Oracle RDBMS

Oracle is a commercial RDBMS. It strongly conforms to the ANSI SQL-92/99 standards. It is the most widely used RDBMS. The Oracle company sells and supports the Oracle RDBMS. There are many other companies that also offer support for Oracle RDBMS. There are several commercial chemical cartridges available for use with Oracle.5... 

The first release of the D ARC Communication Modules in 1987 was dedicated to Oracle Corporation s ORACLE RDBMS the 2nd release was dedicated to CompuServe Software House s System 1032. 

The relational database model was developed by Codd at IBM in 1970 [9]. Oracle provided the first implementation in 1979. The hierarchical database IMS was replaced by DB2, which is also an RDBMS. There exist himdreds of other DBMSs, such as SQL/DS, XDB, My SQL, and Ingres. 

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. 

MACCS-II enables direct interface with other database management systems, such as Ihe Relational Database Management System RDBMS) and Oracle, so that databases that contain text and numeric data, for which special interfaces arc normally needed, can be constructed. 

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. 

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... 

Python is a general-purpose computer language with no built-in capabilities to access an RDBMS. There are modules that extend python to allow interaction with an RDBMS, for example, pygresql12 for PostgreSQL or cx oracle for Oracle. Once pygresql is installed, the following python script will fetch some rows and columns from a PostgreSQL database. 

Personal Computers. IBM PC s (personal computers) and clones with the MS-DOS operating system have become a popular microcomputing environment for the chemical/pharmaceutical industry. Many software products are available for this system including MDL s ChemText chemical word processor, ChemBase chemical database, and ChemTalk terminal program, ORACLE S RDBMS, and BBN s RS/1 statistics program. 

ORACLE could become the de facto standard RDBMS for the chemical/pharmaceutical industry. In February of 1985, nearly 20% of those chemical/pharmaceutical companies using MACCS and a DBMS for research preferred ORACLE, while INQUIRE and System 1032 tied for second place with slightly more than 10%. By the time of writing, the figure for ORACLE has risen to nearly 30% and the other systems are each less than 10%. The only system besides ORACLE that made even modest gains in this area is RTFs INGRES. 

Versions of the ORACLE and INGRES RDBMSs have been announced for distributed use. These will utilise PCs, workstations, or mini/mainframes as nodes. Work done at the University of California, Berkeley on the academic version of INGRES is indicative of the features of these RDBMS s. A user may submit a query at his node that requests information that is distributed over several other nodes. The retrieval algorithm polls the nodes for availability, optimises the query for retrieval speed, and retrieves the requested data across the network. When mature, this technology should be useful in chemical/pharmaceutical companies that are multidepartment, multisite, and multinational organisations. 

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