Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged.Results: To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles.Availability: http://getutopia.comContact: teresa.k.attwood@manchester.ac.uk
Use of transcranial Doppler (TCD) to diagnose vasospasm has been criticised. We examined reproducibility of TCD middle cerebral artery (MCA) velocity measurements. Thirty-six healthy adult volunteers were recruited. Four operators, two experienced and two inexperienced, participated. MCA velocity was measured twice by one operator and once by a second operator. Mean (95% limits of agreement) interoperator agreement was 2.4(+/-36.7) cm/s. Experienced vs. inexperienced, inexperienced vs. inexperienced, and experienced vs. experienced operators were -2.8(+/-39.3), -5.6(+/-40.1), 1.8(+/-22.1) cm/s, respectively. Intraoperator agreement across all operators, experienced and inexperienced were -0.5(+/-16.9), -1.6(+/-19.3), 0.7(+/-13.7) cm/s, respectively. Interoperator limits of agreement for experienced operators were almost half that of inexperienced operators. Intraoperator reproducibility was much better, regardless of level of experience, but aberrant results did occur even with experienced operators. If TCD measurements are used to guide management it is essential that operators are adequately trained, and readings repeated before potentially harmful treatments are instituted.
We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard – too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here – a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers…
The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.
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