Disease metadata table

Modified on Fri, 22 Mar 2024 at 12:56 PM


With a disease metadata table you can explore additional information on your diseases of interest via an interactive table. This information can be acquired from a variety of databases, access to which is determined by your subscription. 

1. Creating a plot 

To create a disease metadata table first click on the create plot icon in your analysis track. This will open the Create plot page. You can then fill in the plot name and the rest of the plot template.

In the Create plot field you can set a name and description of the plot. Subsequently under Choose algorithm to run your analysis select "Disease metadata table". Once you have selected this option, a new field called "Select database" will appear. 

2. Select data

Disease metadata tables can either be created by fetching data directly from a database or from previously uploaded disease metadata datasets.

Depending on the input source the remainder of the workflow for creating a disease metadata table will differ slighly. Thus we wiill examine the subsequent steps side by side for each of the input sources.

2.1 Selecting a database as an input source

In the field Select data, you can pick from which source to acquire the disease metadata. Select the "Database" option to retrieve disease metadata from a database. In the "Choose a database" menu you can select from which database you would like to fetch disease metadata. Once you have selected a database from the dropdown menu confirm you selection by clicking on the Select database button. This will open the "Set parameters" menu.

2.2 Selecting the dataset library as input source

Select the "Dataset library" option to to select a disease metadata dataset that has been assigned to the current workspace by clicking the "Select dataset from workspace dataset library" button. Once you have selected a database from the dropdown menu confirm you selection by clicking on the "Select dataset" button. This will open the "Set parameters" menu.

3. Setting parameters

The set parameters menu witll be different depending on previously selected input source.

3.1 Set parameters for database input source

In the Set parameters field you can specify for which diseases of interest you want to acquire which disease metadata attributes. The diseases you specify in the Disease of interest tab will be available in the disease metadata table. The available choices here are are "All" and "Custom", with the former being default.


If you select the "Custom" option a new multi-select menu will appear where you can enter the disease names of your diseases of interest.

In the Attribute of interest tab, all of the attributes of the disease metadata database are displayed in a dropdown menu. From here you can select one or more attribute of interest.

If you select multiple attributes of interest a separate plot will be created for each of the selected attributes. This feature allows you to easily explore multiple attributes for your disease of interest. The newly created plots will have the following naming convention:"Plot name | Atrribute name". 

3.2 Set parameters for dataset libary input source

There are no additional parameters to set when selecting the a dataset from the dataset library as input source. You can proceed by clicking the "Run" button

4. Creating the disease metadata table

When you have these settings set you can click the Run button to create the disease metadata table. I will appear as a new plot in your track from which you can select it and view it as an interactive plot.


5. Disease metadata table interactive plot page

In the interactive plot page you can explore the results of the disease metadata table via a pivot table.

6. Disease metadata table as input for the rule- based meta-analysis

This newly created disease metadata table can be selected as input in the rule-based meta-analysis. 

When setting up the rule-based you can set the rules for the disease metadata table via a disease selection pivot table by clicking the "Select diseases" button

You can use the pivot table to make a selection of your disease of interest based on if they satisfy disease metadata criteria. You can make a selection based on both categorical and numerical variables. The resulting disease selection table will display all your diseases of interest and wheter they pass your selection criteria. 

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