A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

Fine-Grained Access Control Within NoSQL Document-Oriented Datastores

The recent years have seen the birth of several NoSQL datastores, which are getting more and more popularity for their ability to handle high volumes of heterogeneous and unstructured data in a very efficient way. In several cases, NoSQL databases proved to outclass in terms of performance, scalability, and ease of use relational database management systems, meeting the requirements of a variety of today ICT applications. However, recent surveys reveal that, despite their undoubted popularity, NoSQL datastores suffer from some weaknesses, among which the lack of effective support for data protection appears among the most serious ones. Proper data protection mechanisms are therefore required to fill this void. In this work, we start to address this issue by focusing on access control and discussing the definition of a fine-grained access control framework for document-oriented NoSQL datastores. More precisely, we first focus on issues and challenges related to the definition of such a framework, considering theoretical, implementation, and integration aspects. Then, we discuss the reasons for which state-of-the-art fine-grained access control solutions proposed for relational database management systems cannot be used within the NoSQL scenario. We then introduce possible strategies to address the identified issues, which are at the basis of the framework development. Finally, we shortly report the outcome of an experience where the proposed framework has been used to enhance the data protection features of a popular NoSQL database

Integration-oriented ontology

The purpose of an integration-oriented ontology is to provide a conceptualization of a domain of interest for automating the data integration of an evolving and heterogeneous set of sources using Semantic Web technologies. It links domain concepts to each of the underlying data sources via schema mappings. Data analysts, who are domain experts but not necessarily have technical data management skills, pose ontology-mediated queries over the conceptualization, which are automatically translated to the appropriate query language for the sources at hand. Following well-established rules when designing schema mappings allows to automate the process of query rewriting and execution.Postprint (author's final draft

Model transformations and Tool Integration

Model transformations are increasingly recognised as being of significant importance to many areas of software development and integration. Recent attention on model transformations has particularly focused on the OMGs Queries/Views/Transformations (QVT) Request for Proposals (RFP). In this paper I motivate the need for dedicated approaches to model transformations, particularly for the data involved in tool integration, outline the challenges involved, and then present a number of technologies and techniques which allow the construction of flexible, powerful and practical model transformations