Analysis and visualisation of RDF resources in Ondex

An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a distributed knowledge base which has the potential to advance biomedical research [1]. This potential, however, cannot be realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need for tools that provide data reduction, visualization and interactive analysis capabilities.
Ondex is a data integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated with ontologies. This data model conforms to the Semantic Web framework, in particular to RDF, and therefore Ondex is ideally positioned as a platform that can exploit the semantic web. 
The Ondex system offers a range of features and analysis methods of potential value to semantic web users, including:
-	An interactive graph visualization interface (Ondex user client), which provides data reduction and representation methods that leverage the ontological annotation.
-	A suite of importers from a variety of data sources to Ondex (http://ondex.org/formats.html)
-	A collection of plug-ins which implement graph analysis, graph transformation and graph-matching functions.
-	An integration toolkit (Ondex Integrator) which allows users to compose workflows from these modular components
-	In addition, all importers and plug-ins are available as web-services which can be integrated in other tools, as for instance Taverna [3].
The developments that will be presented in this demo have made this functionality interoperable with the Semantic Web framework. In particular we have developed an interactive importer, based on SPARQL that allows the query-driven construction of datasets which brings together information from different RDF data resources into Ondex.
These datasets can then be further refined, analysed and annotated both interactively using the Ondex user client and via user-defined workflows. The results of these analyses can be exported in RDF, which can be used to enrich existent knowledge bases, or to provide application-specific views of the data. Both importer and exporter only focus on a subset of the Ondex and RDF data models, which are shared between these two data representations [4].
In this demo we will show how Ondex can be used to query, analyse and visualize Semantic Web knowledge bases. In particular we will present real use cases focused, but not limited to, resources relevant to plant biology. 
We believe that Ondex can be a valid contribution to the adoption of the Semantic Web in Systems Biology research and in biomedical investigation more generally. We welcome feedback on our current import/export prototype and suggestions for the advancement of Ondex for the Semantic Web.

References

1.	Ruttenberg, A. et. al.: Advancing translational research with the Semantic Web, BMC Bioinformatics, 8 (Suppl. 3): S2 (2007).
2.	Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Ruegg, A., Rawlings, C., Verrier, P., Philippi, S.: Graph-based analysis and visualization of experimental results with Ondex. Bioinformatics 22 (11):1383-1390 (2006).
3.	Rawlings, C.: Semantic Data Integration for Systems Biology Research, Technology Track at ISMB’09, http://www.iscb.org/uploaded/css/36/11846.pdf (2009).
4.	Splendiani, A. et. al.: Ondex semantic definition, (Web document) http://ondex.svn.sourceforge.net/viewvc/ondex/trunk/doc/semantics/ (2009).
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The sustainable management of museums. An italian perspective

Purpose \u2013 The theme of sustainability in museums has not been sufficiently explored in the international literature on cultural heritage management as well as few museums are already involved in programs to promote sustainable development. Considering this gap, the purpose of this study is twofold. Firstly, to provide a conceptual model applying the principles of sustainable development to the enhancement of cultural heritage and, secondly, to analyze the case of Marche Region. Design \u2013 After analysing the three dimensions of sustainability \u2013 environmental, social and economic \u2013 and their possible application to museum management, the research tested the theoretical assumptions through an exploratory qualitative/ quantitative survey. Methodology \u2013The structured questionnaire was submitted to a sample of museums and consisted of a wide range of questions, primarily, although not exclusively, quantitative, which examined both museum management and sustainability orientation. Approach \u2013 The analysis focused on two different dimensions: the first aimed at understanding the perception of sustainability and the value of its components, the second aimed at investigating museums\u2019 willingness and reasons to engage in concrete sustainability-oriented actions. Finding \u2013 The field research showed Marche Region\u2019s museums have a full awareness of the benefits of sustainable management. However, the lack of a managerial approach to the museums\u2019 development compromises their ability to transfer this orientation in operational policies. Originality of research \u2013 The paper provides a multidimensional model for measuring the level of museum sustainability, able to analyze cultural and behavioral components. This analysis identifies possible areas of intervention for regional policies aimed at improving sustainability orientation of museums

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

Valley light-emitting transistor

published_or_final_versio

Two dimensional crystals in three dimensions: electronic decoupling of single-layered platelets in colloidal nanoparticles

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Voice support in reading skills in higher education: report of the project 'campus multimodal' at the Universitat de Barcelona

Se presentan los resultados de una prueba piloto de estudio e impulso de dos herramientas de apoyo de voz en la lectura, ClaroRead y ReadSpeak, en la Universitat de Barcelona, como ejemplo de aplicación de los principios de diseño curricular universal. Para valorar su impacto se realizan diferentes modalidades de encuestas y tests de uso en las que participó una muestra de alumnos bastante numerosa, y también una entrevista orientada al profesorado. Los resultados permiten conocer problemas de lectura de los usuarios, y las mejoras aportadas por la lectura multimodal

Haplotype characterization of a stranded common minke whale calf (Balaenoptera acutorostrata lacépède, 1804): Is the mediterranean sea a potential calving or nursery ground for the species?

The stranding of a suckling calf of Common Minke Whale (Balaenoptera acutorostrata) on the coast near Salerno (Campania, Southern Italy) is reported. The molecular analysis of a partial sequence of the mitochondrial DNA control region shows that the animal bore a haplotype identical to haplotype Ba169 considered as typical of individuals from North Atlantic population. Historical data and our results suggest the possibility that the Mediterranean Sea might be a potential calving or nursery ground for this species

Charge photogeneration in few-layer MoS2

The two-dimensional semiconductor MoS2 in its mono- and few-layer form is expected to have a significant exciton binding energy of several 100 meV, leading to the consensus that excitons are the primary photoexcited species. Nevertheless, even single layers show a strong photovoltaic effect and work as the active material in high sensitivity photodetectors, thus indicating efficient charge carrier photogeneration (CPG). Here we use continuous wave photomodulation spectroscopy to identify the optical signature of long-lived charge carriers and femtosecond pump-probe spectroscopy to follow the CPG dynamics. We find that intitial photoexcitation yields a branching between excitons and charge carriers, followed by excitation energy dependent hot exciton dissociation as an additional CPG mechanism. Based on these findings, we make simple suggestions for the design of more efficient MoS2 photovoltaic and photodetector devices

Optical signature of symmetry variations and spin-valley coupling in atomically thin tungsten dichalcogenides

Motivated by the triumph and limitation of graphene for electronic applications, atomically thin layers of group VI transition metal dichalcogenides are attracting extensive interest as a class of graphene-like semiconductors with a desired band-gap in the visible frequency range. The monolayers feature a valence band spin splitting with opposite sign in the two valleys located at corners of 1st Brillouin zone. This spin-valley coupling, particularly pronounced in tungsten dichalcogenides, can benefit potential spintronics and valleytronics with the important consequences of spin-valley interplay and the suppression of spin and valley relaxations. Here we report the first optical studies of WS2 and WSe2 monolayers and multilayers. The efficiency of second harmonic generation shows a dramatic even-odd oscillation with the number of layers, consistent with the presence (absence) of inversion symmetry in even-layer (odd-layer). Photoluminescence (PL) measurements show the crossover from an indirect band gap semiconductor at mutilayers to a direct-gap one at monolayers. The PL spectra and first-principle calculations consistently reveal a spin-valley coupling of 0.4 eV which suppresses interlayer hopping and manifests as a thickness independent splitting pattern at valence band edge near K points. This giant spin-valley coupling, together with the valley dependent physical properties, may lead to rich possibilities for manipulating spin and valley degrees of freedom in these atomically thin 2D materials

Ontology mapping for semantically enabled applications

In this review, we provide a summary of recent progress in ontology mapping (OM) at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential of semantically enabled or enriched applications and for meaningful insights, such as drug discovery, using machine-learning technologies. We discuss challenges and solutions for better ontology mappings, as well as how to select ontologies before their application. In addition, we describe tools and algorithms for ontology mapping, including evaluation of tool capability and quality of mappings. Finally, we outline the requirements for an ontology mapping service (OMS) and the progress being made towards implementation of such sustainable services