13.7 Relational Databases

Relational databases are another area Perl programmers and bioinformaticians need to explore. There comes a time when flat files or DBM just won't do for managing the data of a medium- or large-sized project, and you must turn to relational databases. Although they take a bit more effort to set up and program, they offer a standard and reliable way to store data and ask questions about it. In this book, we briefly discussed relational databases and actually used a simple DBM database. In the course of your work, however, you're likely to encounter Oracle, MySQL, PostgreSQL, Sybase, and others.The Perl module DBI, which stands for Database Independence, makes it possible to write code for manipulating relational databases that doesn't depend (too much) on which database you're actually using.

The fact is, writing code to handle databases isn't hard to do. The hardest part is making sure that the database is installed with the proper libraries, that the proper Perl modules are in place, and that you know how to connect to the database from your program. Once you have those things in place, using the database is generally easy.

That said, relational databases have their own lore, and there is a substantial body of knowledge about designing and managing good databases. Many programmers specialize in these issues, and that's true for plenty of bioinformaticians as well, since there are many interesting research questions related to designing better biological databases.