PHPMyAdmin, there’s really not much there to back up, unless you’re just saying to keep a backup of the container that’s working, in case there’s a failure or the container is accidentally changed? Unless you have a really exotic setup with a heavily customized PMA, that’s pretty simple to reconstitute.
Everything else, should be backed up daily at the very least, remember that every time you store a patient file, like a document, scanned insurance card, ID card, lab result document, etc, that becomes a part of the EMR data.
Likewise with the database, every time something in the patient record is altered and saved, that’s writing updated/new records to the data tables.
Backing up MariaDB or Mysql at the database level is probably going to give you better results and be more efficient than just storing copies of the container. In addition to which if it’s all just running on a single Windows host with no redundancy, you might run into data integrity concerns making copies of a container with a running database. If you do choose to do the backup at the container rather than at the database level, at the very least make sure that the service is stopped so you get a clean backup. I’ve seen some horror stories from people who tried to make backups of databases without using the proper tools/methods.
for Mysql , mysqldump. Or mariadb-dump if you switched to Maria for your database engine.
For the rest of the application/data, it depends on what your backup target is.
Rsync and borg are both very useful, but maybe not so much on Windows.