An object query language for multimedia federations

The Fischlar system provides a large centralised repository of multimedia files. As expansion is difficult in centralised systems and as different user groups have a requirement to define their own schemas, the EGTV (Efficient Global Transactions for Video) project was established to examine how the distribution of this database could be managed. The federated database approach is advocated where global schema is designed in a top-down approach, while all multimedia and textual data is stored in object-oriented (O-O) and object-relational (0-R) compliant databases. This thesis investigates queries and updates on large multimedia collections organised in the database federation. The goal of this research is to provide a generic query language capable of interrogating global and local multimedia database schemas. Therefore, a new query language EQL is defined to facilitate the querying of object-oriented and objectrelational database schemas in a database and platform independent manner, and acts as a canonical language for database federations. A new canonical language was required as the existing query language standards (SQL: 1999 and OQL) axe generally incompatible and translation between them is not trivial. EQL is supported with a formally defined object algebra and specified semantics for query evaluation. The ability to capture and store metadata of multiple database schemas is essential when constructing and querying a federated schema. Therefore we also present a new platform independent metamodel for specifying multimedia schemas stored in both object-oriented and object-relational databases. This metadata information is later used for the construction of a global schemas, and during the evaluation of local and global queries. Another important feature of any federated system is the ability to unambiguously define database schemas. The schema definition language for an EGTV database federation must be capable of specifying both object-oriented and object-relational schemas in the database independent format. As XML represents a standard for encoding and distributing data across various platforms, a language based upon XML has been developed as a part of our research. The ODLx (Object Definition Language XML) language specifies a set of XMLbased structures for defining complex database schemas capable of representing different multimedia types. The language is fully integrated with the EGTV metamodel through which ODLx schemas can be mapped to 0-0 and 0-R databases

An Object-Oriented Heterogeneous Database Architecture

Many data management environments face a critical need to integrate heterogeneous data-data that are stored in varying locations using various data management systems with diverse data formats and schemas. To address this problem, the database research community has developed the concept of a heterogeneous database system (HDB) that provides users with the illusion of a single unified database. However, HDBs rely on the implicit assumption that all data to be integrated into the HDB are stored in full-fledged database management systems (DBMS). This assumption leaves environments that need to integrate non-DBMS data unserved by HDB systems. Furthermore, HDBs are complex software solutions that are not easily lmplementable by database developers wrestling with heterogeneous data. This thesis presents a new, easily implemented HDB architecture that is suitable for integrating non-DBMS data. The key to our architecture is using an object-oriented database management system (OODBMS) as an implementation tool. Rather than developing an HDB from scratch, we leverage the power and facilities of the underlying OODBMS to provide a query language, application programmer interface, interactive query interface, concurrency control, etc. Using object-oriented technology gives us an additional benefit-our HDB becomes an object-oriented HDB (OOHDB) providing users with greater data model expressivity along with a powerful behavioral component. The OOHDB architecture we present is independent of a particular OODBMS and can be implemented using a number of commercial OODBMSs for a variety of data management environments. We describe one implementation of our architecture using the GemStone OODBMS for accessing heterogeneous materials science data. This implementation demonstrates how easily the architecture can be implemented. We use this implementation to analyze the performance of the architecture and examine the effectiveness of strategies for enhancing performance. We conclude that for many environments with heterogeneous non-DBMS data, our OOHDB architecture provides a good solution that is easy to implement using commercial OODBMS technology

Semiautomatic generation of CORBA interfaces for databases in molecular biology

The amount and complexity of genome related data is growing quickly. This highly interrelated data is distributed at many different sites, stored in numerous different formats, and maintained by independent data providers. CORBA, the industry standard for distributed computing, offers the opportunity to make implementation differences and distribution transparent and thereby helps to combine disparate data sources and application programs. In this thesis, the different aspects of CORBA access to molecular biology data are examined in detail. The work is motivated by a concrete application for distributed genome maps. Then, the different design issues relevant to the implementation of CORBA access layers are surveyed and evaluated. The most important of these issues is the question of how to represent data in a CORBA environment using the interface definition language IDL. Different representations have different advantages and disadvantages and the best representation is highly application specific. It is therefore in general impossible to generate a CORBA wrapper automatically for a given database. On the other hand, coding a server for each application manually is tedious and error prone. Therefore, a method is presented for the semiautomatic generation of CORBA wrappers for relational databases. A declarative language is described, which is used to specify the mapping between relations and IDL constructs. Using a set of such mapping rules, a CORBA server can be generated automatically. Additionally, the declarative mapping language allows for the support of ad-hoc queries, which are based on the IDL definitions

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

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)