Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project)

More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information. We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platformsComment: Presented at DEIT, Data Engineering and Internet Technology, 2011 IEEE: CFP1113L-CD

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

Cosmology and Fermion Confinement in a Scalar-Field-Generated Domain Wall Brane in Five Dimensions

We consider a brane generated by a scalar field domain wall configuration in 4+1 dimensions, interpolating, in most cases, between two vacua of the field. We study the cosmology of such a system in the cases where the effective four-dimensional brane metric is de Sitter or anti de Sitter, including a discussion of the bulk coordinate singularities present in the de-Sitter case. We demonstrate that a scalar field kink configuration can support a brane with dS$_4$ cosmology, despite the presence of coordinate singularities in the metric. We examine the trapping of fermion fields on the domain wall for nontrivial brane cosmology.Comment: 29 pages, 12 figures; minor changes, accepted by JHE

Path lengths in turbulence

By tracking tracer particles at high speeds and for long times, we study the geometric statistics of Lagrangian trajectories in an intensely turbulent laboratory flow. In particular, we consider the distinction between the displacement of particles from their initial positions and the total distance they travel. The difference of these two quantities shows power-law scaling in the inertial range. By comparing them with simulations of a chaotic but non-turbulent flow and a Lagrangian Stochastic model, we suggest that our results are a signature of turbulence.Comment: accepted for publication in Journal of Statistical Physic

Challenges in Integrating Biological Data Sources

this report, we examine the technical challenges to integration, critique the available tools and resources, and compare the cost and advantages of various methodologies. We begin by analyzing the basic steps in strict and complete integration: 1) transformation of the various schemas to a common data model; 2) matching of semantically related schema objects; 3) schema integration; 4) transformation of data to the federated database on demand; and 5) matching of semantically equivalent data. Some progress has been made on generic problems such as (1) and (3) within the wider database community, but issues of semantics (steps (2) and (5)) have only been dealt with any degree of success by domain experts within the biological community. We then look at the solution space of integration strategies as defined by two axes, the "tightness" of federation and the "degree" of instantiation, discuss where various solutions fall on this plane, and examine their cost and advantages/disadvantages. Finally, we examine technical challenges that are not -3- July 12, 199

Vector meson production and nucleon resonance analysis in a coupled-channel approach for energies m_N < sqrt(s) < 2 GeV II: photon-induced results

We present a nucleon resonance analysis by simultaneously considering all pion- and photon-induced experimental data on the final states gamma N, pi N, 2 pi N, eta N, K Lambda, K Sigma, and omega N for energies from the nucleon mass up to sqrt(s) = 2 GeV. In this analysis we find strong evidence for the resonances P_{31}(1750), P_{13}(1900), P_{33}(1920), and D_{13}(1950). The omega N production mechanism is dominated by large P_{11}(1710) and P_{13}(1900) contributions. In this second part we present the results on the photoproduction reactions and the electromagnetic properties of the resonances. The inclusion of all important final states up to sqrt(s) = 2 GeV allows for estimates on the importance of the individual states for the GDH sum rule.Comment: 41 pages, 26 figures, discussion extended, typos corrected, references updated, to appear in Phys. Rev.

A Semantics for Complex Objects and Approximate Answers

AbstractA new definition of complex objects is introduced which provides a denotation for incomplete tuples as well as partially described sets. Set values are “sandwiched” between “complete” and “consistent” descriptions (respectively represented in the Smyth and Hoare powerdomains), allowing the maximal values to be arbitrary subsets of maximal elements in the domain of the space of descriptions. We then restrict our attention to complex objects which are in some sense “natural,” i.e., those which represent “views” of entity-relationship databases, and define rules over these objects. The rules can be used not only as an integrity check on the information in the database, but can be used constructively to infer consistent instances of conclusions and to refine complete instances of the hypothesis. The system is shown to extend the power of datalog (without negation) and the relational algebra (with set difference), and to have an efficient implementation

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters