Object-to-Multidimensional Database Mapping Algorithms

BackgroundRobust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration.MethodsA dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of “meta” data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way.ResultsThe results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a “meta” data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.ConclusionsBased on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.

It is widely accepted that object-oriented data models are particularly suitable as canonical models for providing data model transparency. In this paper we address issues of reliability of global object identification in global object views arising from requirements for heterogeneity and autonomy. We propose a taxonomy of object identity management policies for providing reliable global OIDs based on (possibly) unreliable local identities. Based on our analysis of the problem domain, we outline a generic object oriented framework for object view implementations that can be refined and configured to the object management needs of a specific data repository. We also argue for the need for some general design guidelines for object views of heterogenous data repositories in which the reliability of local identity plays a major role. >

The future of computer aided design is in object oriented programming. If the database community hopes to participate in this future, it must reexamine some basic assumptions about the architecture of database systems. Database system functionality can be added to object systems but if the performance cost is too high, it will never survive. Below are some suggestions for what can be done at a reasonable performance cost. The object oriented paradigm provides a more practical approach to the partitioning of the global database than horizontal and vertical partitioning of relational tables. Each partition should itself be an independent database containing related data such as the geometry of a part or the spacial relationship of parts in an assembly. A meta-database would be used to control access to collections of these partitions. A collection of partitions comprise the database for a user's design session. The overhead of traditional database transaction management is not acceptable for high performance CAD systems. With the partitioning scheme described above, transaction management can be performed at a partition/session granularity. Once the user has composed the collection of partitions, he has a single user database. There is no need for concurrency control or transaction logging except at the meta-database level. This type of transaction management can in fact be more functional than traditional transaction management, allowing for versioning, long transactions, integrity checking and archival. Object oriented databases need a message model, not a data model. Any object which responds to the same messages as an object of “Duck” class (walk and quack) is, for all intents and purposes, a duck. An attempt to design a data model based on instance variables of an object or based on collections of objects of like class violates the data abstraction facilities of object oriented languages and diminishes their power. An attempt to implement a relational database system with an object oriented language yields a relational database system where you get abstract data types for free. It does not yield an object oriented database system. For object oriented queries, the message is the media. A query can be transformed into an execution plan consisting of messages sent to database objects. Optimization decisions can be made by sending messages to referenced objects. Collection classes can be implemented for new access methods with cost and selectivity methods to provide optimization information. In this way, the query language can grow with the application. Data representation is an important aspect of object oriented systems. Most object systems are typeless in that all instance variables of an object are object references. For performance sake, object systems should provide enough of a type mechanism to allow simple data items (integers, floats, characters … ) to be represented in the form intrinsic to the machine. Methods can then be compiled for access to typed data. In conclusion, object systems provide enormous potential for the development of CAD systems. Performance influences the approach taken to an application. WYSIWYG publishing applications were not attempted until performance was adequate. Functionality is what sells CAD systems. Database system functionality can be added to object systems at a reasonable cost.

With the tremendous growth of large scale data repositories, a need for integrating the exploratory techniques of data mining with the capabilities of relational systems to efficiently handle large volumes of data has now risen. We look at the performance of the most prevalent association rule mining algorithm-Apriori with IBM's DB2 Universal Database system. We show that a multi-column (MC) data model is preferable over the commonly used single column (SC) data model for association rule mining. We obtain factors of 4.8 to 6 improvement in performance for the MC data model over commercial implementations for the SC data model. We provide a new relational operator called Combinations, for efficient SQL implementation of Apriori in the database engine-this results in trivial parallelizability, reliability, and portability for the mining application.

A bi-level object-oriented data model together with a user query language called OFQL is designed which can support applications like GIS (geographic information systems). The data model is divided into two layers, the higher-level data model and the lower-level data model. The higher-level data model or the geographic object data model primarily consists of the geographic objects and a set of semantic spatial functions through which the topological relationships of the geographic objects are defined or derived. The lower-level data model or the geometric object data model has geometric objects which are the actual spatial representations of the geographic objects in the higher-level data model. It also has a set of geometric functions that retrieve, manipulate, and compute for geometric objects. The general architecture of a GIS system using this data modeling approach consists of two modules: the query processor and the function implementor. With the OFQL user-interface, the user is able to pose queries of a geographic nature without knowing the details of the spatial representation and computation of the geographic objects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

Developing a three-dimensional (3D) data model for Geographic Information Systems (GIS) is an essential and complex issue. 3D modelling in GIS is becoming ever more important for the development of cyber cities and digital earth, which have recently become feasible. A competent 3D model forms an efficient foundation for 3D visualization, query and spatial analysis. As a development of the existing 3D models, this study proposes particular improvements in handling complex 3D objects. We present an object-oriented data model for handling complex 3D objects in GIS. First, the conceptual data model is developed based on the principle of object-oriented (OO) data modelling. This model is designed based on the following three basic geometric elements: node, segment and triangle. Accordingly, the abstract geometric objects are defined: including points, lines, surfaces and volumes. Second, the corresponding 3D logical model is designed based on the defined abstract objects and the relationships between them. Third, a formal representation of the 3D spatial objects is described in detail. Fourth, a prototype 3D GIS is developed based on the proposed 3D data model. Finally, we describe the results of an experimental study to reconstruct 3D objects using this 3D GIS and a comparison with the performance of other 3D data models. The proposed model is able to handle complex objects, such as complex buildings and TV towers, which is an essential functionality for building large-scale cyber cities, such as for Hong Kong. The proposed data model proves to be very efficient, particularly in visualization and rendering. The experimental results show which the data volume of the proposed model is compacted and the visualization speed for 3D objects is improved, compared with the existing models.

Integration of object-oriented programming languages and database systems in KOPERNIK

Semantic and object-oriented data models, such as ER, OMT, IFO, and others, have been extensively used for modeling geographic applications. Despite their semantic expressiveness, such models present limitations to adequately model those applications, since they do not provide appropriate primitives for representing spatial data. This paper presents OMT-G, an object oriented data model for geographic applications. OMT-G provides primitives for modeling the geometry and the topology of spatial data, supporting different topological structures, multiple views of objects, and spatial relationships. OMT-G also includes tools to specify transformation processes and presentation alternatives, that allow, among many other possibilities, modeling for multiple representations and multiple presentations. In this way, it overcomes the main limitations of the existing models, thus providing more adequate tools for modeling geographic applications. A comparison with other data models is also presented in order to stress the main advantages of OMT-G.

The wide adoption of semistructured data has created a growing need for effective ways to ensure the correctness of its organization. One effective way to achieve this goal is through formal specification and automated verification. This paper presents a theorem proving approach towards verifying that a particular design or organization of semistructured data is correct. We formally specify the semantics of the Object Relationship Attribute data model for Semistructured Data (ORA-SS) modeling notation and its correctness criteria for semistructured data normalization using the Prototype Verification System (PVS). The result is that effective verification on semistructured data models and their normalization can be carried out using the PVS theorem prover.

Applications have an increasing need to manage semistructured data (such as data encoded in XML) along with conventional structured data. We extend the structured object database model ODMG and its query language OQL with the ability to handle semistructured data based on the OEM model and Lorel language, and we implement our extensions in a system called Ozone. In our approach, structured data may contain entry points to semistructured data, and vice-versa. The unified representation and querying of such “hybrid” data is the main contribution of our work. We retain strong typing and access to all properties of structured portions of the data while allowing exible navigation of semistructured data without requiring full knowledge of structure. Ozone also enhances both ODMG/OQL and OEM/Lorel by virtue of their combination. For instance, Ozone allows OEM semantics to be applied to ODMG data, thus supporting semistructured-style navigation of structured data. Ozone also enables ODMG views of OEM data, allowing standard ODMG applications to access semistructured data without losing the benefits of structure. Ozone is implemented on top of the ODMG-compliant O2 database system, and it fully supports our extensions to the ODMG model and OQL.KeywordsQuery LanguageHybrid DataPath ExpressionSpeci CationSemistructured DataThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Large software systems are expensive to develop and maintain. A significant amount of programmer activity in understanding, changing, and debugging these systems is information management. To support these activities more directly, we have designed a programming environment, called OMEGA, that provides powerful mechanisms for accessing and displaying the information in a large software system. OMEGA uses successful ideas from existing programming environments while trying to correct deficiencies. The major deficiency in these systems is that programmers can only view and manipulate a single logical representation of programs. To support multiple representations, OMEGA uses a relational database system to manage all program information. Using a database system provides a powerful mechanism for efficient access to a variety of cross-sections of program information, as well as providing traditional database facilities such as concurrency control, data integrity, and crash recovery. The user interface to OMEGA separates input specification from output display, relies on pointing rather than typing, and exploits interaction in semantic analysis to detect many errors as soon as they are made. By eliminating the traditional textual interface to programs, OMEGA also allows the unification of the different abstraction mechanisms present in traditional programming environments. We have experimented with the ideas in OMEGA by designing a relational schema for software written in a particular programming language, and by implementing a program that transfers existing programs, stored as text, into a database managed by an off-the-shelf database system. A prototype visual interface to the program database has also been implemented. The results of this thesis are new models of program representation and user interaction for software development systems. The model of program representation can be expressed in the relational data model, and software can therefore be manipulated easily and powerfully using relational calculus. Our experimental implementation demonstrates the feasibility of using a relational database system, and provides insights into potential problems and how they might be solved.

To deal with issues of data model transformation and to make combined use of different data models, this paper proposed a database reengineering scheme which includes schema translation and data conversion from object-oriented data model to flattened XML data model with is-a and cardinality data semantics preservation. In this paper, conceptual schema of object-oriented data model and flattened XML data model are elaborated by UML class diagram and XML Schema Definition(XSD) graph respectively. Logical schema is described by UNISQL class definition and XSD respectively. This paper firstly analyzes class definitions from OODB and sorts them from most independent classes to most dependent classes. Secondly schema translation is processed by mapping class to complexType and then creating element definitions in XSD file. Thirdly data conversion is processed automatically. Performance tests have shown that the proposed database reengineering scheme is reliable and efficient.

Today many e-learning systems achieve high standards in delivering online courses via Web technologies and database system. However, these systems are constrained by rigid data model or schema that was pre-defined in the database to provide data storage structure for contents in e-learning applications. In the development of database driven e-learning system, the schema is crucial in analysing the data requirement for the system. However, many disadvantages are the results of system being developed on top of a static data model structure. The most concern issue includes the inflexibility of the data model that leads to unalterable contents data structure and its layout format, because the attributes in the data model are expected to be hard coded during the development in most cases. To avoid such inflexibility and improve the performance in the e-learning system, this paper introduces an approach of generic data model scheme in the database structure and interface-design toolkits, which allow the users to make modifications on the data structure and the system has the ability to adapt these changes. It achieves the adaptability, extensibility and reusability of database structure in the e-learning system.

In May, 1990, a small workshop was held in New Hope, Pennsylvania, to discuss the fundamental issues raised by continuing work on the interface between databases and programming languages. Four topics were addressed: new directions stemming from object-oriented data models, contributions of type theory to database programming languages (DBPLs), applications of logic to DBPL issues, and DBPL implementations. This workshop was organized under the auspices of the INRIA-NSF program, Languages for Databases and Knowledge Bases .