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Data Browser features

QUERY DATASETS via the Data Browser > Data Browser features

[ 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 currently 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 in which you can select the alternate dataset.

[ 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.

[ 3 ] Create new query

Click to delete all previous queries and open a new query canvas.

[ 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 Seven Bridges team, or save your current query.

Learn more about:

[ 5 ] Save a query

You can save any query on the Data Browser. Note that empty canvases cannot be saved as queries.

This feature is still in Beta, and we will continue to make improvements.

To save a query:

  1. Click Queries on the top of the Data Browser canvas next to the help icon.
  2. Select Save from the drop-down menu.
  3. In the pop-up window which appears, you can name your query, as shown below. Click Add description to add a brief description of your query.
  4. Then, click Save Query.

All saved queries can be accessed by selecting Existing queries from the Queries drop-down menu.

Learn more about accessing existing queries.

[ 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.

For instance, you can search for TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam.bai. This will populate the Data Browser with a query starting from the file TCGA-OR-A5JW-01A-11D-A29I-10_Illumina.bam.bai. You can use this as the starting point of your query.

If you mix two types of search terms (such a UUID and file name), you will be asked to choose one
Learn more about ways to search in the Data Browser.

[ 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.

[ 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 which satisfy your query. For example, the count card for Case shows how many cases are returned by your query.

The number of entities returned change 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 Listview 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.

[ 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. 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 metadata corresponding in the rightmost column.

[ 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. 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.