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https://www.readbyqxmd.com/read/28298238/biofed-federated-query-processing-over-life-sciences-linked-open-data
#1
Ali Hasnain, Qaiser Mehmood, Syeda Sana E Zainab, Muhammad Saleem, Claude Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann
BACKGROUND: Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints...
March 15, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28283999/a-semantic-based-model-for-triage-patients-in-emergency-departments
#2
Guilherme Wunsch, Cristiano A da Costa, Rodrigo R Righi
Triage is a process performed in an emergency department that aims to sort patients according to their need for care. When performed speedily and correctly, this process can potentially increase the chances of survival for a patient with serious complications. This study aims to develop a computer model, called UbiTriagem, which supports the process of triage using the concepts of web semantics and ubiquitous computing focused on healthcare. For evaluating the proposal, we performed an analysis of scenario-driven triage based on previously determined ratings...
April 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28270198/large-scale-adverse-effects-related-to-treatment-evidence-standardization-laertes-an-open-scalable-system-for-linking-pharmacovigilance-evidence-sources-with-clinical-data
#3
(no author information available yet)
BACKGROUND: Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integrate multiple disparate evidence sources while making the evidence computable from a knowledge representation perspective (i.e., semantic enrichment). Existing frameworks suggest well-promising outcomes for such integration but employ a rather limited number of sources...
March 7, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28265499/exploring-biomedical-ontology-mappings-with-graph-theory-methods
#4
Simon Kocbek, Jin-Dong Kim
BACKGROUND: In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies...
2017: PeerJ
https://www.readbyqxmd.com/read/28257498/text-mining-for-improved-exposure-assessment
#5
Kristin Larsson, Simon Baker, Ilona Silins, Yufan Guo, Ulla Stenius, Anna Korhonen, Marika Berglund
Chemical exposure assessments are based on information collected via different methods, such as biomonitoring, personal monitoring, environmental monitoring and questionnaires. The vast amount of chemical-specific exposure information available from web-based databases, such as PubMed, is undoubtedly a great asset to the scientific community. However, manual retrieval of relevant published information is an extremely time consuming task and overviewing the data is nearly impossible. Here, we present the development of an automatic classifier for chemical exposure information...
2017: PloS One
https://www.readbyqxmd.com/read/28243197/computer-aided-experiment-planning-toward-causal-discovery-in-neuroscience
#6
Nicholas J Matiasz, Justin Wood, Wei Wang, Alcino J Silva, William Hsu
Computers help neuroscientists to analyze experimental results by automating the application of statistics; however, computer-aided experiment planning is far less common, due to a lack of similar quantitative formalisms for systematically assessing evidence and uncertainty. While ontologies and other Semantic Web resources help neuroscientists to assimilate required domain knowledge, experiment planning requires not only ontological but also epistemological (e.g., methodological) information regarding how knowledge was obtained...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28236811/neuropsychological-performance-changes-following-subthalamic-versus-pallidal-deep-brain-stimulation-in-parkinson-s-disease-a-systematic-review-and-metaanalysis
#7
Ahmed Elgebaly, Mohamed Elfil, Attia Attia, Mayar Magdy, Ahmed Negida
BACKGROUND: Studies comparing subthalamus (STN) and globus pallidus internus (GPi) deep brain stimulation (DBS) for the management of Parkinson's disease in terms of neuropsychological performance are scarce and heterogeneous. Therefore, we performed a systematic review and metaanalysis to compare neuropsychological outcomes following STN DBS versus GPi DBS. METHODS: A computer literature search of PubMed, the Web of Science, and Cochrane Central was conducted. Records were screened for eligible studies, and data were extracted and synthesized using Review Manager (v...
February 27, 2017: CNS Spectrums
https://www.readbyqxmd.com/read/28230725/towards-a-semantic-web-of-things-a-hybrid-semantic-annotation-extraction-and-reasoning-framework-for-cyber-physical-system
#8
Zhenyu Wu, Yuan Xu, Yunong Yang, Chunhong Zhang, Xinning Zhu, Yang Ji
Web of Things (WoT) facilitates the discovery and interoperability of Internet of Things (IoT) devices in a cyber-physical system (CPS). Moreover, a uniform knowledge representation of physical resources is quite necessary for further composition, collaboration, and decision-making process in CPS. Though several efforts have integrated semantics with WoT, such as knowledge engineering methods based on semantic sensor networks (SSN), it still could not represent the complex relationships between devices when dynamic composition and collaboration occur, and it totally depends on manual construction of a knowledge base with low scalability...
February 20, 2017: Sensors
https://www.readbyqxmd.com/read/28224131/tashkeela-novel-corpus-of-arabic-vocalized-texts-data-for-auto-diacritization-systems
#9
Taha Zerrouki, Amar Balla
Arabic diacritics are often missed in Arabic scripts. This feature is a handicap for new learner to read َArabic, text to speech conversion systems, reading and semantic analysis of Arabic texts. The automatic diacritization systems are the best solution to handle this issue. But such automation needs resources as diactritized texts to train and evaluate such systems. In this paper, we describe our corpus of Arabic diacritized texts. This corpus is called Tashkeela. It can be used as a linguistic resource tool for natural language processing such as automatic diacritics systems, dis-ambiguity mechanism, features and data extraction...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28214993/scaleus-semantic-web-services-integration-for-biomedical-applications
#10
Pedro Sernadela, Lorena González-Castro, José Luís Oliveira
In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web...
April 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28213144/modeling-and-validating-hl7-fhir-profiles-using-semantic-web-shape-expressions-shex
#11
Harold R Solbrig, Eric Prud'hommeaux, Grahame Grieve, Lloyd McKenzie, Joshua C Mandel, Deepak K Sharma, Guoqian Jiang
BACKGROUND: HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging open standard for the exchange of electronic healthcare information. FHIR resources are defined in a specialized modeling language. FHIR instances can currently be represented in either XML or JSON. The FHIR and Semantic Web communities are developing a third FHIR instance representation format in Resource Description Framework (RDF). Shape Expressions (ShEx), a formal RDF data constraint language, is a candidate for describing and validating the FHIR RDF representation...
February 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28203277/semantics-based-plausible-reasoning-to-extend-the-knowledge-coverage-of-medical-knowledge-bases-for-improved-clinical-decision-support
#12
Hossein Mohammadhassanzadeh, William Van Woensel, Samina Raza Abidi, Syed Sibte Raza Abidi
BACKGROUND: Capturing complete medical knowledge is challenging-often due to incomplete patient Electronic Health Records (EHR), but also because of valuable, tacit medical knowledge hidden away in physicians' experiences. To extend the coverage of incomplete medical knowledge-based systems beyond their deductive closure, and thus enhance their decision-support capabilities, we argue that innovative, multi-strategy reasoning approaches should be applied. In particular, plausible reasoning mechanisms apply patterns from human thought processes, such as generalization, similarity and interpolation, based on attributional, hierarchical, and relational knowledge...
2017: BioData Mining
https://www.readbyqxmd.com/read/28187413/dato-an-atlas-of-biological-databases-and-tools
#13
Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen
This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28155727/an-improved-method-for-functional-similarity-analysis-of-genes-based-on-gene-ontology
#14
Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu, Zhixia Teng
BACKGROUND: Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recent years, many gene functional similarity methods have been proposed based on the semantic similarity of GO terms. However, these leading approaches may make errorprone judgments especially when they measure the specificity of GO terms as well as the IC of a term set. Therefore, how to estimate the gene functional similarity reliably is still a challenging problem...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28151816/mobile-technology-in-the-perioperative-arena-rapid-evolution-and-future-disruption
#15
Brian S Rothman, Rajnish K Gupta, Matthew D McEvoy
Throughout the history of medicine, physicians have relied upon disruptive innovations and technologies to improve the quality of care delivered, patient outcomes, and patient satisfaction. The implementation of mobile technology in health care is quickly becoming the next disruptive technology. We first review the history of mobile technology over the past 3 decades, discuss the impact of hardware and software, explore the rapid expansion of applications (apps), and evaluate the adoption of mobile technology in health care...
March 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28122056/vigi4med-scraper-a-framework-for-web-forum-structured-data-extraction-and-semantic-representation
#16
Bissan Audeh, Michel Beigbeder, Antoine Zimmermann, Philippe Jaillon, Cédric Bousquet
The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource...
2017: PloS One
https://www.readbyqxmd.com/read/28120406/generalization-and-maintenance-of-treatment-gains-in-primary-progressive-aphasia-ppa-a-systematic-review
#17
REVIEW
Inês Cadório, Marisa Lousada, Paula Martins, Daniela Figueiredo
BACKGROUND: Cognitive-linguistic treatments and interventions targeting communication have been developed within the context of primary progressive aphasia (PPA), however knowledge about the scope of generalization and maintenance of therapy gains considering PPA subtypes remains scarce and awaits systematic investigation. AIMS: To analyse the effects of semantic therapy on generalization and maintenance of treatment outcomes in individuals with PPA, considering its different subtypes...
January 24, 2017: International Journal of Language & Communication Disorders
https://www.readbyqxmd.com/read/28114069/web-video-event-recognition-by-semantic-analysis-from-ubiquitous-documents
#18
Litao Yu, Yang Yang, Zi Huang, Peng Wang, Jingkuan Song, Heng Shen
In recent years, the task of event recognition from videos has attracted increasing interest in multimedia area. While most of the existing research was mainly focused on exploring visual cues to handle relatively small-granular events, it is difficult to directly analyse video content without any prior knowledge. Therefore, synthesizing both the visual and semantic analysis is a natural way for video event understanding. In this paper, we study the problem of web video event recognition, where web videos often describe largegranular events and carry limited textual information...
September 27, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28077170/prosodic-processing-post-traumatic-brain-injury-a-systematic-review
#19
Gabriela Ilie, Michael D Cusimano, Wenshan Li
BACKGROUND: Traumatic brain injury (TBI) survivors often report difficulties with understanding and producing paralinguistic cues, as well as understanding and producing basic communication tasks. However, a large range of communicative deficits in this population cannot be adequately explained by linguistic impairment. The review examines prosodic processing performance post-TBI, its relationship with injury severity, brain injury localization, recovery and co-occurring psychiatric or mental health issues post-TBI METHODS: A systematic review using several databases including MEDLINE, EMBASE, Cochrane, LLBA (Linguistics and Language Behaviour Abstract) and Web of Science (January 1980 to May 2015), as well as a manual search of the cited references of the selected articles and the search cited features of PubMed was performed...
January 4, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/28062448/ontologyx-a-suite-of-r-packages-for-working-with-ontological-data
#20
Daniel Greene, Sylvia Richardson, Ernest Turro
Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three packages which aim to simplify such procedures. The ontologyIndex package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies. ontologySimilarity and ontologyPlot extend ontologyIndex with functionality for straightforward visualization and semantic similarity calculations, including statistical routines...
January 5, 2017: Bioinformatics
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