104 research outputs found
Previewing Semantic Web Pipes
Get PDFIn this demo we present a first implementation of Semantic Web Pipes, a powerful tool to build RDF-based mashups. Semantic Web pipes are defined in XML and when executed they fetch RDF graphs on the Web, operate on them, and produce an RDF output which is itself accessible via a stable URL. Humans can also use pipes directly thanks to HTML wrapping of the pipe parameters and outputs. The implementation we will demo includes an online AJAX pipe editor and execution engine. Pipes can be published and combined thus fostering collaborative editing and reuse of data mashups
Review: Dystroglycan in the Nervous System
Get PDFDystroglycan is part of a large complex of proteins, the dystrophin-glycoprotein complex, which has been implicated in the pathogenesis of muscular dystrophies for a long time. Besides muscular degeneration many patients manifest symptoms of neurological and cognitive dysfunction. Newer findings suggest that dystroglycan is implicated in brain development, synapse formation and plasticity, nerve-glia interactions and maintenance of the blood-brain barrier.
Most research so far has focused on the functions of dystroglycan in muscle and neuromuscular junctions, while its role in the brain and interneuronal synapses has been largely neglected. 
This review will give an overview of the biochemistry of dystroglycan, its interaction with other proteins as well as its confirmed and hypothetical functions in the nervous system in health and diesease
Linked Data approach for selection process automation in Systematic Reviews
Get PDFBackground: a systematic review identifies, evaluates and synthesizes the available literature on a given topic using scientific and repeatable methodologies. The significant workload required and the subjectivity bias could affect results. Aim: semi-automate the selection process to reduce the amount of manual work needed and the consequent subjectivity bias. Method: extend and enrich the selection of primary studies using the existing technologies in the field of Linked Data and text mining. We define formally the selection process and we also develop a prototype that implements it. Finally, we conduct a case study that simulates the selection process of a systematic literature published in literature. Results: the process presented in this paper could reduce the work load of 20% with respect to the work load needed in the fully manually selection, with a recall of 100%. Conclusions: the extraction of knowledge from scientific studies through Linked Data and text mining techniques could be used in the selection phase of the systematic review process to reduce the work load and subjectivity bia
Examining perceptions of the usefulness and usability of a mobile-based system for pharmacogenomics clinical decision support: A mixed methods study
Get PDFBackground. Pharmacogenomic testing has the potential to improve the safety and efficacy of pharmacotherapy, but clinical application of pharmacogenetic knowledge has remained uncommon. Clinical Decision Support (CDS) systems could help overcome some of the barriers to clinical implementation. The aim of this study was to evaluate the perception and usability of a web- and mobile-enabled CDS system for pharmacogenetics-guided drug therapy-the Medication Safety Code (MSC) system-among potential users (i.e., physicians and pharmacists). Furthermore, this study sought to collect data on the practicability and comprehensibility of potential layouts of a proposed personalized pocket card that is intended to not only contain the machine-readable data for use with the MSC system but also humanreadable data on the patient's pharmacogenomic profile. Methods. We deployed an emergent mixed methods design encompassing (1) qualitative interviews with pharmacists and pharmacy students, (2) a survey among pharmacogenomics experts that included both qualitative and quantitative elements and (3) a quantitative survey among physicians and pharmacists. The interviews followed a semistructured guide including a hypothetical patient scenario that had to be solved by using the MSC system. The survey among pharmacogenomics experts focused on what information should be printed on the card and how this information should be arranged. Furthermore, the MSC system was evaluated based on two hypothetical patient scenarios and four follow-up questions on the perceived usability. The second survey assessed physicians' and pharmacists' attitude towards the MSC system. Results. In total, 101 physicians, pharmacists and PGx experts coming from various relevant fields evaluated the MSC system. Overall, the reaction to the MSC system was positive across all investigated parameters and among all user groups. The majority of participants were able to solve the patient scenarios based on the recommendations displayed on the MSC interface. A frequent request among participants was to provide specific listings of alternative drugs and concrete dosage instructions. Negligence of other patient-specific factors for choosing the right treatment such as renal function and co-medication was a common concern related to the MSC system, while data privacy and cost-benefit considerations emerged as the participants' major concerns regarding pharmacogenetic testing in general. The results of the card layout evaluation indicate that a gene-centered and tabulated presentation of the patient's pharmacogenomic profile is helpful and well-accepted. Conclusions. We found that the MSC system was well-received among the physicians and pharmacists included in this study. A personalized pocket card that lists a patient's metabolizer status along with critically affected drugs can alert physicians and pharmacists to the availability of essential therapy modifications
Life sciences on the semantic web: the neurocommons and beyond
No full textTranslational research, the effort to couple the results of basic research to clinical applications, depends on the ability to effectively answer questions using information that spans multiple disciplines. The Semantic Web, with its emphasis on combining information using standard representation languages, access to that information via standard web protocols, and technologies to leverage computation, such as in the form of inference and distributable query, offers a social and technological basis for assembling, integrating and making available biomedical knowledge at Web scale. In this article, we discuss the use of Semantic Web technology for assembling and querying biomedical knowledge from multiple sources and disciplines. We present the Neurocommons prototype knowledge base, a demonstration intended to show the feasibility and benefits of using these technologies. The prototype knowledge base can be used to experiment with and assess the scalability of current tools and methods for creating such a resource, and to elicit issues that will need to be addressed in order to expand the scope and use of it. We demonstrate the utility of the knowledge base by reviewing a few example queries that provide answers to precise questions relevant to the understanding of disease. All components of the knowledge base are freely available at http://neurocommons.org/, enabling readers to reconstruct the knowledge base and experiment with this new technology.peer-reviewe
Life sciences on the semantic web: the neurocommons and beyond
No full textTranslational research, the effort to couple the results of basic research to clinical applications, depends on the ability to effectively answer questions using information that spans multiple disciplines. The Semantic Web, with its emphasis on combining information using standard representation languages, access to that information via standard web protocols, and technologies to leverage computation, such as in the form of inference and distributable query, offers a social and technological basis for assembling, integrating and making available biomedical knowledge at Web scale. In this article, we discuss the use of Semantic Web technology for assembling and querying biomedical knowledge from multiple sources and disciplines. We present the Neurocommons prototype knowledge base, a demonstration intended to show the feasibility and benefits of using these technologies. The prototype knowledge base can be used to experiment with and assess the scalability of current tools and methods for creating such a resource, and to elicit issues that will need to be addressed in order to expand the scope and use of it. We demonstrate the utility of the knowledge base by reviewing a few example queries that provide answers to precise questions relevant to the understanding of disease. All components of the knowledge base are freely available at http://neurocommons.org/, enabling readers to reconstruct the knowledge base and experiment with this new technology
Breaking-down the Ontology Alignment Task with a Lexical Index and Neural Embeddings
Get PDFLarge ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In the paper we present an approach that combines a lexical index, a neural embedding model and locality modules to effectively divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed methods are adequate in practice and can be integrated within the workflow of state-of-the-art systems
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