MySQL RDBMS

MySQL is an open-source RDBMS. It conforms in part to the SQL 92/99 standards. The MySQL company sells and support the MySQL RDBMS. There are other companies that support MySQL and offer products that use MySQL as the underlying database. Tharun Kumar Allu describes a small molecule chemical database cartridge extension for MySQL.6... 

An introduction to SQL is provided in Chapter 3, but with an emphasis on examples relevant to chemical information rather than business information, which is often used in other books. Chapter 4 discusses some of the RDBMS that are available, namely Oracle, MySQL, and PostgreSQL. All of them use SQL to insert, delete, update, and select data. Chapter 5 shows ways in which client programs, including Web-based applications, are used to connect to the database server. Chapter 6 examines ways in which RDBMS are typically used to handle numerical and textual chemical information using relational tables. An example of using data files from the PubChem project is included. 

Much of this book discusses ways in which the RDBMS can be used and even extended to handle chemical structures correctly, quickly, and conveniently. Extensions of the capabilities of PostgreSQL are simply called extensions. Oracle uses the term data cartridge. There are chemical extensions or cartridges available for PostgreSQL, Oracle, and MySQL. 

Some of the more advanced methods described in this book require a more specific use of the RDBMS. The choice made for this book is PostgreSQL. In cases where a particular feature of PostgreSQL is used, a note is added to alert the reader. For example, the array data type in SQL2003 is implemented in PostgreSQL very differently than in Oracle. The list matches function described in a later chapter of this book returns an array of integers that denote which atoms in a structure match a substructure query. The integration of this function into SQL would be handled quite differently in PostgreSQL, Oracle and MySQL. 

Because of the flexibility and familiarity of Web browsers, Web-based applications have become very popular and powerful. There are many Web-based interfaces to RDBMS. For example, phpPgAdmin1 is a popular Web application for PostgreSQL. PhpMyAdmin2 is popular with users of MySQL. These applications allow one to connect to a chosen database server, browse the schemas and tables in the database, and enter SQL commands. The output from SQL commands, especially table output, is formatted nicely. Other operations, such as creating, altering, or dropping tables and schemas, are also provided. These use an HTML form interface, with text boxes, radio buttons, check boxes, and other form elements familiar to all uses of the Web. 

PgAdmin are available to be run on Linux, Windows, Mac, and other clients. Oracle users typically use Oracle s SQL Developer or Toad (Toad also works with MySQL). SQL Developer4 is a Java application that uses JDBC to mediate the communication to the database. A typical user need not be concerned with this, but a later chapter of this book discusses ways to construct new client applications using JDBC, ODBC, and other methods to communicate with the RDBMS. Toad is a Windows only application with a free version and a full-featured pay version.5... 

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