GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

BACKGROUND: A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. RESULTS: GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. CONCLUSION: GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at [email protected]. A commercial licence form can be obtained for profit company at [email protected]. See also

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Multimedia search without visual analysis: the value of linguistic and contextual information

This paper addresses the focus of this special issue by analyzing the potential contribution of linguistic content and other non-image aspects to the processing of audiovisual data. It summarizes the various ways in which linguistic content analysis contributes to enhancing the semantic annotation of multimedia content, and, as a consequence, to improving the effectiveness of conceptual media access tools. A number of techniques are presented, including the time-alignment of textual resources, audio and speech processing, content reduction and reasoning tools, and the exploitation of surface features

Approaches to visualising linked data: a survey

The uptake and consumption of Linked Data is currently restricted almost entirely to the Semantic Web community. While the utility of Linked Data to non-tech savvy web users is evident, the lack of technical knowledge and an understanding of the intricacies of the semantic technology stack limit such users in their ability to interpret and make use of the Web of Data. A key solution in overcoming this hurdle is to visualise Linked Data in a coherent and legible manner, allowing non-domain and non-technical audiences to obtain a good understanding of its structure, and therefore implicitly compose queries, identify links between resources and intuitively discover new pieces of information. In this paper we describe key requirements which the visualisation of Linked Data must fulfil in order to lower the technical barrier and make the Web of Data accessible for all. We provide an extensive survey of current efforts in the Semantic Web community with respect to our requirements, and identify the potential for visual support to lead to more effective, intuitive interaction of the end user with Linked Data. We conclude with the conclusions drawn from our survey and analysis, and present proposals for advancing current Linked Data visualisation efforts

TLAD 2010 Proceedings:8th international workshop on teaching, learning and assesment of databases (TLAD)

This is the eighth in the series of highly successful international workshops on the Teaching, Learning and Assessment of Databases (TLAD 2010), which once again is held as a workshop of BNCOD 2010 - the 27th International Information Systems Conference. TLAD 2010 is held on the 28th June at the beautiful Dudhope Castle at the Abertay University, just before BNCOD, and hopes to be just as successful as its predecessors.The teaching of databases is central to all Computing Science, Software Engineering, Information Systems and Information Technology courses, and this year, the workshop aims to continue the tradition of bringing together both database teachers and researchers, in order to share good learning, teaching and assessment practice and experience, and further the growing community amongst database academics. As well as attracting academics from the UK community, the workshop has also been successful in attracting academics from the wider international community, through serving on the programme committee, and attending and presenting papers.This year, the workshop includes an invited talk given by Richard Cooper (of the University of Glasgow) who will present a discussion and some results from the Database Disciplinary Commons which was held in the UK over the academic year. Due to the healthy number of high quality submissions this year, the workshop will also present seven peer reviewed papers, and six refereed poster papers. Of the seven presented papers, three will be presented as full papers and four as short papers. These papers and posters cover a number of themes, including: approaches to teaching databases, e.g. group centered and problem based learning; use of novel case studies, e.g. forensics and XML data; techniques and approaches for improving teaching and student learning processes; assessment techniques, e.g. peer review; methods for improving students abilities to develop database queries and develop E-R diagrams; and e-learning platforms for supporting teaching and learning