RDBMS

A disadvantage of the relational database management system (RDBMS) might be the overload of hardware and operating systems, which make the system slower. 

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. 

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]. 

The main difference from the relational DBS is that the data are now stored in object types with a unique identity number (ID), attributes, and operations. Therefore, the relationship between objects is completely different from that in an RDBMS. 

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. 

The Data Persistence Layer can be a thick layer that resides in the application middleware or a thin layer in the application middleware combined with some stored procedures in the database. The former makes the Data Persistence Layer independent of the underline RDBMS that is being used. The latter provides better performance because the number of network calls can be reduced. Either way, a wed-defined interface between the Business Layer and the Data Storage Layer is the key. 

RDBMS (relational database management system) read/write permission real time (noun) real-time (unit modifier) reboot... 

Laboratory Information Management Systems (LIMS) are widely used in the laboratories of pharmaceuticals and related industries. LIMS is typically based on client server technology supported by a Relational Database Management System (RDBMS) as a storage repository (see Figure 21.1). They can be used to manage and process large amounts of electroiuc analysis data locally within a laboratory or company-wide between sites. 

The raw data required to be retained for GLP is composed of both structured and unstructured data. Some of the raw data in a laboratory resides in relational databases (RDBMS),... 

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. 

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. 

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. 

New SQL functions and data types can be used to extend a relational database. This is explained in Chapter 10 using PostgreSQL as an example. Ways in which three-dimensional molecular structures can be stored are examined in Chapter 11. This chapter also advocates using an RDBMS instead of molecular structure files and shows how this transition might be accomplished. 

The nature of the data in each column must be specified by providing a data type. The data type must be one of a fixed set of types available in the relational database management system (RDBMS) being used. A discussion of several common RDBMS follows in Chapter 4. Some of the frequently used data types are... 

A data type is necessary to allow the RDBMS to accurately convert the data from an external representation, most often text in a file, to an internal representation of the data. For example, the external representation of a numeric value is a text string containing at least one numeral, and possibly a plus or minus sign or a decimal point. A text value may contain any valid text character, usually only printable characters from the ASCII set. The internal representation of the data is dependent upon the particular RDBMS and hardware being used. It is not necessary to know the exact internal representation of the data. The important thing to consider is which data type accurately represents the data for your purposes. 

The internal representation of data is not entirely unimportant. When the float data type is used, the data are typically converted to the internal floating-point representation used by the computer on which the RDBMS is installed. This may have unintended consequences because of the rounding that occurs, especially if several mathematical operations are... 

It is not necessary to do any sorting or other operations on the data to create the index. Every RDBMS has built-in indexing capabilities that apply to numerical, text, or even other data types. Most implementations of numerical indexing do not necessarily rearrange the table rows in a sorted order. The exact method used to create the index is not usually of interest to the database designer. 

A table is said to be in first normal form if each row has the same number of columns, each column has a value, and there are no duplicate rows. Because an RDBMS uses a table defined with a fixed number of columns, it is always true that each row contains the same number of columns. If one allows that null is a value, then every column will have a value. It should be obvious that repeating a row in a table is wasteful, but also potentially confusing and prone to error. For example, if two rows in a table of logP contained the same name and logP, one row may have the logP changed at some point. Then which row would be the correct row This condition also illustrates the final aspect of first normal form There should be at least one column, or combination of columns, that could function as a key that uniquely identifies the row. This is the name column or compound id column in the above examples. The data in this column must be unique. 

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... 

In Chapter 2, the concept of relational tables was introduced. In this chapter, the most common way of working with tables in an RDBMS is introduced. The SQL language provides ways to create tables, insert data, select data, delete data, update data, join tables, create table schemas, define functions, etc. SQL has many other features, not all of which are covered here. 

A database can be thought of as a collection of schemas. It is possible to have many databases managed by one RDBMS, but each database is independent of any other. SQL was not designed to facilitate access to data in different databases. Recently, methods such as dbSwitch1 or dblink2 have made it possible to link together different databases. However, these are not considered here because they do not conform to the SQL standard and are implemented is various ways in different RDBMS. In the examples in this book, all schemas, table, functions, etc., are contained within one database. 

An essential use of the Select command is to select data from different tables using the joining capabilities of RDBMS. Suppose there is another table of assay data defined using... 

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. 

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... 

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... 

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