I want to backup and restore only important data from database.
Do you which tables are must have or any other idea how to restore?
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this is really not a good idea to split the database backup. It really doesnt take very long to dump the database. If your concerned, what about running a mysql master and slave database, and then dumping the slave database.
Also suggest backing up off the server, I use a small script s3cmd which allows me to dump the database and backup to S3 all in one go. It also allows you to keep days/weeks/months of sql backups
As stated, you shouldn't split up the Magento database. If you've really got your heart set on it, you'll want to spend some time looking at http://www.magereverse.com/ . You will need to be sure that a partial DB backup won't cause issues elsewhere due to constraints. Not an endeavor for the faint of heart.