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Semantic web

M Britel, M Bourguignon, N Foray
PURPOSES: The term "radiosensitivity" appeared for the first time at the beginning of the 20th century, few years after the discovery of X-rays. Initially used by French and German radiologists, it illustrated the risk of radiation-induced (RI) skin reactions. From the 1950's, "radiosensitivity" was progressively found to describe other features of RI response such as RI cancers or cataracts. To date, such confusion may raise legal issues and complexify the message addressed to general public...
March 13, 2018: International Journal of Radiation Biology
Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange
In order to access and filter content of life-science databases, full text search is a widely applied query interface. But its high flexibility and intuitiveness is paid for with potentially imprecise and incomplete query results. To reduce this drawback, query assistance systems suggest those combinations of keywords with the highest potential to match most of the relevant data records. Widespread approaches are syntactic query corrections that avoid misspelling and support expansion of words by suffixes and prefixes...
March 12, 2018: PLoS Computational Biology
Feixiang Xu, Xinhui Liu, Wei Chen, Chen Zhou, Bingwei Cao
This paper proposes an ontology-based fault diagnosis method which overcomes the difficulty of understanding complex fault diagnosis knowledge of loaders and offers a universal approach for fault diagnosis of all loaders. This method contains the following components: (1) An ontology-based fault diagnosis model is proposed to achieve the integrating, sharing and reusing of fault diagnosis knowledge for loaders; (2) combined with ontology, CBR (case-based reasoning) is introduced to realize effective and accurate fault diagnoses following four steps (feature selection, case-retrieval, case-matching and case-updating); and (3) in order to cover the shortages of the CBR method due to the lack of concerned cases, ontology based RBR (rule-based reasoning) is put forward through building SWRL (Semantic Web Rule Language) rules...
February 28, 2018: Sensors
Maulik R Kamdar, Mark A Musen
Integrated approaches for pharmacology are required for the mechanism-based predictions of adverse drug reactions that manifest due to concomitant intake of multiple drugs. These approaches require the integration and analysis of biomedical data and knowledge from multiple, heterogeneous sources with varying schemas, entity notations, and formats. To tackle these integrative challenges, the Semantic Web community has published and linked several datasets in the Life Sciences Linked Open Data (LSLOD) cloud using established W3C standards...
April 2017: Proceedings of the International World-Wide Web Conference
Henry W Chen, Jingcheng Du, Hsing-Yi Song, Xiangyu Liu, Guoqian Jiang, Cui Tao
BACKGROUND: Today, there is an increasing need to centralize and standardize electronic health data within clinical research as the volume of data continues to balloon. Domain-specific common data elements (CDEs) are emerging as a standard approach to clinical research data capturing and reporting. Recent efforts to standardize clinical study CDEs have been of great benefit in facilitating data integration and data sharing. The importance of the temporal dimension of clinical research studies has been well recognized; however, very few studies have focused on the formal representation of temporal constraints and temporal relationships within clinical research data in the biomedical research community...
February 22, 2018: JMIR Medical Informatics
Wenquan Jin, Do Hyeun Kim
Recently, healthcare services can be delivered effectively to patients anytime and anywhere using e-Health systems. e-Health systems are developed through Information and Communication Technologies (ICT) that involve sensors, mobiles, and web-based applications for the delivery of healthcare services and information. Remote healthcare is an important purpose of the e-Health system. Usually, the eHealth system includes heterogeneous sensors from diverse manufacturers producing data in different formats. Device interoperability and data normalization is a challenging task that needs research attention...
February 20, 2018: Sensors
Shaker El-Sappagh, Daehan Kwak, Farman Ali, Kyung-Sup Kwak
BACKGROUND: Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this process and enhance its accuracy. The most important component of any CDSS is its knowledge base. This knowledge base can be formulated using ontologies. The formal description logic of ontology supports the inference of hidden knowledge. Building a complete, coherent, consistent, interoperable, and sharable ontology is a challenge...
February 6, 2018: Journal of Biomedical Semantics
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E Shooshan, Laritza Rodriguez, Kate Masterton, Dina Demner-Fushman
BACKGROUND: Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding)...
February 6, 2018: BMC Bioinformatics
Rebecca A Gilbert, Matthew H Davis, M Gareth Gaskell, Jennifer M Rodd
Research has shown that adults' lexical-semantic representations are surprisingly malleable. For instance, the interpretation of ambiguous words (e.g., bark) is influenced by experience such that recently encountered meanings become more readily available (Rodd et al., 2016, 2013). However, the mechanism underlying this word-meaning priming effect remains unclear, and competing accounts make different predictions about the extent to which information about word meanings that is gained within one modality (e...
February 1, 2018: Journal of Experimental Psychology. Learning, Memory, and Cognition
Martin Sudmanns, Dirk Tiede, Stefan Lang, Andrea Baraldi
The challenge of enabling syntactic and semantic interoperability for comprehensive and reproducible online processing of big Earth observation (EO) data is still unsolved. Supporting both types of interoperability is one of the requirements to efficiently extract valuable information from the large amount of available multi-temporal gridded data sets. The proposed system wraps world models, (semantic interoperability) into OGC Web Processing Services (syntactic interoperability) for semantic online analyses...
2018: International Journal of Digital Earth
Fred Hohman, Nathan Hodas, Duen Horng Chau
Deep learning is the driving force behind many recent technologies; however, deep neural networks are often viewed as "black-boxes" due to their internal complexity that is hard to understand. Little research focuses on helping people explore and understand the relationship between a user's data and the learned representations in deep learning models. We present our ongoing work, ShapeShop, an interactive system for visualizing and understanding what semantics a neural network model has learned. Built using standard web technologies, ShapeShop allows users to experiment with and compare deep learning models to help explore the robustness of image classifiers...
May 2017: Extended Abstracts on Human Factors in Computing Systems
Jean-Emmanuel Bibault, Eric Zapletal, Bastien Rance, Philippe Giraud, Anita Burgun
PURPOSE: Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources...
2018: PloS One
Nicolas Matentzoglu, James Malone, Chris Mungall, Robert Stevens
BACKGROUND: Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description reports. There appears to be, however, a high degree of variability in the content of these reports. Often, important details are omitted such that it is difficult to gain a sufficient understanding of the ontology, its content and method of creation...
January 18, 2018: Journal of Biomedical Semantics
Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A Overton, Edison Ong
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles...
January 12, 2018: Journal of Biomedical Semantics
Minji Kim, Mona Choi, Yoosik Youm
PURPOSE: As comprehensive nursing care service has gradually expanded, it has become necessary to explore the various opinions about it. The purpose of this study is to explore the large amount of text data regarding comprehensive nursing care service extracted from online news and social media by applying a semantic network analysis. METHODS: The web pages of the Korean Nurses Association (KNA) News, major daily newspapers, and Twitter were crawled by searching the keyword 'comprehensive nursing care service' using Python...
December 2017: Journal of Korean Academy of Nursing
Alexander Garcia, Federico Lopez, Leyla Garcia, Olga Giraldo, Victor Bucheli, Michel Dumontier
A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology...
2018: PeerJ
Miguel Ángel Rodríguez-García, Robert Hoehndorf
BACKGROUND: Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained...
January 5, 2018: BMC Bioinformatics
Marc Jamoulle, Melissa Resnick, Julien Grosjean, Ashwin Ittoo, Elena Cardillo, Robert Vander Stichele, Stefan Darmoni, Marc Vanmeerbeek
BACKGROUND: While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. OBJECTIVES: To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC...
December 15, 2017: European Journal of General Practice
Pedro Sernadela, José Luís Oliveira
Computational annotation of textual information has taken on an important role in knowledge extraction from the biomedical literature, since most of the relevant information from scientific findings is still maintained in text format. In this endeavour, annotation tools can assist in the identification of biomedical concepts and their relationships, providing faster reading and curation processes, with reduced costs. However, the separate usage of distinct annotation systems results in highly heterogeneous data, as it is difficult to efficiently combine and exchange this valuable asset...
January 1, 2017: Database: the Journal of Biological Databases and Curation
Tiffany J Callahan, William A Baumgartner, Michael Bada, Adrianne L Stefanski, Ignacio Tripodi, Elizabeth K White, Lawrence E Hunter
Our knowledge of the biological mechanisms underlying complex human disease is largely incomplete. While Semantic Web technologies, such as the Web Ontology Language (OWL), provide powerful techniques for representing existing knowledge, well-established OWL reasoners are unable to account for missing or uncertain knowledge. The application of inductive inference methods, like machine learning and network inference are vital for extending our current knowledge. Therefore, robust methods which facilitate inductive inference on rich OWL-encoded knowledge are needed...
2018: Pacific Symposium on Biocomputing
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