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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A Proposal for the Inclusion of Accessibility Criteria in the Publishing Workflow of Images in Biomedical Academic Articles

AbstractIn spite of the importance of visual content in academic publishing, biomedical articles do not offer accessible images, mainly because of the lack of text alternatives. According to a process-oriented accessibility philosophy, this article proposes the use of image-related texts, such as captions or mentions, as text alternatives of images, since they are solutions based on the current practices of authors of biomedical images. We also present two tools created to guide authors in writing comprehensive text alternatives. The aim of this proposal is to increase the opportunities of an actual application of accessibility principles within the biomedical academic publishing

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

Towards linked open gene mutations data

<p>Abstract</p> <p>Background</p> <p>With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework.</p> <p>In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data.</p> <p>Methods</p> <p>A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest.</p> <p>Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite.</p> <p>Results</p> <p>We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application.</p> <p>Conclusions</p> <p>This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.</p> <p>The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.</p

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

MEASURING PROPENSITY OF ONLINE PURCHASE BY USING THE TAM MODEL: EVIDENCE FROM ITALIAN UNIVERSITY STUDENTS

The study aims to investigate the dynamics of online purchasing behavior through the analysis of a sample of students from Italy. The objective is twofold: firstly, to outline a descriptive picture of the type of relationship with the web and the use of the TAM model to highlight the propensity to use electronic commerce by the analyzed sample. An interesting evidence is the prevalence of using the Internet for social activities rather than for purchases. In fact, the propensity to purchase online is still very limited and mainly concerns cultural and tourist services rather than physical products. Mobile devices are the main devices for connecting students to the Web and, consequently, the most used for purchasing online

Valley light-emitting transistor

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Mapping and Evaluating the Attractiveness of Pilgrim Routes from an Experiential Perspective: the Case of the ‘Paths through Italy’

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The stuffed crocodile of "Castel Nuovo" in Naples (Italy): new insights from ancient DNA and radiocarbon

In the present study, a stuffed crocodile displayed for centuries at the "Castel Nuovo" (New Castle) in Naples was radiocarbon dated and examined using ancient DNA analysis. The specimen was classified as Crocodylus niloticus based on its large body size and the mitochondrial DNA haplotype obtained, already described for a living population in Lake Nasser (Egypt). Radiocarbon analysis indicated an age of 585 ± 40 14C year BP, which coincides with the end of the Middle Ages. These results are commented in the light of Medieval religious symbolism and ancient legends which link the crocodile to the history of Naples during the mid-fifteenth century. The data obtained seem to confirm the explanation found in an old guidebook to Naples, according to which the stuffed crocodile was offered by a soldier returning from Egypt as an ex-voto to the image of the "Madonna del Parto" in the chapel of the castle. In addition, the radiocarbon dating shows that the individual analysed could be the oldest taxidermied vertebrate in Europe

Los protestantes y la inquisición

El estudio del protestantismo que llegó a América en el Siglo XVII debe partir del análisis de los criterios que impuso la Inquisición Española para juzgar a los cristianos no católicos en su condición de herejes, en un momento histórico en que las monarquías protestantes representaron para España el enemigo religioso, político y económico; extendiendo a América la enemistad que se agudizó en el continente europeo. La Inquisición, con respecto a las Indias, incluyó en sus estatutos y en sus manuales de procedimiento una casuística local, y fundamentándose en ella fue emitiendo instrucciones particulares según el territorio y la época en los cuales debieron aplicarse. Todo lo cual demuestra la flexibilidad del Santo Oficio en adaptarse a las circunstancias de tiempo y lugar y justifica la larga vida de la institución