Object-oriented querying of existing relational databases

In this paper, we present algorithms which allow an object-oriented querying of existing relational databases. Our goal is to provide an improved query interface for relational systems with better query facilities than SQL. This seems to be very important since, in real world applications, relational systems are most commonly used and their dominance will remain in the near future. To overcome the drawbacks of relational systems, especially the poor query facilities of SQL, we propose a schema transformation and a query translation algorithm. The schema transformation algorithm uses additional semantic information to enhance the relational schema and transform it into a corresponding object-oriented schema. If the additional semantic information can be deducted from an underlying entity-relationship design schema, the schema transformation may be done fully automatically. To query the created object-oriented schema, we use the Structured Object Query Language (SOQL) which provides declarative query facilities on objects. SOQL queries using the created object-oriented schema are much shorter, easier to write and understand and more intuitive than corresponding S Q L queries leading to an enhanced usability and an improved querying of the database. The query translation algorithm automatically translates SOQL queries into equivalent SQL queries for the original relational schema

Genomic characterisation of an endometrial pathogenic <i>Escherichia coli</i> strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity

&lt;b&gt;Background&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Strains of &lt;i&gt;Escherichia coli&lt;/i&gt; cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylogenetic relationship exists that distinguishes most &lt;i&gt;E. Coli&lt;/i&gt; causing intestinal disease from those that cause extra-intestinal disease, however, isolates within a recently described subclass of Extra-Intestinal Pathogenic &lt;i&gt;E. Coli&lt;/i&gt; (ExPEC), termed endometrial pathogenic &lt;i&gt;E. Coli&lt;/i&gt;, tend to be phylogenetically distant from the vast majority of characterised ExPECs, and more closely related to human intestinal pathogens. In this work, we investigate the genetic basis for ExPEC infection in the prototypic endometrial pathogenic &lt;i&gt;E. Coli&lt;/i&gt; strain MS499.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt;&lt;p&gt;&lt;/p&gt; By investigating the genome of MS499 in comparison with a range of other E. coli sequences, we have discovered that this bacterium has acquired substantial lengths of DNA which encode factors more usually associated with ExPECs and less frequently found in the phylogroup relatives of MS499. Many of these acquired factors, including several iron acquisition systems and a virulence plasmid similar to that found in several ExPECs such as APEC O1 and the neonatal meningitis &lt;i&gt;E. Coli&lt;/i&gt; S88, play characterised roles in a variety of typical ExPEC infections and appear to have been acquired recently by the evolutionary lineage leading to MS499.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Taking advantage of the phylogenetic relationship we describe between MS499 and several other closely related &lt;i&gt;E. Coli&lt;/i&gt; isolates from across the globe, we propose a step-wise evolution of a novel clade of sequence type 453 ExPECs within phylogroup B1, involving the recruitment of ExPEC virulence factors into the genome of an ancestrally non-extraintestinal &lt;i&gt;E. Coli&lt;/i&gt;, which has repurposed this lineage with the capacity to cause extraintestinal disease. These data reveal the genetic components which may be involved in this phenotype switching, and argue that horizontal gene exchange may be a key factor in the emergence of novel lineages of ExPECs.&lt;p&gt;&lt;/p&gt

Safer in the Clouds (Extended Abstract)

We outline the design of a framework for modelling cloud computing systems.The approach is based on a declarative programming model which takes the form of a lambda-calculus enriched with suitable mechanisms to express and enforce application-level security policies governing usages of resources available in the clouds. We will focus on the server side of cloud systems, by adopting a pro-active approach, where explicit security policies regulate server's behaviour.Comment: In Proceedings ICE 2010, arXiv:1010.530