Ontology-based data access: ontop of databases

We present the architecture and technologies underpinning the OBDA system Ontop and taking full advantage of storing data in relational databases. We discuss the theoretical foundations of Ontop: the tree-witness query rewriting, T-mappings and optimisations based on database integrity constraints and SQL features. We analyse the performance of Ontop in a series of experiments and demonstrate that, for standard ontologies, queries and data stored in relational databases, Ontop is fast, efficient and produces SQL rewritings of high quality

Circuit Complexity Meets Ontology-Based Data Access

Ontology-based data access is an approach to organizing access to a database augmented with a logical theory. In this approach query answering proceeds through a reformulation of a given query into a new one which can be answered without any use of theory. Thus the problem reduces to the standard database setting. However, the size of the query may increase substantially during the reformulation. In this survey we review a recently developed framework on proving lower and upper bounds on the size of this reformulation by employing methods and results from Boolean circuit complexity.Comment: To appear in proceedings of CSR 2015, LNCS 9139, Springe

A Comparison of Techniques Measuring Stress in Birds

Free-living birds are subjected to both external and internal stresses which can affect their health, activity, and reproductive success. To study stress in free living birds, they must be captured in nets and handled by the researcher to take blood samples for commonly used measures of stress, an activity which itself can induce stress and confound results. This study compares the effects of handling time on three different measures of stress: levels of the stress hormone corticosterone (CORT), levels of Heat Shock Protein 60 (HSP 60) and the ratio of heterophils to lymphocytes (H/L ratio) in tufted titmouse (Baeolophus bicolor) captured at feeders between December and January (2011-2013) in Fredericksburg, VA. Blood samples collected between two and 15 minutes from 12 birds were assayed for levels of CORT and HSP and from 24 birds for H/L ratios. Relationships were examined between these stress indicators and handling time, body mass and body condition. CORT was significantly correlated with handling time (p\u3c0.01), which reinforces existing evidence of CORT’s sensitivity to the way subjects are handled immediately prior to blood collection. HSP or H/L ratios were not affected by handling time, suggesting that they may be preferable indicators of stress in free living birds under some circumstances

Ontology-based data access with databases: a short course

Ontology-based data access (OBDA) is regarded as a key ingredient of the new generation of information systems. In the OBDA paradigm, an ontology defines a high-level global schema of (already existing) data sources and provides a vocabulary for user queries. An OBDA system rewrites such queries and ontologies into the vocabulary of the data sources and then delegates the actual query evaluation to a suitable query answering system such as a relational database management system or a datalog engine. In this chapter, we mainly focus on OBDA with the ontology language OWL 2QL, one of the three profiles of the W3C standard Web Ontology Language OWL 2, and relational databases, although other possible languages will also be discussed. We consider different types of conjunctive query rewriting and their succinctness, different architectures of OBDA systems, and give an overview of the OBDA system Ontop

Substitution in a sense

The Reference Principle (RP) states that co-referring expressions are everywhere intersubstitutable salva congruitate. On first glance, (RP) looks like a truism, but a truism with some bite: (RP) transforms difficult philosophical questions about co-reference into easy grammatical questions about substitutability. This has led a number of philosophers to think that we can use (RP) to make short work of certain longstanding metaphysical debates. For example, it has been suggested that all we need to do to show that the predicate ‘( ) is a horse’ does not refer to a property is point out that ‘( ) is a horse’ and ‘the property of being a horse’ are not everywhere intersubstitutable salva congruitate. However, when we understand ‘substitution’ in the simplest and most straightforward way, (RP) is no truism; in fact, natural languages are full of counterexamples to the principle. In this paper, I introduce a new notion of substitution, and then develop and argue for a version of (RP) that is immune to these counterexamples. Along the way I touch on the following topics: the relation between argument forms and their natural language instances; the reification of sense; the difference between terms and predicates; and the relation between reference and disquotation. I end by arguing that my new version of (RP) cannot be used to settle metaphysical debates quite as easily as some philosophers would like

Answering SPARQL queries over databases under OWL 2 QL entailment regime

We present an extension of the ontology-based data access platform Ontop that supports answering SPARQL queries under the OWL 2 QL direct semantics entailment regime for data instances stored in relational databases. On the theoretical side, we show how any input SPARQL query, OWL 2 QL ontology and R2RML mappings can be rewritten to an equivalent SQL query solely over the data. On the practical side, we present initial experimental results demonstrating that by applying the Ontop technologies—the tree-witness query rewriting, T-mappings compiling R2RML mappings with ontology hierarchies, and T-mapping optimisations using SQL expressivity and database integrity constraints—the system produces scalable SQL queries

Sex and the Cinema: What American Pie Teaches the Young

This paper focuses upon the wildly successful blockbuster American Pie teenpics, especially American Pie 3 – the Wedding. I argue that these films, which are sited so securely within the visual and pedagogical machinery of Hollywood culture, are specifically designed to appeal to teenage male audiences, and to provide lessons in sex and romance. Movies like this are especially important as they are experienced by far more teenagers than, for example, instructional films or other classroom materials; indeed, as Henry Giroux has observed, "teens and youth learn how to define themselves outside of the traditional sites of instruction, such as the home and the school… Learning in the postmodern age is located elsewhere – in popular spheres that shape their identities, through forms of knowledge and desires that appear absent from what is taught in schools" (Giroux, 1997, p.49). In this paper I discuss whether the American Pie series is actually a "new age" effort which, via insubordinate performances of gender, contests the hegemonic field of signification which regulates the production of sex, gender and desire, or whether it is more accurately described as a retrogressive hetero-conservative opus with a veneer of sexual radicalism. In short, I intend to probe whether this filmic vector for sex education is all about the shaping of responsible, caring, vulnerable men, or is it guiding them to become just like their heterosexual, middle-class fathers? And whether, despite its riotous and raunchy advertising, American Pie really dishes up something spicy or something terribly wholesome instead

Microscopic self-consistent theory of Josephson junctions including dynamical electron correlations

We formulate a fully self-consistent, microscopic model to study the retardation and correlation effects of the barrier within a Josephson junction. The junction is described by a series of planes, with electronic correlation included through a local self energy for each plane. We calculate current-phase relationships for various junctions, which include non-magnetic impurities in the barrier region, or an interfacial scattering potential. Our results indicate that the linear response of the supercurrent to phase across the barrier region is a good, but not exact indicator of the critical current. Our calculations of the local density of states show the current-carrying Andreev bound states and their energy evolution with the phase difference across the junction. We calculate the figure of merit for a Josephson junction, which is the product of the critical current, Ic, and the normal state resistance, R(N), for junctions with different barrier materials. The normal state resistance is calculated using the Kubo formula, for a system with zero current flow and no superconducting order. Semiclassical calculations would predict that these two quantities are determined by the transmission probabilities of electrons in such a way that the product is constant for a given superconductor at fixed temperature. Our self-consistent solutions for different types of barrier indicate that this is not the case. We suggest some forms of barrier which could increase the Ic.R(N) product, and hence improve the frequency response of a Josephson device.Comment: 46 pages, 21 figure

P352 A propensity score-matched, real-world comparison of ustekinumab vs vedolizumab as a second-line treatment for Crohn's disease. The Cross Pennine study II

Abstract Background The best choice of biological agents after failure to an anti-tumour necrosis factor (TNF)α agent in patients with Crohn's disease (CD) is yet to be defined. Real-world data dealing with this issue are still emerging. Methods This is a multicentre retrospective study including eight UK hospitals (August 2014-April 2020). We retrospectively collected data of patients treated with ustekinumab. Clinical response and remission at 14 and 52 weeks evaluated through Physician Global Assessment (PGA) and adverse events were recorded. Predictors of clinical response were examined, and a propensity score-matched analysis with a cohort of patients treated with vedolizumab was performed. Results Overall, 282 patients (mean age 40±15, F:M ratio 1.7:1) treated with ustekinumab were included. Clinical response or remission was reached by 200/282 patients (70.9%) at 14 weeks, and by 162/259 patients (62.5%) at 52 weeks. The most common reason for discontinuation was either primary failure or loss of response, followed by the occurrence of adverse events and by the need for surgery. The rate of non-adherence was rather low (1.4%). Current smoking (OR 2.48, 95% CI 1.13-5.44; p=0.02), baseline PGA (OR 2.4, 95% CI 1.55-3.69, p<0.001), and use of steroids (OR 2.42, 95% CI 1.26-4.65, p=0.008) were associated with 52-week treatment failure. Overall, 74 adverse events occurred, of which 26 were labelled as serious (8.3 per 100 person-year). After exclusion of patients without anti-TNFα exposure prior to starting ustekinumab or vedolizumab and exclusion of patients previously exposed to vedolizumab or ustekinumab, we analysed 275/282 patients (97.5%) from the ustekinumab cohort and 118/135 patients (87.4%) from the vedolizumab cohort. Propensity score analysis revealed that at 14 weeks, patients treated with ustekinumab were 38% (95% CI 25-50%; p<0.001) more likely to achieve a clinical remission, while at 52 weeks, the difference of 9% (95% CI -15-33%; p=0.462) was not significant. Conclusion Ustekinumab was effective and well tolerated in this real-world cohort. While ustekinumab proved more effective at 14-week follow-up, we found no statistically significant differences in outcomes at 52 weeks