by selecting **Open saved** from the **Queries** drop-down menu. \n\nLearn more about [accessing existing queries](doc:data-browser-query-start-from-an-existing-query).\n\n<a name=\"search\"></a>\n##[ 6 ] The Search Box\n\nClick on **Search by ID** to reveal the search box. The search box allows you to search by UUID, ID (TCGA Barcodes), or file name.\n\nYou can enter more than one UUID, ID (TCGA Barcode), or file name (separated by commas) into the search box and click **Search**.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/00e4ad4-pCjCMJJgTch86oJV1Vns_Screen_Shot_2016-05-10_at_4.33.51_PM_1.jpeg\",\n        \"pCjCMJJgTch86oJV1Vns_Screen Shot 2016-05-10 at 4.33.51 PM (1).jpeg\",\n        984,\n        604,\n        \"#e8e8e8\"\n      ]\n    }\n  ]\n}\n[/block]\nFor instance, you can search for **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam**. This will populate the Data Browser with a query starting from the file **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam**. You can use this as the starting point of your query.\n\nIf you mix two types of search terms (such as a UUID and file name), you will be asked to choose one before proceeding.\n\n##[ 7 ] Copy files to project\n\nThe **+Copy files to project** button allows you to copy files that satisfy your query to your desired project. Learn more about [accessing data for use in your project](doc:access-data-from-the-data-browser).\n\n<a name=\"count\"></a>\n##[ 8 ] Count\n\nThe Count feature quantifies the scope of the data returned by your query.\n\nA count card at the bottom of the Data Browser displays the entity and number of instances of that entity that satisfy your query. For example, the count card for **Case** shown below displays how many cases are returned by this specific query.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/769e210-case-count.png\",\n        \"case-count.png\",\n        610,\n        258,\n        \"#f0e8e7\"\n      ]\n    }\n  ]\n}\n[/block]\nThe number of entities returned changes as you add filters to your query. The count cards at the bottom of the page gray out to let you know the represented quantities need to be refreshed.\n\nTo refresh the number of instances of each entity returned by your query, click the circular arrows next to the count cards.\n\n##[ 9 ] Export query results\n\nExport query results as a CSV, JSON, or XML file from this table by clicking **Export**. All query results are exported simultaneously but are separated into a different file for each branch. You can only export up to 3000 rows from the table results for each branch.\n \n##[ 10 ] Table of results: List view\n\nThe table below the Data Browser contains further details about your query. The **List**view displays a list of UUIDs for the entities which match your query. This allows you to review returned results, but it does not allow you to select or filter results. All selection and filtering have to be done via the query on the Data Browser canvas.\n\n<a name=\"details-view\"></a>\n##[ 11 ] Table of results: Details view\nThe table below the Data Browser contains further details about your query. The **Details** view displays details of the selected entity in the context of your query, as shown below for the **Sample 1** entity of this query. The lefthand column, **Connections**, displays the inbound and outbound connections for the selected entity in the context of your query. The middle column displays a list of UUIDs corresponding to the selected entity that match your query. Click on any one UUID in the middle column to view its corresponding metadata in the rightmost column.  \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/fd80870-cgc-data-browser-ed.png\",\n        \"cgc-data-browser-ed.png\",\n        1362,\n        386,\n        \"#f8f8f8\"\n      ]\n    }\n  ]\n}\n[/block]\n<a name=\"distribution-graphs\"></a>\n\n##[ 12 ] Table of results: Analytics view\nThe table below the Data Browser contains further details about your query. The **Analytics** view displays the distributions of the members of each entity, as shown below for this query. These graphs are an alternative way to visualize query results and reflect the same information as is displayed in the table. Note that currently only pre-defined, selectable values of a property can be visualized.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/930cf2c-Screen_Shot_2017-01-16_at_4.10.14_PM.png\",\n        \"Screen Shot 2017-01-16 at 4.10.14 PM.png\",\n        876,\n        259,\n        \"#8d1fb0\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]","excerpt":"<a href=\"query-datasets\" style=\"color:#132c56\">QUERY DATASETS</a> ><a href=\"about-the-data-browser\" style=\"color:#132c56\">About the Data Browser</a> > Data Browser features","slug":"data-browser-features","type":"basic","title":"↳ Data Browser features"}

↳ Data Browser features

<a href="query-datasets" style="color:#132c56">QUERY DATASETS</a> ><a href="about-the-data-browser" style="color:#132c56">About the Data Browser</a> > Data Browser features

[block:callout] { "type": "warning", "title": "On this page:", "body": "[ 1 ] Dataset name](#dataset-name)\n[ 2 ] Query name](#query-name)\n[ 3 ] Queries](#queries)\n[ 4 ] Save a query](#save-a-query)\n[ 5 ] The Search Box](#search)\n[ 6 ] Count](#count)\n[ 7 ] Clear All](#clear-all)\n[ 8 ] Copy files to project](#copy-files-to-project) \n[ 9 ] Table of results: List view](#table-of-results)\n[ 10 ] Table of results: Details view](#details-view)\n[ 11 ] Table of results: Analytics view](#distribution-graphs) \n[ 12 ] Export query results](#export-query-results)" } [/block] [block:image] { "images": [ { "image": [ "https://files.readme.io/a315a99-data-browser-features-cgc.jpg", "data-browser-features-cgc.jpg", 1296, 813, "#4d4f79" ], "border": true } ] } [/block] <a name="dataset-name"></a> ##[ 1 ] Dataset name The name of the dataset you are querying is on the left side of the top navigation bar. In the image above, you are querying the TCGA dataset. To clear your canvas and switch to another dataset (e.g. CCLE), simply click on the visible dataset name (e.g. TCGA). This opens a dialog box in which you can select the alternate dataset. <div align="right"><a href="#top">top</a></div> <a name="query-name"></a> ##[ 2 ] Query name The name of your query is also on the left side of the top navigation bar. This defaults to **New query** if your query is unsaved. <a name="create-new-query"></a> ##[ 3 ] Create new query Click to delete all previous queries and open a new query canvas. <a name="queries"></a> ##[ 4 ] Queries Click on **Queries** to reveal different actions relating to queries, as shown above. Choose to open a previously saved query, open an example query provided by the CGC team, or save your current query. Learn more about: * [Starting from an example query](doc:data-browser-query-start-from-an-example-query) * [Building a query from search terms](doc:data-browser-query-start-by-searching-through-a-dataset) * [Building a query from scratch](doc:data-browser-query-start-from-scratch) * [Working from an existing query](doc:data-browser-query-start-from-an-existing-query) <a name="save-a-query"></a> ##[ 5 ] Save a query You can save any query generated in the Data Browser. Note that empty canvases cannot be saved as queries. To save a query: 1. Click **Queries** on the top right of the Data Browser canvas. 2. Select **Save** from the drop-down menu. 3. In the pop-up window that appears, you can name and, if you wish, add a brief description of your query. 4. Then click **Save as new query**. All saved queries can be accessed by selecting **Open saved** from the **Queries** drop-down menu. Learn more about [accessing existing queries](doc:data-browser-query-start-from-an-existing-query). <a name="search"></a> ##[ 6 ] The Search Box Click on **Search by ID** to reveal the search box. The search box allows you to search by UUID, ID (TCGA Barcodes), or file name. You can enter more than one UUID, ID (TCGA Barcode), or file name (separated by commas) into the search box and click **Search**. [block:image] { "images": [ { "image": [ "https://files.readme.io/00e4ad4-pCjCMJJgTch86oJV1Vns_Screen_Shot_2016-05-10_at_4.33.51_PM_1.jpeg", "pCjCMJJgTch86oJV1Vns_Screen Shot 2016-05-10 at 4.33.51 PM (1).jpeg", 984, 604, "#e8e8e8" ] } ] } [/block] For instance, you can search for **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam**. This will populate the Data Browser with a query starting from the file **TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam**. You can use this as the starting point of your query. If you mix two types of search terms (such as a UUID and file name), you will be asked to choose one before proceeding. ##[ 7 ] Copy files to project The **+Copy files to project** button allows you to copy files that satisfy your query to your desired project. Learn more about [accessing data for use in your project](doc:access-data-from-the-data-browser). <a name="count"></a> ##[ 8 ] Count The Count feature quantifies the scope of the data returned by your query. A count card at the bottom of the Data Browser displays the entity and number of instances of that entity that satisfy your query. For example, the count card for **Case** shown below displays how many cases are returned by this specific query. [block:image] { "images": [ { "image": [ "https://files.readme.io/769e210-case-count.png", "case-count.png", 610, 258, "#f0e8e7" ] } ] } [/block] The number of entities returned changes as you add filters to your query. The count cards at the bottom of the page gray out to let you know the represented quantities need to be refreshed. To refresh the number of instances of each entity returned by your query, click the circular arrows next to the count cards. ##[ 9 ] Export query results Export query results as a CSV, JSON, or XML file from this table by clicking **Export**. All query results are exported simultaneously but are separated into a different file for each branch. You can only export up to 3000 rows from the table results for each branch. ##[ 10 ] Table of results: List view The table below the Data Browser contains further details about your query. The **List**view displays a list of UUIDs for the entities which match your query. This allows you to review returned results, but it does not allow you to select or filter results. All selection and filtering have to be done via the query on the Data Browser canvas. <a name="details-view"></a> ##[ 11 ] Table of results: Details view The table below the Data Browser contains further details about your query. The **Details** view displays details of the selected entity in the context of your query, as shown below for the **Sample 1** entity of this query. The lefthand column, **Connections**, displays the inbound and outbound connections for the selected entity in the context of your query. The middle column displays a list of UUIDs corresponding to the selected entity that match your query. Click on any one UUID in the middle column to view its corresponding metadata in the rightmost column. [block:image] { "images": [ { "image": [ "https://files.readme.io/fd80870-cgc-data-browser-ed.png", "cgc-data-browser-ed.png", 1362, 386, "#f8f8f8" ] } ] } [/block] <a name="distribution-graphs"></a> ##[ 12 ] Table of results: Analytics view The table below the Data Browser contains further details about your query. The **Analytics** view displays the distributions of the members of each entity, as shown below for this query. These graphs are an alternative way to visualize query results and reflect the same information as is displayed in the table. Note that currently only pre-defined, selectable values of a property can be visualized. [block:image] { "images": [ { "image": [ "https://files.readme.io/930cf2c-Screen_Shot_2017-01-16_at_4.10.14_PM.png", "Screen Shot 2017-01-16 at 4.10.14 PM.png", 876, 259, "#8d1fb0" ], "border": true } ] } [/block]