MySQL is a database system yes. What you do is supply it with the necessary commands to create a database with it, tables, fields, run queries against the databases, etc. You can read more about it in the reference manual:
MySQL is a Relational Database Management System (RDBMS) (although not a true one). It is not an interface to some other database. It creates database and manages those databases. Server side languages such as PHP and Perl create interfaces to connect to MySQL which is designed to manage commands sent to it.
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