Exploring Data

On this page, we walk you through the visualization UI where you can:

Explore Database

You can find database data objects in your project by adding a class filter and selecting option 'Database'.

Filter Database

Select a database and new action buttons will appear on the top right corner. Click the 'View in Explorer' button to enter the visualization UI.

Explore Database

To visualize a database, a special type of record, called DatabaseExplorer, is used. A DatabaseExplorer record with the same tag as the database is picked for visualization. You can explore data from the database in all dashboards defined by the DatabaseExplorer record. You can also change any filters defined on the dashboard.

All unsaved changes are marked by an asterisk next to the dataset title and some actions may be disabled when there are unsaved changes. If you would like to preserve the filtered data and save them as a cohort, simply click 'Save Cohort' button in the top right corner and select a project and folder where the cohort should be saved.

Save Cohort

Create Cohorts

A new cohort will be saved in a selected project and folder as a closed record of type DatabaseQuery. Select a cohort and new action buttons will appear on the top right corner. Click the 'View in Explorer' button to explore a cohort in the visualization UI.

Explore Cohort

You can apply more filters or change already applied filters on the cohort and save changes as a completely new cohort based on the same database, DatabaseExplorer record and view (dashboard) which you used for data visualization.

Most cohorts can be created in the UI. If a combination of complex ANDs and ORs are desired, Complex Cohorts can be created from the command line.

Note: Please note that you need to have access to cohort's source database to be able to explore a cohort in the visualization UI.

Change Views

If DatabaseExplorer record defines multiple dashboards for data visualization, you can switch between the different views by clicking on the ellipsis button in the top right corner. Select a view name to explore data in a different dashboard. Selected filters will be preserved by view change only if the dashboard in the selected view has the same filters defined. The warning icon appears next to the every view which does not conform to the same filters definition.

Change Views

Download Data

Viewed data can be anytime downloaded in various formats. To download data, hover over a tile from which you would like to get data, click the vertical ellipsis button, select the 'Download Data...' option and choose an output format and destination where to save the selected data.

Note: Please note that downloading data via visualization UI is not suitable for large datasets. You can use SQL Runner app to download data in a more efficient way.

Download Data

Start Analysis

You can start an analysis from any accessible project or directly from the list of all available apps. Visualization UI enables a shortcut way how to run an analysis with saved cohort as an input. You can start an analysis by 'Start Analysis' button. The button is disabled if there are present any unsaved changes.

The analysis selection dialog contains only available executions with cohort as an input. Select the analysis you would like to run and proceed to Run Analysis page by 'Run Selected' button in the bottom right corner.

Start Analysis

The cohort is set automatically as an input. You need to set all other required inputs specified in the 'Analysis Inputs' tab, select an instance type and an output folder on 'App Settings' tab. You can change name and project of your execution.

You can find more information about available apps in the list of Spark apps.

Run Analysis

You can monitor your started analysis in Monitor tab of the project in which context you launched the job. Once job finishes, you can see all information about the job, including inputs, outputs and log.

Done Analysis

If job produces a result database, the job output will contain a link to the visualization UI for further exploration of data from the result database.

Result Database

Combine Cohorts

You can combine multiple saved cohorts to create a new cohort as a union, an intersection or a difference of source cohorts.

To combine a viewed cohort, click the ellipsis button in the top right corner and select the 'Combine Cohort...' option. If the option is disabled, check that all of your changes are saved and that the DatabaseExplorer record used for the visualization of cohort is combinable.

The Combine Cohort dialog contains list of selected cohorts to be combined and combination logic. You can choose one from supported operations: UNION, INTERSECTION, and DIFFERENCE. The selected cohorts list is populated by current cohort automatically. You can remove it by 'Remove' button which appears on the right side on hover. You add more cohorts to the list by 'Add Cohorts' button.

Requirements for cohorts combination:

  • cohorts must be from the same database and use the same DatabaseExplorer record for visualization
  • number of cohorts at least 2 and at most 10
  • cohorts can be already combined cohorts

You can view a combined cohort by 'Combine Cohorts' button in the bottom right corner. The button is enabled only when all selected cohorts are compatible. If the button is still disabled after you have two or more cohorts in the list, refer to the error message above selected cohorts list.

Combine Cohort

If the combination of cohorts was successful, data from the combination are available to explore in the dashboard of the first cohort of the combination. Click the info button behind the dataset title to show the tooltip with additional information about the combination. You can see the source database, source cohorts and SQL query generated as a base query to retrieve data from the combination. You can navigate to the location of source database or any of the source cohorts by highlighted links. Only the cohorts used for the combination are listed as source cohorts.

The shown filters are not persisted from the source cohorts. You can apply additional filters on data from the combination.

Note: Viewed data from the combination are unsaved. You need to click 'Save Cohort' button in the top right corner if you would like to persist the data as a new combined cohort.

Combined Cohort

Apply New Database

You can change a database of already saved cohort and create a new cohort based on a selected database with the same tag as the database of original cohort. Databases with the same tag are compatible and can be visualized using the same DatabaseExplorer record.

Click the ellipsis button in the top right corner and select 'Apply New Database...' option. Then, you can select a database with the same tag as cohort's database from any of your accessible projects. Click 'Apply New Database' button and explore data from the new database with applied filters from original cohort. You can modify or apply additional filters. You can check the database as a source of visualized data in the tooltip shown by the info button behind the dataset title.

Note: Viewed data from the applied new database are unsaved. You need to click 'Save Cohort' button in the top right corner if you would like to persist the data as a new cohort with the selected database as a source database.

Apply New Database

Variant Details

Ellipsis icons behind values of allele id present in some dashboards represent links to variant detail page. Click the link to open the variant detail page in a new browser tab.

Variant Details

The variant detail page contains annotations and links to external references.

Variant Detail Page

Last edited by Elena Duranova, 2018-10-24 22:03:29