Molecular database management

Dubois J-E, Carrier G, Panaye A. DARC topological descriptors for pattern recognition in molecular database management systems and design. J Chem Inf Comput Sci 1991 31 574-578. 

MDL Information Systems, Inc. MDL provides modular software systems for managing chemical information, as weU as related molecular and reaction databases for use with the software. MDL s database management programs, MACCS-II and REACCS, provide access to compound and reaction databases and also have the capabiHty to manage user-created databases (37). Although MDL is not considered to be an on-line database vendor, it is mentioned here because of the value of its information products and services to the chemical industry. 

MACCS-II enables direct interface with other database management systems, such as the Relational Database Management System (RDBMS) and Oracle, so that databases which contain text and numeric data for which special interfaces are normally needed can be constmcted. Eor example, an Oracle MACCS-II linked system is currendy being used by the National Institute on Dmg Abuse (113) to develop a database that will allow scientists to determine the molecular stmctures of cocaine and other controlled substances as well as designer dmgs. 

The implementation of efficient and updated 2D and 3D structure databases is one major challenge in molecular diversity management. In addition to the compound design and selection criteria used for the compilation, the quality of the compound storage, manipulation, and logistics systems used for the management of the collection are key factors to yield reproducible results. ... 

MAECIS contains five major sections that are integrated into a single system. At its center is a database management system that handles the storage and updating of data and chemical structures. Associated with this section is an information retrieval section that allows one to search the database for specific information composed of any combination of data and/or substructures. Once information is retrieved, it can be displayed on a computer terminal or sent to a printer for hardcopy output using the display section of MAECIS which includes the ability to display chemical structures in various formats. The final two sections of MAECIS allow for the manipulation of chemical structures and the calculation of various molecular properties that are related to chemical structures. 

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. 

If SMILES is used to store molecular structures in a relational database management system(RDBMS), it may be necessary to extract the symbol and bond information for some client programs that expect a connection table. The smiles to symbol and smiles to bonds function shown in the next sections allow the symbol and bond information in a SMILES to be extracted as an array. Some client programs may prefer to process this information in rows, as if they were records in a file. The following plpgsql functions can be used to present the array elements as rows. Two functions are shown ctable (connection table) and symbol coords. The symbol coords function requires an array of coordinates in addition to the symbols. 

Notice in Figure 1 the little peak in 1985 and the much larger one around 1989-1990 these peaks are due mainly to expansion at software companies catering to the pharmaceutical industry. However, in the early 1990s when these software companies saw the prospect of slower sales of programs for molecular modeling and compound database management, the total number of ad-... 

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