Object-Relational Database

Object Relational Database. A relational database in which data can be collected and combined with methods to fit an object oriented model. Searching in the database is conducted in the context of the objects and their methods, rather than the raw data fields and stored procedures. There is usually considerable overhead in building, maintaining, and using an object relational database, so this type of organization has not so far been widely used in chemical or biological databases. 

PostgreSQL is generally referred to as an Object Relational Database Management System (ORDBMS). The use of the word object implies objects in the sense of an object-oriented computer language. While not intended to be fully object-oriented in the same sense as a computer language, an ORDBMS shares the essential aspects of objects. These include composite data types, methods (functions), and inheritance. 

Grimes, S. 1998. Modeling object/relational databases, http / /www.dbmsmag. com/9804dl3.html (accessed April 18, 2008). 

Darwen, H., and Date, C. J. (1998), Foundation for Object/Relational Databases The Third Manifesto, Addison-Wesley, Reading MA. 

The proposed standard for object-relational database languages is SQL-99. Figure 14 shows how Fig. 4 could be specified in SQL-99. Note the use of ROW TYPE to specify a complex domain, the use of REF to denote tuple identifiers and the use of type constructors such as SET and LIST. Note also that, unlike ODL (cf. Fig. 12), in SQL-99 inverse relationships are not declared. Note, finally, how gene is modeled as including operations, as indicated by the keyword FUNCTION introducing the behavioral part of the specification of gene. 

The internal structure of a full-text database is significantly different from that of other types such as relational (row/column/table-oriented) or object-oriented databases. The domain of a full-text database is the indexing and storage of large amounts of textual data. Indexes based on words occurring in the text corpus, proximity operators to locate phrases and close spatial relationships between words, and probabilistic thesauri to define word, concept, and content clusters are important characteristics of this type of database. See Bibliographic Database Object-oriented Database Object-Relational Database Relational Database and Textual Database. 

A relatively new class of database which has developted from the traditional table-oriented model of relational databases in order to cope with information with complex inner structure and complicated data interconnections or inheritance relationships. See Full-text Database Object-Relational Database and Relational Database. 

One of the oldest types of database and still the most widespread. A relational database organizes the stored data items into tables in which the columns are fields of a specific type and the rows are data entries. The typical query language for relational databases is SQL (systems query language), which is powerful, well defined and, within the domain of the SQL standard, independent of the database vendor. See. Full-text Database Object-oriented Databa.se and Object-Relational Database. 

The characteristic of a relational database model is the organization of data in different tables that have relationships with each other. A table is a two-dimensional consti uction of rows and columns. All the entries in one column have an equivalent meaning (c.g., name, molecular weight, etc. and represent a particular attribute of the objects (records) of the table (file) (Figure 5-9). The sequence of rows and columns in the tabic is irrelevant. Different tables (e.g., different objects with different attributes) in the same database can be related through at least one common attribute. Thus, it is possible to relate objects within tables indirectly by using a key. The range of values of an attribute is called the domain, which is defined by constraints. Schemas define and store the metadata of the database and the tables. 

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 hierarical, network, relational, and object-oriented database models are the four fundamental ones. 

A database (or data base) is a collection of data that is organised so that its contents can easily be accessed, managed, and modified by a computer. The most prevalent type of database is the relational database which organises the data in tables multiple relations can be mathematically defined between the rows and columns of each table to yield the desired information. An object-oriented database stores data in the form of obj ects which are organised in hierarchical classes that may inherit properties from classes higher in the tree structure. 

The first section is an overview of what a static model is about. Section 2.2 introduces objects, their attributes, and snapshots and distinguishes the concept of object identity from object equality. The attributes that model an object s state can be implemented in very different ways. Section 2.3 outlines some implementation variations using Java, a relational database, and a real-world implementation. 

In a relational database, we might have separate tables, Session, Instructor, and Client. Each object is one row in its corresponding table (see Figure 2.4). 

Object behaviors have no clear counterpart in this world of relational databases, which are concerned primarily with storing the attributes and links between objects. The database can be driven with something such as SQL, but the queries and commands are not encapsulated with specific relations. 

For example, C++ works with an OO model in main memory but leaves persistent data up to you you can t send a message to an object in filestore. If you can secure a good OO database you re in luck but otherwise, typically you re stuck with plain old files or a relational database and must to think how to encode the objects. Your class-layer design should initially defer the question of how objects are distributed between hosts and media. 

In using a relational database, the interlinked object structure is translated into a representation based on tables and rows. Each object typically is a row in a table one table is defined for each class (sans inheritance). 

Object-oriented databases scale to very large datasets but they do not have the maturity of relational products. 

The Microsoft Access database (http //www.microsoft.com/) is a collection of data and objects related to a particular topic (Hutchinson and Giddeon, 2000). The data represent the information stored in the database, and the objects help users define the structure of that information and automate the data manipulating tasks. Access supports SQL (Structured Query Language) to create, modify, and manipulate records in the table to facilitate the process. It is a table-oriented processing. The user is referred to the Microsoft Access User s Guide or online Help for information. 

CLOB. A Character Large Object data type. This data type is used in Oracle, for instance, to store large amounts (e.g., up to several Gigabytes) of character data. Storage of structures in a relational database in mole-cule-file format is an example. 

In this paper we describe the basic design of a microarray gene expression database to help microarray users and their informatics teams set up their information services. The first version of the microarray database object model ArrayExpress, which is described here, was developed at the European Bioinformatics Institute (EBI) in collaboration with the German Cancer Research Centre (DKFZ) and posted on the Internet in November, 1999 (see (http //www.ebi.ac.uk/arrayexpress)). A relational database implementation maxd based on the ArrayExpress object model was conducted at the University of Manchester (http //bioinf.man.ac.uk/microarray/resources.html) and is widely used for microarray laboratory informatics support. 

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