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https://www.readbyqxmd.com/read/29111222/ssel-ade-a-semi-supervised-ensemble-learning-framework-for-extracting-adverse-drug-events-from-social-media
#1
Jing Liu, Songzheng Zhao, Gang Wang
With the development of Web 2.0 technology, social media websites have become lucrative but under-explored data sources for extracting adverse drug events (ADEs), which is a serious health problem. Besides ADE, other semantic relation types (e.g., drug indication and beneficial effect) could hold between the drug and adverse event mentions, making ADE relation extraction - distinguishing ADE relationship from other relation types - necessary. However, conducting ADE relation extraction in social media environment is not a trivial task because of the expertise-dependent, time-consuming and costly annotation process, and the feature space's high-dimensionality attributed to intrinsic characteristics of social media data...
October 27, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/29106550/the-oma-orthology-database-in-2018-retrieving-evolutionary-relationships-among-all-domains-of-life-through-richer-web-and-programmatic-interfaces
#2
Adrian M Altenhoff, Natasha M Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio M de Farias, Karina Zile, Charles Stevenson, Jiao Long, Henning Redestig, Gaston H Gonnet, Christophe Dessimoz
The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29076113/a-knowledge-modeling-approach-to-integrate-multiple-clinical-practice-guidelines-to-provide-evidence-based-clinical-decision-support-for-managing-comorbid-conditions
#3
Samina Abidi
Clinical management of comorbidities is a challenge, especially in a clinical decision support setting, as it requires the safe and efficient reconciliation of multiple disease-specific clinical procedures to formulate a comorbid therapeutic plan that is both effective and safe for the patient. In this paper we pursue the integration of multiple disease-specific Clinical Practice Guidelines (CPG) in order to manage co-morbidities within a computerized Clinical Decision Support System (CDSS). We present a CPG integration framework-termed as COMET (Comorbidity Ontological Modeling & ExecuTion) that manifests a knowledge management approach to model, computerize and integrate multiple CPG to yield a comorbid CPG knowledge model that upon execution can provide evidence-based recommendations for handling comorbid patients...
October 26, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29065602/graph-based-semantic-web-service-composition-for-healthcare-data-integration
#4
Ngamnij Arch-Int, Somjit Arch-Int, Suphachoke Sonsilphong, Paweena Wanchai
Within the numerous and heterogeneous web services offered through different sources, automatic web services composition is the most convenient method for building complex business processes that permit invocation of multiple existing atomic services. The current solutions in functional web services composition lack autonomous queries of semantic matches within the parameters of web services, which are necessary in the composition of large-scale related services. In this paper, we propose a graph-based Semantic Web Services composition system consisting of two subsystems: management time and run time...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29063554/best-paper-selection
#5
(no author information available yet)
Lin FP, Pokorny A, Teng C, Dear R, Epstein RJ. Computational prediction of multidisciplinary team decision-making for adjuvant breast cancer drug therapies: a machine learning approach. BMC Cancer 2016 Dec 1;16(1):929 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131452/ Marco-Ruiz L, Pedrinaci C, Maldonado JA, Panziera L, Chen R, Bellika JG. Publication, discovery and interoperability of Clinical Decision Support Systems: A Linked Data approach. J Biomed Inform 2016 Aug;62:243-64 http://www.sciencedirect.com/science/article/pii/S153204641630065X?via%3Dihub McEvoy DS, Sittig DF, Hickman TT, Aaron S, Ai A, Amato M, Bauer DW, Fraser GM, Harper J, Kennemer A, Krall MA, Lehmann CU, Malhotra S, Murphy DR, O'Kelley B, Samal L, Schreiber R, Singh H, Thomas EJ, Vartian CV, Westmorland J, McCoy AB, Wright A...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29063553/contributions-from-the-2016-literature-on-clinical-decision-support
#6
V Koutkias, J Bouaud
Objectives: To summarize recent research and select the best papers published in 2016 in the field of computerized clinical decision support for the Decision Support section of the IMIA yearbook. Methods: A literature review was performed by searching two bibliographic databases for papers related to clinical decision support systems (CDSSs). The aim was to identify a list of candidate best papers from the retrieved papers that were then peer-reviewed by external reviewers. A consensus meeting of the IMIA editorial team finally selected the best papers on the basis of all reviews and section editor evaluation...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29035605/a-two-staged-approach-to-developing-and-evaluating-an-ontology-for-delivering-personalized-education-to-diabetic-patients
#7
Susan Quinn, Raymond Bond, Chris Nugent
Ontologies are often used in biomedical and health domains to provide a concise and consistent means of attributing meaning to medical terminology. While they are novices in terms of ontology engineering, the evaluation of an ontology by domain specialists provides an opportunity to enhance its objectivity, accuracy, and coverage of the domain itself. This paper provides an evaluation of the viability of using ontology engineering novices to evaluate and enrich an ontology that can be used for personalized diabetic patient education...
October 16, 2017: Informatics for Health & Social Care
https://www.readbyqxmd.com/read/28971431/opinion-mining-for-educational-video-lectures
#8
Dimitrios Kravvaris, Katia Lida Kermanidis
The search for relevant educational videos is a time consuming process for the users. Furthermore, the increasing demand for educational videos intensifies the problem and calls for the users to utilize whichever information is offered by the hosting web pages, and choose the most appropriate one. This research focuses on the classification of user views, based on the comments on educational videos, into positive or negative ones. The aim is to give users a picture of the positive and negative comments that have been recorded, so as to provide a qualitative view of the final selection at their disposal...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28969593/biocarian-search-engine-for-exploratory-searches-in-heterogeneous-biological-databases
#9
Nazar Zaki, Chandana Tennakoon
BACKGROUND: There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web...
October 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28968812/metsigdis-a-manually-curated-resource-for-the-metabolic-signatures-of-diseases
#10
Liang Cheng, Haixiu Yang, Hengqiang Zhao, Xiaoya Pei, Hongbo Shi, Jie Sun, Yunpeng Zhang, Zhenzhen Wang, Meng Zhou
Complex diseases cannot be understood only on the basis of single gene, single mRNA transcript or single protein but the effect of their collaborations. The combination consequence in molecular level can be captured by the alterations of metabolites. With the rapidly developing of biomedical instruments and analytical platforms, a large number of metabolite signatures of complex diseases were identified and documented in the literature. Biologists' hardship in the face of this large amount of papers recorded metabolic signatures of experiments' results calls for an automated data repository...
August 22, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28968713/an-automated-tool-for-obtaining-qsar-ready-series-of-compounds-using-semantic-web-technologies
#11
Oriol López-Massaguer, Ferran Sanz, Manuel Pastor
Summary: We describe an application (Collector) for obtaining series of compounds annotated with bioactivity data, ready to be used for the development of quantitative structure-activity relationships (QSAR) models. The tool extracts data from the 'Open Pharmacological Space' (OPS) developed by the Open PHACTS project, using as input a valid name of the biological target. Collector uses the OPS ontologies for expanding the query using all known target synonyms and extracts compounds with bioactivity data against the target from multiple sources...
September 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28962670/analysis-and-visualization-of-disease-courses-in-a-semantically-enabled-cancer-registry
#12
Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis, Martin Boeker
BACKGROUND: Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cancer registries nowadays. However, the lack of a well-defined common semantic model is a problem when user-defined analyses and data linking to external resources are required. The objectives of this study are: (1) design of a semantic model for local cancer registries; (2) development of a semantically-enabled cancer registry based on this model; and (3) semantic exploitation of the cancer registry for analysing and visualising disease courses...
September 29, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28945577/analytic-an-active-learning-system-for-trajectory-classification
#13
Amilcar Soares Junior, Chiara Renso, Stan Matwin
The increasing availability and use of positioning devices has resulted in large volumes of trajectory data. However, semantic annotations for such data are typically added by domain experts, which is a time-consuming task. Machine-learning algorithms can help infer semantic annotations from trajectory data by learning from sets of labeled data. Specifically, active learning approaches can minimize the set of trajectories to be annotated while preserving good performance measures. The ANALYTiC web-based interactive tool visually guides users through this annotation process...
2017: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/28935617/the-adverse-drug-reactions-from-patient-reports-in-social-media-project-five-major-challenges-to-overcome-to-operationalize-analysis-and-efficiently-support-pharmacovigilance-process
#14
Cedric Bousquet, Badisse Dahamna, Sylvie Guillemin-Lanne, Stefan J Darmoni, Carole Faviez, Charles Huot, Sandrine Katsahian, Vincent Leroux, Suzanne Pereira, Christophe Richard, Stéphane Schück, Julien Souvignet, Agnès Lillo-Le Louët, Nathalie Texier
BACKGROUND: Adverse drug reactions (ADRs) are an important cause of morbidity and mortality. Classical Pharmacovigilance process is limited by underreporting which justifies the current interest in new knowledge sources such as social media. The Adverse Drug Reactions from Patient Reports in Social Media (ADR-PRISM) project aims to extract ADRs reported by patients in these media. We identified 5 major challenges to overcome to operationalize the analysis of patient posts: (1) variable quality of information on social media, (2) guarantee of data privacy, (3) response to pharmacovigilance expert expectations, (4) identification of relevant information within Web pages, and (5) robust and evolutive architecture...
September 21, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28931422/pibas-fedsparql-a-web-based-platform-for-integration-and-exploration-of-bioinformatics-datasets
#15
Marija Djokic-Petrovic, Vladimir Cvjetkovic, Jeremy Yang, Marko Zivanovic, David J Wild
BACKGROUND: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources...
September 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28929028/fish-ontology-framework-for-taxonomy-based-fish-recognition
#16
Najib M Ali, Haris A Khan, Amy Y-Hui Then, Chong Ving Ching, Manas Gaur, Sarinder Kaur Dhillon
Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval...
2017: PeerJ
https://www.readbyqxmd.com/read/28922135/learning-from-short-text-streams-with-topic-drifts
#17
Peipei Li, Lu He, Haiyan Wang, Xuegang Hu, Yuhong Zhang, Lei Li, Xindong Wu
Short text streams such as search snippets and micro blogs have been popular on the Web with the emergence of social media. Unlike traditional normal text streams, these data present the characteristics of short length, weak signal, high volume, high velocity, topic drift, etc. Short text stream classification is hence a very challenging and significant task. However, this challenge has received little attention from the research community. Therefore, a new feature extension approach is proposed for short text stream classification with the help of a large-scale semantic network obtained from a Web corpus...
September 18, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28883200/optimizing-a-query-by-transformation-and-expansion
#18
Katrin Glocker, Alexander Knurr, Julia Dieter, Friederike Dominick, Melanie Forche, Christian Koch, Analie Pascoe Pérez, Benjamin Roth, Frank Ückert
In the biomedical sector not only the amount of information produced and uploaded into the web is enormous, but also the number of sources where these data can be found. Clinicians and researchers spend huge amounts of time on trying to access this information and to filter the most important answers to a given question. As the formulation of these queries is crucial, automated query expansion is an effective tool to optimize a query and receive the best possible results. In this paper we introduce the concept of a workflow for an optimization of queries in the medical and biological sector by using a series of tools for expansion and transformation of the query...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28883194/light-weighted-automatic-import-of-standardized-ontologies-into-the-content-management-system-drupal
#19
Christoph Beger, Alexandr Uciteli, Heinrich Herre
The amount of ontologies, which are utilizable for widespread domains, is growing steadily. BioPortal alone, embraces over 500 published ontologies with nearly 8 million classes. In contrast, the vast informative content of these ontologies is only directly intelligible by experts. To overcome this deficiency it could be possible to represent ontologies as web portals, which does not require knowledge about ontologies and their semantics, but still carries as much information as possible to the end-user. Furthermore, the conception of a complex web portal is a sophisticated process...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28883193/expert2owl-a-methodology-for-pattern-based-ontology-development
#20
Kais Tahar, Jie Xu, Heinrich Herre
The formalization of expert knowledge enables a broad spectrum of applications employing ontologies as underlying technology. These include eLearning, Semantic Web and expert systems. However, the manual construction of such ontologies is time-consuming and thus expensive. Moreover, experts are often unfamiliar with the syntax and semantics of formal ontology languages such as OWL and usually have no experience in developing formal ontologies. To overcome these barriers, we developed a new method and tool, called Expert2OWL that provides efficient features to support the construction of OWL ontologies using GFO (General Formal Ontology) as a top-level ontology...
2017: Studies in Health Technology and Informatics
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