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https://www.readbyqxmd.com/read/28883200/optimizing-a-query-by-transformation-and-expansion
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28881973/biosses-a-semantic-sentence-similarity-estimation-system-for-the-biomedical-domain
#4
Gizem Sogancioglu, Hakime Öztürk, Arzucan Özgür
Motivation: The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881224/accent-modulates-access-to-word-meaning-evidence-for-a-speaker-model-account-of-spoken-word-recognition
#5
Zhenguang G Cai, Rebecca A Gilbert, Matthew H Davis, M Gareth Gaskell, Lauren Farrar, Sarah Adler, Jennifer M Rodd
Speech carries accent information relevant to determining the speaker's linguistic and social background. A series of web-based experiments demonstrate that accent cues can modulate access to word meaning. In Experiments 1-3, British participants were more likely to retrieve the American dominant meaning (e.g., hat meaning of "bonnet") in a word association task if they heard the words in an American than a British accent. In addition, results from a speeded semantic decision task (Experiment 4) and sentence comprehension task (Experiment 5) confirm that accent modulates on-line meaning retrieval such that comprehension of ambiguous words is easier when the relevant word meaning is dominant in the speaker's dialect...
September 4, 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/28873820/non-visually-performing-analytical-tasks-on-statistical-charts
#6
Tomas Murillo-Morales, Klaus Miesenberger
This article proposes a natural language-based approach to accessibility of charts. Formal underpinnings are used to semantically annotate the constituent elements of a vector graphic to support accessing and modifying the content by natural language queries in a web interface. A prototype which lets blind users perform a number of analytical activities on bar charts is introduced.
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28870259/rdfio-extending-semantic-mediawiki-for-interoperable-biomedical-data-management
#7
Samuel Lampa, Egon Willighagen, Pekka Kohonen, Ali King, Denny Vrandečić, Roland Grafström, Ola Spjuth
BACKGROUND: Biological sciences are characterised not only by an increasing amount but also the extreme complexity of its data. This stresses the need for efficient ways of integrating these data in a coherent description of biological systems. In many cases, biological data needs organization before integration. This is not seldom a collaborative effort, and it is thus important that tools for data integration support a collaborative way of working. Wiki systems with support for structured semantic data authoring, such as Semantic MediaWiki, provide a powerful solution for collaborative editing of data combined with machine-readability, so that data can be handled in an automated fashion in any downstream analyses...
September 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28838066/mouse-genome-informatics-mgi-resource-genetic-genomic-and-biological-knowledgebase-for-the-laboratory-mouse
#8
Janan T Eppig
The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI...
July 1, 2017: ILAR Journal
https://www.readbyqxmd.com/read/28828200/pathedex-uncovering-high-explanatory-visual-diagnostics-heuristics-using-digital-pathology-and-multiscale-gaze-data
#9
Dmitriy Shin, Mikhail Kovalenko, Ilker Ersoy, Yu Li, Donald Doll, Chi-Ren Shyu, Richard Hammer
BACKGROUND: Visual heuristics of pathology diagnosis is a largely unexplored area where reported studies only provided a qualitative insight into the subject. Uncovering and quantifying pathology visual and nonvisual diagnostic patterns have great potential to improve clinical outcomes and avoid diagnostic pitfalls. METHODS: Here, we present PathEdEx, an informatics computational framework that incorporates whole-slide digital pathology imaging with multiscale gaze-tracking technology to create web-based interactive pathology educational atlases and to datamine visual and nonvisual diagnostic heuristics...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28819351/a-systematic-analysis-of-term-reuse-and-term-overlap-across-biomedical-ontologies
#10
Maulik R Kamdar, Tania Tudorache, Mark A Musen
Reusing ontologies and their terms is a principle and best practice that most ontology development methodologies strongly encourage. Reuse comes with the promise to support the semantic interoperability and to reduce engineering costs. In this paper, we present a descriptive study of the current extent of term reuse and overlap among biomedical ontologies. We use the corpus of biomedical ontologies stored in the BioPortal repository, and analyze different types of reuse and overlap constructs. While we find an approximate term overlap between 25-31%, the term reuse is only <9%, with most ontologies reusing fewer than 5% of their terms from a small set of popular ontologies...
2017: Semantic Web
https://www.readbyqxmd.com/read/28791315/retracted-generating-personalized-web-search-using-semantic-context
#11
The Scientific World Journal
[This retracts the article DOI: 10.1155/2015/462782.].
2017: TheScientificWorldJournal
https://www.readbyqxmd.com/read/28766103/protocol-driven-decision-support-within-e-referral-systems-to-streamline-patient-consultation-triaging-and-referrals-from-primary-care-to-specialist-clinics
#12
Ehsan Maghsoud-Lou, Sean Christie, Samina Raza Abidi, Syed Sibte Raza Abidi
Patient referral is a protocol where the referring primary care physician refers the patient to a specialist for further treatment. The paper-based current referral process at times lead to communication and operational issues, resulting in either an unfulfilled referral request or an unnecessary referral request. Despite the availability of standardized referral protocols they are not readily applied because they are tedious and time-consuming, thus resulting in suboptimal referral requests. We present a semantic-web based Referral Knowledge Modeling and Execution Framework to computerize referral protocols, clinical guidelines and assessment tools in order to develop a computerized e-Referral system that offers protocol-based decision support to streamline and standardize the referral process...
September 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28764813/an-ontology-driven-tool-for-structured-data-acquisition-using-web-forms
#13
Rafael S Gonçalves, Samson W Tu, Csongor I Nyulas, Michael J Tierney, Mark A Musen
BACKGROUND: Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining eligibility for disability benefits) based on conclusions derived from acquired data (e.g., assessment of impaired motor function). To use data in these settings, we need it structured in a way that can be exploited by automated reasoning systems, for instance, in the Web Ontology Language (OWL); the de facto ontology language for the Web...
August 1, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28750030/minimally-inconsistent-reasoning-in-semantic-web
#14
Xiaowang Zhang
Reasoning with inconsistencies is an important issue for Semantic Web as imperfect information is unavoidable in real applications. For this, different paraconsistent approaches, due to their capacity to draw as nontrivial conclusions by tolerating inconsistencies, have been proposed to reason with inconsistent description logic knowledge bases. However, existing paraconsistent approaches are often criticized for being too skeptical. To this end, this paper presents a non-monotonic paraconsistent version of description logic reasoning, called minimally inconsistent reasoning, where inconsistencies tolerated in the reasoning are minimized so that more reasonable conclusions can be inferred...
2017: PloS One
https://www.readbyqxmd.com/read/28679928/semantic-web-reusable-learning-objects-personal-learning-networks-in-health-key-pieces-for-digital-health-literacy
#15
Stathis Th Konstantinidis, Heather Wharrad, Richard Windle, Panagiotis D Bamidis
The knowledge existing in the World Wide Web is exponentially expanding, while continuous advancements in health sciences contribute to the creation of new knowledge. There are a lot of efforts trying to identify how the social connectivity can endorse patients' empowerment, while other studies look at the identification and the quality of online materials. However, emphasis has not been put on the big picture of connecting the existing resources with the patients "new habits" of learning through their own Personal Learning Networks...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28679487/issues-associated-with-the-use-of-semantic-web-technology-in-knowledge-acquisition-for-clinical-decision-support-systems-systematic-review-of-the-literature
#16
Seyedjamal Zolhavarieh, David Parry, Quan Bai
BACKGROUND: Knowledge-based clinical decision support system (KB-CDSS) can be used to help practitioners make diagnostic decisions. KB-CDSS may use clinical knowledge obtained from a wide variety of sources to make decisions. However, knowledge acquisition is one of the well-known bottlenecks in KB-CDSSs, partly because of the enormous growth in health-related knowledge available and the difficulty in assessing the quality of this knowledge as well as identifying the "best" knowledge to use...
July 5, 2017: JMIR Medical Informatics
https://www.readbyqxmd.com/read/28650813/knowledge-based-topic-model-for-unsupervised-object-discovery-and-localization
#17
Zhenxing Niu, Gang Hua, Le Wang, Xinbo Gao
Unsupervised object discovery and localization is to discover some dominant object classes and localize all of object instances from a given image collection without any supervision. Previous work has attempted to tackle this problem with vanilla topic models such as Latent Dirichlet Allocation (LDA). However, in those methods no prior knowledge for the given image collection is exploited to facilitate object discovery. On the other hand, the topic models used in those methods suffer from the topic coherence issue-some inferred topics do not have clear meaning, which limits the final performance of object discovery...
June 22, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641261/robust-web-image-annotation-via-exploring-multi-facet-and-structural-knowledge
#18
Mengqiu Hu, Yang Yang, Fumin Shen, Luming Zhang, Heng Tao Shen, Xuelong Li
Driven by the rapid development of Internet and digital technologies, we have witnessed the explosive growth of Web images in recent years. Seeing that labels can reflect the semantic contents of the images, automatic image annotation, which can further facilitate the procedure of image semantic indexing, retrieval, and other image management tasks, has become one of the most crucial research directions in multimedia. Most of the existing annotation methods, heavily rely on well-labeled training data (expensive to collect) and/or single view of visual features (insufficient representative power)...
October 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28583204/building-a-semantic-web-based-metadata-repository-for-facilitating-detailed-clinical-modeling-in-cancer-genome-studies
#19
Deepak K Sharma, Harold R Solbrig, Cui Tao, Chunhua Weng, Christopher G Chute, Guoqian Jiang
BACKGROUND: Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains...
June 5, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28549446/-gnparser-a-powerful-parser-for-scientific-names-based-on-parsing-expression-grammar
#20
Dmitry Y Mozzherin, Alexander A Myltsev, David J Patterson
BACKGROUND: Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role...
May 26, 2017: BMC Bioinformatics
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