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

Migrating relational databases into object-based and XML databases

Rapid changes in information technology, the emergence of object-based and WWW applications, and the interest of organisations in securing benefits from new technologies have made information systems re-engineering in general and database migration in particular an active research area. In order to improve the functionality and performance of existing systems, the re-engineering process requires identifying and understanding all of the components of such systems. An underlying database is one of the most important component of information systems. A considerable body of data is stored in relational databases (RDBs), yet they have limitations to support complex structures and user-defined data types provided by relatively recent databases such as object-based and XML databases. Instead of throwing away the large amount of data stored in RDBs, it is more appropriate to enrich and convert such data to be used by new systems. Most researchers into the migration of RDBs into object-based/XML databases have concentrated on schema translation, accessing and publishing RDB data using newer technology, while few have paid attention to the conversion of data, and the preservation of data semantics, e.g., inheritance and integrity constraints. In addition, existing work does not appear to provide a solution for more than one target database. Thus, research on the migration of RDBs is not fully developed. We propose a solution that offers automatic migration of an RDB as a source into the recent database technologies as targets based on available standards such as ODMG 3.0, SQL4 and XML Schema. A canonical data model (CDM) is proposed to bridge the semantic gap between an RDB and the target databases. The CDM preserves and enhances the metadata of existing RDBs to fit in with the essential characteristics of the target databases. The adoption of standards is essential for increased portability, flexibility and constraints preservation. This thesis contributes a solution for migrating RDBs into object-based and XML databases. The solution takes an existing RDB as input, enriches its metadata representation with the required explicit semantics, and constructs an enhanced relational schema representation (RSR). Based on the RSR, a CDM is generated which is enriched with the RDB's constraints and data semantics that may not have been explicitly expressed in the RDB metadata. The CDM so obtained facilitates both schema translation and data conversion. We design sets of rules for translating the CDM into each of the three target schemas, and provide algorithms for converting RDB data into the target formats based on the CDM. A prototype of the solution has been implemented, which generates the three target databases. Experimental study has been conducted to evaluate the prototype. The experimental results show that the target schemas resulting from the prototype and those generated by existing manual mapping techniques were comparable. We have also shown that the source and target databases were equivalent, and demonstrated that the solution, conceptually and practically, is feasible, efficient and correct

HOOD : a Higher-Order Object-Oriented Database model and its implementation

Bibliography: pages 133-140.There is no accepted standard for the object-oriented database paradigm at present, which has led to different definitions of features and conformance requirements. HOOD is a Higher-Order Object-Oriented Database system which defines a meta-data model for specifying the requirements of an Object-Oriented Database, which provides uniformity and extensibility. From this specification and by making use of a comprehensive structure system, an exemplar or implementation model is defined. Among the constructs provided by the model are types, instances, objects, values, methods, base types, generic types and metatypes. The mechanisms of instantiation and subtyping allow for relationships between these constructs. Extensibility is provided in the model for types, base types, structures and methods. Uniformity is achieved by defining all constructs as instances and through the use of messages for all operations. There is only one form of object construct which provides persistence and identities. The complex values and extensibility of the model allow it to adapt in order to model the real world instead of adapting the real world to fit the model. We have implemented a subset of the structures and values defined in the model, provided persistence and identities for object, and included the various constructs mentioned above. The method language allows for the specification of methods, the passing of messages, and the use of complex values. The compiler performs type checking and resolution and generates instructions for an abstract machine which manipulates the database

The advantages and cost effectiveness of database improvement methods

Relational databases have proved inadequate for supporting new classes of applications, and as a consequence, a number of new approaches have been taken (Blaha 1998), (Harrington 2000). The most salient alternatives are denormalisation and conversion to an object-oriented database (Douglas 1997). Denormalisation can provide better performance but has deficiencies with respect to data modelling. Object-oriented databases can provide increased performance efficiency but without the deficiencies in data modelling (Blaha 2000). Although there have been various benchmark tests reported, none of these tests have compared normalised, object oriented and de-normalised databases. This research shows that a non-normalised database for data containing type code complexity would be normalised in the process of conversion to an objectoriented database. This helps to correct badly organised data and so gives the performance benefits of de-normalisation while improving data modelling. The costs of conversion from relational databases to object oriented databases were also examined. Costs were based on published benchmark tests, a benchmark carried out during this study and case studies. The benchmark tests were based on an engineering database benchmark. Engineering problems such as computer-aided design and manufacturing have much to gain from conversion to object-oriented databases. Costs were calculated for coding and development, and also for operation. It was found that conversion to an object-oriented database was not usually cost effective as many of the performance benefits could be achieved by the far cheaper process of de-normalisation, or by using the performance improving facilities provided by many relational database systems such as indexing or partitioning or by simply upgrading the system hardware. It is concluded therefore that while object oriented databases are a better alternative for databases built from scratch, the conversion of a legacy relational database to an object oriented database is not necessarily cost effective

Migrating relational databases into object-based and XML databases

Rapid changes in information technology, the emergence of object-based and WWW applications, and the interest of organisations in securing benefits from new technologies have made information systems re-engineering in general and database migration in particular an active research area. In order to improve the functionality and performance of existing systems, the re-engineering process requires identifying and understanding all of the components of such systems. An underlying database is one of the most important component of information systems. A considerable body of data is stored in relational databases (RDBs), yet they have limitations to support complex structures and user-defined data types provided by relatively recent databases such as object-based and XML databases. Instead of throwing away the large amount of data stored in RDBs, it is more appropriate to enrich and convert such data to be used by new systems. Most researchers into the migration of RDBs into object-based/XML databases have concentrated on schema translation, accessing and publishing RDB data using newer technology, while few have paid attention to the conversion of data, and the preservation of data semantics, e.g., inheritance and integrity constraints. In addition, existing work does not appear to provide a solution for more than one target database. Thus, research on the migration of RDBs is not fully developed. We propose a solution that offers automatic migration of an RDB as a source into the recent database technologies as targets based on available standards such as ODMG 3.0, SQL4 and XML Schema. A canonical data model (CDM) is proposed to bridge the semantic gap between an RDB and the target databases. The CDM preserves and enhances the metadata of existing RDBs to fit in with the essential characteristics of the target databases. The adoption of standards is essential for increased portability, flexibility and constraints preservation. This thesis contributes a solution for migrating RDBs into object-based and XML databases. The solution takes an existing RDB as input, enriches its metadata representation with the required explicit semantics, and constructs an enhanced relational schema representation (RSR). Based on the RSR, a CDM is generated which is enriched with the RDB's constraints and data semantics that may not have been explicitly expressed in the RDB metadata. The CDM so obtained facilitates both schema translation and data conversion. We design sets of rules for translating the CDM into each of the three target schemas, and provide algorithms for converting RDB data into the target formats based on the CDM. A prototype of the solution has been implemented, which generates the three target databases. Experimental study has been conducted to evaluate the prototype. The experimental results show that the target schemas resulting from the prototype and those generated by existing manual mapping techniques were comparable. We have also shown that the source and target databases were equivalent, and demonstrated that the solution, conceptually and practically, is feasible, efficient and correct.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Grifon: a graphical interface to an object oriented database

The aim of the research outlined in this thesis is to establish what type of interface would be most suitable for object oriented databases. In particular it examines how graphical interface technologies might be used to present the database in a clearer form. In support of the research, a prototype interface system has also been developed to a commercial database to illustrate the practicality of the development of such an interface, and the increased effectiveness of the resultant system. The thesis outlines the features provided by the interface, the benefits accrued from such a system, and the problems associated with its development. Finally, it examines how such a system fits into the current work being carried out in the area of user interaction with databases

Electronic marketplace

Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1999.Includes bibliographical references (leaf 34).by David Yi Wang.M.Eng

A feature-based approach to the Computer-Aided Design of sculptured products

Computer-Aided Design systems offer considerable potential for improving design process efficiency. To reduce the 'ease of use' barrier hindering full realisation of this potential amongst general mechanical engineering industries, many commercial systems are adopting a Feature-Based Design (FBD) metaphor. Typically the user is allowed to define and manipulate the design model using interface elements that introduce and control parametric geometry clusters, with engineering meaning, representing specific product features (such as threaded holes, slots, pockets and bosses). Sculptured products, such as golf club heads, shoe lasts, crockery and sanitary ware, are poorly supported by current FBD systems and previous research, because their complex shapes cannot be accurately defined using the geometrically primitive feature sets implemented. Where sculptured surface regions are allowed for, the system interface, data model and functionality are little different from that already provided in many commercial surface modelling systems, and so offer very little improvement in ease of use, quality or efficiency. This thesis presents research to propose and develop an FBD methodology and system suitable for sculptured products. [Continues.

Self-adjusting multi-granularity locking protocol for object-oriented databases

Object-oriented databases have the potential to be used for data-intensive, multi-user applications that are not well served by traditional applications. Despite the fact that there has been extensive research done for relational databases in the area of concurrency control; many of the approaches are not suitable for the complex data model of object-oriented databases. This thesis presents a self-adjusting multi-granularity locking protocol (SAML) which facilitates choosing an appropriate locking granule according to the requirements of the transactions and encompasses less overhead and provides better concurrency compared to some of the existing protocols. Though there has been another adaptive multi-granularity protocol called AMGL [1] which provides the same degree of concurrency as SAML: SAML has been proven to have significantly reduced the number of locks and hence the locking overhead compared to AMGL. Experimental results show that SAML performs the best when the workload is high in the system and transactions are long-lived