This is a question I've gotten asked in nearly all the Liferay System Administrator trainings I've given. Most people will just backup their database and Liferay data directory separately but any competent system admin will tell you that it's not guaranteed to be consistent because someone could upload or delete files between the time you took the database dump and the time you copied the data directory. Now I'm assuming that you are storing your document library binaries to filesystem instead of database.
Now to achieve a consistent backup with minimal interruption to your portal what you need to do is get a read lock on all your Liferay tables. This will prevent writes to the database. Then you dump the database to file with a tool like mysqldump and then you take a quick snapshot of the filesystem before you unlock the tables. You need to keep the connection that locked the tables open until this whole process is done. Once you have the database dump and filesystem snapshot ready only then you can release the lock and then you can backup the data directory using what ever method you would normally use.
For the PoC I'm using MySQL and my filesystem is on Linux LVM volume which supports taking snapshots. I've written a Perl script to execute all the commands. I'm sharing the script under GPL and it's available in Github. Feel free to fork it and modify it to suit your needs and if you have good ideas send me a pull request.
The way the script works is you pass in bunch of parameters like database details, lvm volume location, source and target directories. Here's an example:
backup_liferay.pl -u dba-backup -p mypassword -d lportal -h localhost \
--lvm-volume-path /dev/vg0/opt --lvm-snapshot-volume-path /dev/vg0/opt-snapshot \
--lvm-snapshot-volume-name opt-snapshot --lvm-snapshot-volume-size 50G \
--snapshot-mount-path /backups/snapshot \
--source-path /liferay-portal-6.1.0/data/document_library \
--db-target-path /backups/mysql/lportal.sql.gz \
--data-target-path /backups/liferay --compress
Now even if that doesn't exactly match your system I hope it gives you an idea how to roll your own Liferay backup.