Mastering Perl for Bioinformatics

Chapter 6. Perl and Relational Databases

Relational database systems are extremely important in all kinds of computing—commercial as well as scientific. The Perl programmer can perform most database manipulations from Perl programs using modules written for this purpose. I’ll briefly review database lore and then concentrate on an introduction to the Perl modules that provide an interface to relational databases.

This and the remaining chapters of this book will continue to look at fundamental Perl topics but with this difference: these topics rely on Perl modules, not on new Perl syntax. The reason for this is a deliberate decision by the Perl language designers to keep the language itself fairly small and to move as much functionality as possible into modules. This decision is interesting and important, and it has the practical effect of making modules quite important in Perl.

First, I’ll provide a quick explanation of database terminology and acronyms. Since I’ll be discussing only relational databases, I sometimes say database to mean relational database. (They aren’t synonymous in general, however.) I say DBMS (or database management system(s)) to refer to the software that provides database capabilities, such as MySQL or Oracle. Database or relational database refers to the definition and implementation of a particular collection of data in a DBMS, such as the examples I show later in the chapter. These terms, database for the data itself, and database management ...