Object-oriented Database

Parsaye, K., Chignell, M., Khoshafian, S., and Wong, H. (1989), Intelligent Databases Object-Oriented, Deductive, Hypermedia Technologies, John WUey Sons, New York. 

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 type of database which combines aspects of the classical relational database (rows, columns, tables) with features of object-oriented databases (support for data of unusual types or with inner structure, inheritance relationships, or user-defined functions which perform complex operations on data). See Full-text Database Object-oriented 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. 

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. 

If you ve done any database design, you ll be familiar with the idea that every entity must have a unique key, which it is up to you to assign. The key is an explicit combination of the entity s attributes, and any two entities with the same attribute values are actually the same one. But in object-oriented design, we always assume an imphcit unique key. If you implement in an OO language or on an OO database, it provides the key for you otherwise, you make it explicit when you get to coding. 

In the early days of object-oriented programming, attention was focused on the class as the fundamental unit of modularity. But there are other equally valid units of design work. Think of all the different pieces of work you could usefully transmit to a colleague or store in a database here s a list of things a package might contain. 

With object-oriented databases, the interlinked object model is transparently carried over to persistence, and the developer is concerned with logical things—transaction boundaries, concurrency, how far to propagate locks—rather than mapping between two dissimilar models. 

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

Visual basic-based interface and knowledge base Object oriented system implemented in C++ Implemented as a conventional structured program Object-oriented program using lab data and numerical relationships Object-oriented expert system implemented in C++ interfacing with a database on materials and compositions... 

Ghosh, D. (1999). Object oriented Transcription Factors Database (ooTFD). Nucleic Acids Res 27,315-7. 

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. 

Thomas, M.B. An analysis of the Patax6 pharmacopoeia of Bahia, Brazil, using an object oriented database model, Ph.D. Thesis, University of Florida, USA, 2001. 

ROME has been implemented using C-h+ [985] and the object-oriented database management system VERSANT [1022. It provides an API for external services through the CORBA [877, 1024] middleware standard. This communication layer has been implemented using omniORB [701]. 

For the time being, Comos PT strongly focuses on the product part of a design process. The tool is based on an object-oriented database, which allows to store all relevant parts of a chemical plant. All stored objects can be enriched with attributes and relationships between each other. Furthermore, Comos PT provides dedicated views on these objects (e.g. flow sheets) which show the two-dimensional layout of a (part of a) chemical plant. The support for the coordination of engineers is currently restricted to administrative attributes of objects, which represent the progress of a certain product according to a certain phase in the design process. 

The API interfaces to SRS provide an object oriented programmers interface into an SRS system. This allows programmers to access the databases in their SRS system from their programs written in C++, Perl, Java or Python. The databases can be queried and information retrieved about the set of entries. The SRS system itself can be interrogated about the databases available and the fields which can be queried within those databases. 

The Protein Function and Biochemical Pathways project, and its aMAZE database [van Helden 2000] are an ongoing effort since 1998 under the leadership of Shoshana Wodak of the European Bioinformatics Institute and the Free University of Brussels. It includes an encompassing object-oriented data model and has begun development of pathway visualization and analysis tools. 

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. 

This chapter has shown how composite data types can be of great use in chemical databases. The components of a composite data type are either basic SQL data types, or other composite data types. This is the same way an object is defined in an object-oriented computer language. This level of abstraction can help simplify the development of complex databases. 

Figure 2.11 presents the concept of an open integrated system. The simulation environment could come from the Vendor A, to which in-house unit operations can be coupled. One of the user-model unit calls the library of the vendor B, which is linked to a thermo-server supplied by the vendor C, who in turn could consider an equation-of-state model from the supplier D. The vendor E might supply a special solver, while the database with information about physical properties could come from the vendor F, etc. It is clear that the PMC s should be provided with compatible plug-and-play interfaces. This can be done nowadays at best with an object-oriented technology. 

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