Extension RDBMS

For a variety of appHcations such as computer-aided engineering systems, software development, or hypermedia, the relational database model is insufficient. In an RDBMS, it is difficult to model complex objects and environments the various extensive tables become complicated, the integrity is problematic to observe, and the performance of the system is reduced. This led to two sophisticated object-based models, the object-oriented and the object-relational model, which are mentioned only briefly here. For further details see Refs. [10] and [11]. 

There are many books that describe relational database management systems (RDBMS) and the structured query language (SQL) used to manipulate the data. Understanding SQL is important, and this book contains an introduction to SQL. However, the focus is on the concepts of relational data. One goal is to show how a proper integration of a new molecular structure data type yields a powerful, extended relational database for use in chemistry. For those of you new to relational databases, it is expected that the SQL introduction will suffice for your understanding of the concepts in this book. For those of you already familiar with SQL, it is hoped that you will see how the extensions described here provide a powerful, integrated way to handle molecular structures within the database. In either case, there are plenty of practical SQL examples contained in this book. 

Chapter 7 introduces ways in which RDBMS can be used to handle chemical structural information using SMILES and SMARTS representations. It shows how extensions to relational databases allow chemical structural information to be stored and searched efficiently. In this way, chemical structures themselves can be stored in data columns. Once chemical structures become proper data types, many search and computational options become available. Conversion between different chemical structure formats is also discussed, along with input and output of chemical structures. 

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. 

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... 

There is a smaller set of tools that are typically run on the server. Any SQL commands and any procedural language functions are run on the server. In principle, there is complete flexibility of the server side tools, since in principle any computer program can be written in any computer language. Later chapters of this book show how the RDBMS server itself can be extended using server side programming to handle chemical information. These extensions may directly solve the needs of a particular project, but more importantly they increase the flexibility of the RDBMS to handle chemical information. Client programs can use the results of chemical searches and other computations as well. 

Many other uses of the xform function are possible. Because the function is an extension of SQL, it can be easily used with all the other features of the SQL language and capabilities of an RDBMS. 

The previous section shows how molecular structures stored in an RDBMS can be made available to client programs that traditionally read molecular structure files. The advantage of storing molecular structures in an RDBMS is that the information can be used from within the database, as well as by external clients. For example, it would be possible to search a table of molecular structures for three-dimensional overlap, much like it might be searched for substructure match. Of course, such search functions need to be written and installed as extensions to an RDBMS, just like the matches functions was done for substructure searches. This section shows some possible ways this might be accomplished. 

One disadvantage of using client programs is that data must be transferred to and from the server. Depending on how much data is required, this can cause a client program to run less efficiently than a server function run as an extension of the RDBMS. 

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