Data access and integration in the ISPIDER proteomics grid

Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources

M2ORM2: A Model for the Transparent Management of Relationally Persistent Objects

Object-oriented application development often involves storing application objects in a relational database. Sometimes it is desirable to develop the persistent classes and the relational database in an independent way, and to use an object persistent manager to connect them in a suitable way. This paper introduces {M2ORM2, a model for describing meet-in-the-middle mappings between object schemas and relational schemas, to support the transparent management of object persistence by means of relational databases

The Real Benefits of Object-Relational DB-Technology for Object-Oriented Software Development

Abstract: Object-oriented programming languages (OOPLs like C++, Java, etc.) have established themselves in the development of complex software systems for more than a decade. With the integration of object-oriented concepts, object-relational database management systems (ORDBMSs) aim at supporting new generation software systems better and more efficiently. Facing the situation that nowadays more and more software development teams use OOPLs ‘on top of’ (O)RDBMSs, i. e., access (object-)relational databases from applications developed in OOPLs, this paper reports on our investigations on assessing the contribution of object-relational database technology to object-oriented software development. First, a conceptual examination shows that there is still a considerable gap between the object-relational paradigm (as represented by the SQL:1999 standard) and the object-oriented paradigm. Second, empirical studies (performed by using our new benchmark approach) point at mechanisms, which are not part of SQL:1999 but would allow to reduce the mentioned gap. Thus, we encourage the integration of such mechanisms, e. g., support for navigation and complex objects (structured query results), into ORDBMSs in order to be really beneficial for new generation software systems.

Evaluating partition selection policies using the PMOS garbage collector

Implementors of garbage collection algorithms are, in general, faced with determining a number of policy decisions such as when to collect, how to collect space or how to interact with the running application. With main memory collectors such decisions are usually influenced by results and experiences from a wealth of previous work. However, with partitioned collection of persistent objects stores, the implementor has a much smaller base to draw from. This is due not just to the small number of existing incremental object store collector implementations but also because the tradeoffs are significantly different from main-memory collection. This paper reports on investigations, using the PMOS collector, into policy choices determining which partition should be chosen for collection. A previous study on partition selection postulated that a flexible selection policy can significantly reduce I/O and increase the amount of space reclaimed. That study was based on simulations on a synthetic object database. Here we test these conclusions by repeating the experiments using real applications, a partitioned store collector and an implemented persistent object store.David S. Munro, Alfred L. Brow

Interactive Query and Search in Semistructured Databases

Semistructured graph-based databases have been proposed as well-suited stores for World-Wide Web data. Yet so far, languages for querying such data are too complex for casual Web users. Further, proposed query approaches do not take advantage of the interactivity of typical Web sessions---users are proficient at iteratively refining their Web explorations. In this paper we propose a new model for interactively querying and searching semistructured databases. Users can begin with a simple keyword search, dynamically browse the structure of the result, and then submit further refining queries. Enabling this model exposes new requirements of a semistructured database that are not apparent under traditional database uses. We demonstrate the importance of efficient keyword search, structural summaries of query results, and support for inverse pointers. We also describe some preliminary solutions to these technical issues