How do I select and download sample data?

Who can download data?

Any authenticated user can download published data that they have permission to view. Access to data is determined by your role and the sharing policies of the projects.

Step-by-Step Guide to Downloading Data

Step 1: Navigate to an Isolates Table

You can download data from any Isolates Table in the application. These are found in two main places:

• On a main pathogen dashboard (e.g., Cholera, COVID-19), click the "Isolates table" tab. This table aggregates all published data you can see for that pathogen.
• On a specific project page, click the "Isolates table" tab. This table contains all published data for that specific project.

Step 2: Filter Your Data

Before selecting isolates, use the powerful filter toolbar above the table to narrow down your dataset. You can filter by collection date, country, lineage, and many other parameters. This is a crucial step to ensure your download is targeted and contains only the data you need.

Step 3: Select Isolates

Once you have filtered the data, use the checkboxes on the left side of the table to select the isolates you want to download:

• Select individual isolates: Click the checkbox in each row you want to include.
• Select all on a page: Click the checkbox in the table header to select all visible isolates on the current page.

Your selections are preserved as you navigate between pages, allowing you to build a selection set from across the entire filtered dataset. The text "X of Y row(s) selected" below the table keeps track of your total selection.

Step 4: Initiate the Download

When you have selected at least one isolate, the "Download" button above the table will become active. Click it to begin the download process.

The Downloaded File

• A toast notification will confirm that your download has started.
• Your browser will download a file named something like agari_data_export_YYYY-MM-DD.tsv.
• The file will be in TSV (Tab-Separated Values) format, which can be opened in any spreadsheet software like Excel or Google Sheets.

Important: The downloaded file will contain all metadata columns for the selected isolates, not just the columns that were visible in the table at the time of download.

Audit & Security

Please note that all data downloads are recorded in the corresponding project's activity log. This creates an auditable trail of who downloaded what data and when, ensuring data security and accountability.