Efficiency RDBMS

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. 

Some authors advocate analyzing schemas of tables up to normal form 3 and then backing off to second normal form in order to increase efficiency. With increasing capabilities of computers and RDBMS, this... 

The RDBMS is installed and runs on a computer that functions as a database server. Any SQL commands are executed on the server by the RDBMS. Functions written in SQL or in any of the procedural languages mentioned above are also executed by the RDBMS. This has the advantage that the data tables used by these SQL commands or procedural functions are under the control of the server. This is the most efficient way to access the data. The disadvantage is that the server may have many requests to handle from many users. Another way to operate on data tables is indirectly, using a client program typically (although not necessarily) run from another computer. 

There are other ways to construct an SQL statement that will select exactly the same rows and columns from these tables. These are just syntactical differences or stylistic differences. The methods shown here is just one suggestion. Depending on which RDBMS is used, different approaches may be more or less efficient. 

The CHORD6 chemical cartridge is a commercial product from gNova, Inc. It is written using C functions and the OEChem toolkit from OpenEye. It provides the core functions discussed in this book, such as cansmiles, matches, count matches, list matches, smiles to molfile, molfile to smiles, and xform. CHORD makes it possible to efficiently process RDBMS tables containing many millions of chemical structures. 

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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