Protein Structure Data Management System

With advancement in the development of the new laboratory instruments and experimental techniques, the protein data has an explosive increasing rate. Therefore how to efficiently store, retrieve and modify protein data is becoming a challenging issue that most biological scientists have to face and solve. Traditional data models such as relational database lack of support for complex data types, which is a big issue for protein data application. Hence many scientists switch to the object-oriented databases since object-oriented nature of life science data perfectly matches the architecture of object-oriented databases, but there are still a lot of problems that need to be solved in order to apply OODB methodologies to manage protein data. One major problem is that the general-purpose OODBs do not have any built-in data types for biological research and built-in biological domain-specific functional operations. In this dissertation, we present an application system with built-in data types and built-in biological domain-specific functional operations that extends the Object-Oriented Database (OODB) system by adding domain-specific additional layers Protein-QL, Protein Algebra Architecture and Protein-OODB above OODB to manage protein structure data. This system is composed of three parts: 1) Client API to provide easy usage for different users. 2) Middleware including Protein-QL, Protein Algebra Architecture and Protein-OODB is designed to implement protein domain specific query language and optimize the complex queries, also it capsulates the details of the implementation such that users can easily understand and master Protein-QL. 3) Data Storage is used to store our protein data. This system is for protein domain, but it can be easily extended into other biological domains to build a bio-OODBMS. In this system, protein, primary, secondary, and tertiary structures are defined as internal data types to simplify the queries in Protein-QL such that the domain scientists can easily master the query language and formulate data requests, and EyeDB is used as the underlying OODB to communicate with Protein-OODB. In addition, protein data is usually stored as PDB format and PDB format is old, ambiguous, and inadequate, therefore, PDB data curation will be discussed in detail in the dissertation

Software integration between external game APIs and the GameBus repository

Many games exist to serve a unique purpose for different domains, so is the case with healthcare. However, when it comes to integrating such games to achieve healthcare benefits, and an integrated, enjoyable experience, not enough has been done due to factors such as shortage of resources, time to market and others. This report describes the design and implementation of the GameBus data model to realize such an integrated platform. This model is the technology independent core of the solution. Moreover, the model is a common language for different developers and partners, which contributes to bringing the functional design closer to the software design. This report encompasses and explains all the different aspects of the development throughout this project. These include problem analysis, system architecture, design and its implementation

A flexible approach for mapping between object-oriented databases and xml. A two way method based on an object graph.

One of the most popular challenges facing academia and industry is the development of effective techniques and tools for maximizing the availability of data as the most valuable source of knowledge. The internet has dominated as the core for maximizing data availability and XML (eXtensible Markup Language) has emerged and is being gradually accepted as the universal standard format for platform independent publishing and exchanging data over the Internet. On the other hand, there remain large amount of data held in structured databases and database management systems have been traditionally used for the effective storage and manipulation of large volumes of data. This raised the need for effective methodologies capable of smoothly transforming data between different formats in general and between XML and structured databases in particular. This dissertation addresses the issue by proposing a two-way mapping approach between XML and object-oriented databases. The basic steps of the proposed approach are applied in a systematic way to produce a graph from the source and then transform the graph into the destination format. In other words, the derived graph summarizes characteristics of the source whether XML (elements and attributes) or object-oriented database (classes, inheritance and nesting hierarchies). Then, the developed methodology classifies nodes and links from the graph into the basic constructs of the destination, i.e., elements and attributes for XML or classes, inheritance and nesting hierarchies for object-oriented databases. The methodology has been successfully implemented and illustrative case studies are presented in this document

Exploring parallelism with object oriented database management system

The object oriented approach to database management systems aims to remove the limitations of the current systems by providing enhanced semantic capabilities and more flexible facilities, including the encapsulation of operations as well as data in the specification of an object. Such systems are certainly more complex than existing database management systems. Although, they are complex, the current object oriented database management systems are built for Von-Neumann (purely sequential) machines. Such implementation inevitably leads to major problems involving efficiency and performance. So, new techniques for implementation need to be investigated. One possible solution for the efficiency, and performance problems is to use parallel processing techniques. Thus, the aim of this research is to propose aspects in which parallel processing can be introduced within the scope of object oriented database management systems and identify ways in which the performance can be improved. A prototype of the main components of an object oriented database system called KBZ has been implemented to test out some of the parallel processing aspects. The thesis starts with an introduction and background to the research. It then describes major parallel system architectures for an object oriented database management system. Techniques such as distributing a large volume of data among various processors (transputers), performing processing in the background of the system to reduce response time, and performing input/output parallel processing are presented. The initial prototype, PKBZ version-1, is then described; in particular, the logical and physical representation of object classes, how they communicate through message sending, and the different types of message supported. Two prototype versions exist. The initial prototype was designed to investigate the parallel implementation and general functionality of the system. The second version provides greater flexibility and incorporates enhanced functionality to allow experimentation. The enhancements in the second version are also discussed in the thesis, and the experimental results using different transputer configurations are illustrated and analyzed

Extending information retrieval system model to improve interactive web searching.

The research set out with the broad objective of developing new tools to support Web information searching. A survey showed that a substantial number of interactive search tools were being developed but little work on how these new developments fitted into the general aim of helping people find information. Due to this it proved difficult to compare and analyse how tools help and affect users and where they belong in a general scheme of information search tools. A key reason for a lack of better information searching tools was identified in the ill-suited nature of existing information retrieval system models. The traditional information retrieval model is extended by synthesising work in information retrieval and information seeking research. The purpose of this new holistic search model is to assist information system practitioners in identifying, hypothesising, designing and evaluating Web information searching tools. Using the model, a term relevance feedback tool called ‘Tag and Keyword’ (TKy) was developed in a Web browser and it was hypothesised that it could improve query reformulation and reduce unnecessary browsing. The tool was laboratory experimented and quantitative analysis showed statistical significances in increased query reformulations and in reduced Web browsing (per query). Subjects were interviewed after the experiment and qualitative analysis revealed that they found the tool useful and saved time. Interestingly, exploratory analysis on collected data identified three different methods in which subjects had utilised the TKy tool. The research developed a holistic search model for Web searching and demonstrated that it can be used to hypothesise, design and evaluate information searching tools. Information system practitioners using it can better understand the context in which their search tools are developed and how these relate to users’ search processes and other search tools

IDEAS-1997-2021-Final-Programs

This document records the final program for each of the 26 meetings of the International Database and Engineering Application Symposium from 1997 through 2021. These meetings were organized in various locations on three continents. Most of the papers published during these years are in the digital libraries of IEEE(1997-2007) or ACM(2008-2021)

The 1995 Science Information Management and Data Compression Workshop

This document is the proceedings from the 'Science Information Management and Data Compression Workshop,' which was held on October 26-27, 1995, at the NASA Goddard Space Flight Center, Greenbelt, Maryland. The Workshop explored promising computational approaches for handling the collection, ingestion, archival, and retrieval of large quantities of data in future Earth and space science missions. It consisted of fourteen presentations covering a range of information management and data compression approaches that are being or have been integrated into actual or prototypical Earth or space science data information systems, or that hold promise for such an application. The Workshop was organized by James C. Tilton and Robert F. Cromp of the NASA Goddard Space Flight Center

A cooperative framework for molecular biology database integration using image object selection

The theme and the concept of 'Molecular Biology Database Integration' and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a framework for integrating the molecular biology databases. The framework has proposed to develop a cooperative environment to share information on the basis of common purpose for the molecular biology databases. The research has also reviewed other implementation and interoperability issues for laboratory based, dedicated and target specific database. The research has addressed the following issues: diversity of molecular biology databases schemas, schema constructs and schema implementation multi-database query using image object keying, database integration technologies using context graph, automated navigation among these databases. This thesis has introduced a new approach for database implementation. It has introduced an interoperable component database concept to initiate multidatabase query on gene mutation data. A number of data models have been proposed for gene mutation data which is the basis for integrating the target specific component database to be integrated with the federated information system. The proposed data models are: data models for genetic trait analysis, classification of gene mutation data, pathological lesion data and laboratory data. The main feature of this component database is non-overlapping attributes and it will follow non-redundant integration approach as explained in the thesis. This will be achieved by storing attributes which will not have the union or intersection of any attributes that exist in public domain molecular biology databases. Unlike data warehousing technique, this feature is quite unique and novel. The component database will be integrated with other biological data sources for sharing information in a cooperative environment. This involves developing new tools. The thesis explains the role of these new tools which are: meta data extractor, mapping linker, query generator and result interpreter. These tools are used for a transparent integration without creating any global schema of the participating databases. The thesis has also established the concept of image object keying for multidatabase query and it has proposed a relevant algorithm for matching protein spot in gel electrophoresis image. An object spot in gel electrophoresis image will initiate the query when it is selected by the user. It matches the selected spot with other similar spots in other resource databases. This image object keying method is an alternative to conventional multidatabase query which requires writing complex SQL scripts. This method also resolve the semantic conflicts that exist among molecular biology databases. The research has proposed a new framework based on the context of the web data for interactions with different biological data resources. A formal description of the resource context is described in the thesis. The implementation of the context into Resource Document Framework (RDF) will be able to increase the interoperability by providing the description of the resources and the navigation plan for accessing the web based databases. A higher level construct is developed (has, provide and access) to implement the context into RDF for web interactions. The interactions within the resources are achieved by utilising an integration domain to extract the required information with a single instance and without writing any query scripts. The integration domain allows to navigate and to execute the query plan within the resource databases. An extractor module collects elements from different target webs and unify them as a whole object in a single page. The proposed framework is tested to find specific information e.g., information on Alzheimer's disease, from public domain biology resources, such as, Protein Data Bank, Genome Data Bank, Online Mendalian Inheritance in Man and local database. Finally, the thesis proposes further propositions and plans for future work

Automatic mapping of XML documents into relational database

Extensible Markup Language (XML) nowadays is one of the most important standard media used for exchanging and representing data through the Internet. Storing, updating and retrieving the huge amount of web services data such as XML is an attractive area of research for researchers and database vendors. In this thesis, we propose and develop a new mapping model, called MAXDOR, for storing, rebuilding, updating and querying XML documents using a relational database without making use of any XML schemas in the mapping process. The model addressed the problem of solving the structural hole between ordered hierarchical XML and unordered tabular relational database to enable us to use relational database systems for storing, updating and querying XML data. A multiple link list is used to maintain XML document structure, manage the process of updating document contents and retrieve document contents efficiently. Experiments are done to evaluate MAXDOR model. MAXDOR will be compared with other well-known models available in the literature(Tatarinov et al., 2002) and (Torsten et al., 2004) using total expected value of rebuilding XML document execution time and insertion of token execution time.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Views and concerns and interrelationships : Lessons learned from developing the multi-View software engineering environment PIROL

Software-Entwicklungsumgebungen sind komplexe Systeme mit besonderen Anforderungen an Modularität und Anpaßbarkeit. Diese Arbeit beschreibt die Entwicklung der Umgebung PIROL. Die Beschreibung ist dabei in eine Abfolge der folgenden 12 Themen gegliedert. (1) Metamodellierung ist das Grundkonzept, nach dem PIROL seine Daten gemäß einem objektorientierten Datenmodell zerlegt, so daß beliebige Werkzeuge auch auf die Daten anderer Werkzeuge auf sinnvolle Art und Weise zuzugreifen können. (2) Das Metamodell wird zur persistenten Speicherung der Daten auf Konzepte des Repositories H-PCTE abgebildet. (3) Die Granularität eines Metamodells ist für die Effektivität und Effizienz des Gesamtsystems entscheidend. PIROL unterstützt hybride Modellierung als Kompromiß beider Extreme. (4) Durch Methoden des Metamodells wird Verhaltensmodellierung für verschiedenste Aufgaben unterstützt. (5) Ausnahmebehandlung wird systematisch unterstützt. (6) Verschiedene Mechanismen zur Wahrung der Datenintegrität sind enthalten. (7) Das System wurde nach einer Client-Server Architektur entwickelt, deren zentrale Komponente eine "Workbench" ist, die die Repository-Sprache Lua/P ausführt. (8) Steuerungsintegration erlaubt durch verteilte Steuerflüsse das enge Zusammenspiel lose gekoppelter Komponenten. (9) Die koordinierte Zusammenarbeit mehrerer Benutzer wird unterstützt. (10) Die logische Unabhängigkeit von Werkzeugen wird durch das neue Konzept der Dynamic View Connectors erreicht. (11) Allgemeine Dienste sind in der Umgebung einheitlich verfügbar. (12) Das System unterstützt die Weiterentwicklung. All diese Themengebiete sind sehr eng miteinander verzahnt und die Darstellung ist zu großem Teil der gegenseitigen Beeinflussung gewidmet. Es wird gezeigt, wie eine Großzahl der Entwurfsentscheidungen genau aus diesen Beeinflussungen motiviert sind. Die Beschreibung folgt damit dem Konzept der "Concern Interaction Matrix", das hier zur Bewältigung von Komplexität vorgeschlagen wird. Dabei werden Charakteristika einzelner Anliegen und einzelner Zusammenhänge herausgearbeitet. Die Beschreibung PIROLs wird durch die Liste der integrierten Werkzeuge, Ansätze von Laufzeit-Messungen und einige Betrachtungen zur Beurteilung abgerundet. Abschließend werden verschiedene Konzepte rund um den Begriff "Sichten" erörtert. Sichten sind ein zentrale Anliegen von PIROL. Außerdem generalisiert die Diskussion über die mehrdimensionale Darstellung des Hauptteiles. Es werden Begrifflichkeit, Konzepte und Techniken für Sichten in der Softwaretechnik vorgestellt und diskutiert. Dabei wird die Brücke geschlagen von Sichten in objektorientierten Datenbanken, über aspekt-orientierte Softwareentwicklung bis hin zum allgemeinen "Concern Modeling", zu dem die o.g. Methode einen Beitrag leisten soll. Sichten werden dabei als ein zentrales Konzept der Softwaretechnik neben Abstraktion und Zerlegung beurteilt. Dynamic View Connectors sind ein wesentlicher Beitrag von PIROL, durch den Datenbanksichten und aspektorientierte Programmierung zusammengeführt werden. Zwar ist der Sichten-Begriff längst nicht so scharf definiert, wie die Begriffe Abstraktion und Zerlegung, aber gerade die Überlappungen und Diskrepanzen, die durch Sichten abgebildet werden können, machen dies Konzept zu einem starken Strukturierungsprinzip, das zwar einigen Aufwand zur Behandlung von Inkonsistenzen erfordert, aber andererseits hilft, komplexe Systeme handhabbar und wartbar zu gestalten.Software engineering environments are complex systems with special requirements regarding modularity and adaptability. This thesis describes the development of the environment PIROL. The description is structured as a sequence of the following 12 concerns: (1) Meta modeling is the basic concept by which PIROL decomposes its data in accordance to an object-oriented data model. This allows arbitrary tools to access data of other tools in a meaningful way. (2) For persistent storage the model is mapped to the concepts of the repository H-PCTE. (3) The granularity of a meta model determines effectiveness and efficiency of the system. PIROL supports hybrid modeling as a compromise between extremes. (4) By methods of the meta model behavior modeling is supported for a wide range of tasks. (5) Exception handling is supported systematically. (6) Several mechanisms for preserving data integrity are integrated. (7) The system follows a client-server architecture. As its, central component the "workbench" executes the repository language LuaP. (8) Control integration allows for close cooperation of loosely coupled components by means of distributed control flows. (9) The coordinated cooperation of multiple users is supported. (10) Logical independence of tools is achieved by the novel concept of Dynamic View Connectors. (11) Common services are available throughout the environment in a uniform way. (12) The system is prepared for evolution. All these concerns are tightly interlocked. A considerable share of the presentation is dedicated to such mutual interactions. Is is shown, how a large number of design decisions is motivated exactly by these interactions. The description follows the concept of a "Concern Interaction Matrix" which is proposed for managing complexity. Characteristics of concerns and their interactions are elaborated. The description of PIROL is completed by a list of integrated tools, initial performance measurements and evaluation. Finally, several concepts relating to the notion of "views" are discussed. Views are a central concern of PIROL. Furthermore, the discussion generalizes over the multi-dimensional presentation in the body of this thesis. Notions, concepts and techniques for views in software engineering are presented and discussed. This discussion connects views in object-oriented databases, aspect-oriented software development and general "concern modeling", to which the method of "Concern Interaction Matrices" contributes. Views are regarded as a central concept of software engineering at the same level as abstraction and decomposition. Dynamic View Connectors are a significant contribution of PIROL that combines database views and aspect-oriented programming. The notion of "views" is defined with far less precision than abstraction and decomposition, but indeed by the overlap and mismatches, which can be captured by views, this concept is a strong principle for structuring software and information. Effort is needed for handling inconsistencies as they may arise, but after all, views are a suitable means for managing the complexity of systems and for designing these systems for evolution