10 research outputs found

    An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow

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    <p>Abstract</p> <p>Background</p> <p>Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an <it>ad hoc </it>manner.</p> <p>Results</p> <p>We have developed a simple generic XML schema (GenomicMappingData.xsd – GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows.</p> <p>Conclusion</p> <p>The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.</p

    The Memory Store: A collaborative online fiction, which explores the opportunities for participatory narrative experiences afforded by the shared space of the Internet

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    This practice-led thesis explores the opportunities digital technologies afford for writers to create online fictional spaces to share with readers. The research asks how might authors utilise the shared space of the Internet to offer collaborative narrative experiences? Part One of the thesis is a creative project, The Memory Store, http://thememorystore.org a hypertext, detective fiction, set in Liverpool in 2115, written with contributions from a hundred people. The work experiments with authorship as a collective experience in an online environment, considering ways in which we might collaboratively construct stories. This experimental project differs in its ambition from other collaborative online writing projects, such as MacGuffin (Comma Press and Manchester Metropolitan University, 2015) and Rainy City Stories (Openstories, 2008) by exploring methods to structure writing contributed by participants so that reading can flow from one writer to another with a narrative connection established by the site’s interface. Part Two of the thesis is a critical reflection that explores theories that have informed my creative practice. The research examines what Manovich described as ‘spatial wandering,’ (2001, p49) Nelson’s term ‘intertwingularity’ (1974, p29) and ‘the bricolage’ that Turkle (1995, p51) referred to in respect of the Internet, to approach conceptualisations of digital technology as spatial, creating environments through which readers navigate to interconnected experiences, facilitating exploration, encouraging participation, communication and sharing. The thesis also considers narrative space, detective fiction and the archiving of collective memory in online environments to support the development of the creative project

    Devise: a framework for the evaluation of internet search engines

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    This project investigates the feasibility of the use of user-satisfaction as a multidimensional evaluative construct of search engines. Search engine developments are reviewed to reveal a range of indexing and retrieval techniques that may assist casual users in the information retrieval task. Yet few evaluation studies have considered the impact of system features, in particular those with which the user interacts for search assistance. A broad review of retrieval system evaluation highlights the complex environment in which measures of both the utility of the search results and the usability of the system are sought from a user-perspective. Our proposed approach for a user-centered evaluation is based on a conceptual framework in which user-satisfaction is characterised as a variable dependent on system features and functions and expressed in a moderating context of user-task requirement. Towards this end, the research reported here focuses on the definition of the construct of user satisfaction on the multi dimensions of the retrieval process, an expression of what a typical user is trying to do. Empirical work was then undertaken to test the feasibility and potential value of the implementation of the framework for the evaluation of three search engines. Initial results are presented which provide a degree of understanding of how users are satisfied and on what criteria. This provides the basis on which we make recommendations for the refinement of the multidimensional framework and its use as a methodology for the evaluation of search engines from a user perspective

    The Smart City and the Extraction of Hope

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    Designing navigable information spaces

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    Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998.Includes bibliographical references (p. 159-164).by Mark A. Foltz.M.S

    The Future of Media

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    How do we combat post-truth in the news? Are social media influencers the journalists of today? What is it like to live in a smart city? Does AI really change "everything"? The Future of Media investigates the future of media industries and technologies (journalism, TV, film, photography, radio, publishing, social media), while exploring how media shape our future—on a political, economic, cultural and individual level. Issues of diversity, media reform, labour, activism and art take the discussion into a wider social context. Through this, the book celebrates the importance and vitality of media in the modern world. The Future of Media is also an experiment in collaborative modes of thinking and working. Co-authored by theorists and practitioners from one of the world's most established media departments, it offers a radical, creative and critical take on media industries—and on world affairs

    The development of a reference database of health information resources to facilitate informed lifestyle choice

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    This study investigates, within the current health care situation, the interrelationship of the user, resources and tool in the design of a prototype WELLNESS database-driven web site. A shift has taken place in health care, in which the base of conventional medicine has broadened to integrate other systems, practices and worldviews. These include complementary and alternative medicine, health promotion, disease prevention and wellness. Emphasis is placed on the need to take personal responsibility for one's own health and wellness. The global burden of chronic disease, reaching epidemic proportions, is increasingly linked to risk factors resulting from personal lifestyle choices. The growing evidence of the user's need to make personal, informed, lifestyle choices and their reliance on the Web for health information, required investigation. WELLNESS, a specific orientation to health and wellness, formed the framework within which the user and resources were defined and the tool designed. The user was profiled as the WELLNESS health information seeker, hereby contributing significantly to an understanding of the user in this new context. The user profile informed the establishment of resource selection criteria and tool design. The identification of WELLNESS content selection criteria, within a five-dimensional model, was required to ensure quality, relevant and credible resources. The tool is comprised of the WELLNESS thesaurus and WELLNESS database-driven web site. The WELLNESS thesaurus was constructed based on a combination of relevant thesauri. It will be used as an indexing tool. An investigation of existing health information web sites highlighted the importance of designing a specific WELLNESS database-driven web site. A database host was identified against which the original study's conceptual schema was assessed. A low-fidelity prototype web site was designed as the interface between the WELLNESS health information seeker and the database of WELLNESS health information resources. This study has epidemiological, philosophical, epistemological, sociological and psychological relevance. The provision of access to WELLNESS health information resources, made available in the WELLNESS database-driven web site, for personal, informed lifestyle choice by the WELLNESS health information seeker could potentially contribute to the reduction of the global burden of chronic disease.Information ScienceD.Litt. et Phil. (Information Science
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