keyword
MENU ▼
Read by QxMD icon Read
search

Semantic web

keyword
https://www.readbyqxmd.com/read/29351341/labeling-for-big-data-in-radiation-oncology-the-radiation-oncology-structures-ontology
#1
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
https://www.readbyqxmd.com/read/29347969/miro-guidelines-for-minimum-information-for-the-reporting-of-an-ontology
#2
REVIEW
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
https://www.readbyqxmd.com/read/29329592/the-extensible-ontology-development-xod-principles-and-tool-implementation-to-support-ontology-interoperability
#3
REVIEW
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
https://www.readbyqxmd.com/read/29326411/-semantic-network-analysis-of-online-news-and-social-media-text-related-to-comprehensive-nursing-care-service
#4
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
https://www.readbyqxmd.com/read/29312824/biotea-semantics-for-pubmed-central
#5
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
https://www.readbyqxmd.com/read/29304741/inferring-ontology-graph-structures-using-owl-reasoning
#6
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
https://www.readbyqxmd.com/read/29243572/development-dissemination-and-applications-of-a-new-terminological-resource-the-q-code-taxonomy-for-professional-aspects-of-general-practice-family-medicine
#7
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
https://www.readbyqxmd.com/read/29220478/a-semantic-based-workflow-for-biomedical-literature-annotation
#8
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
https://www.readbyqxmd.com/read/29218876/owl-nets-transforming-owl-representations-for-improved-network-inference
#9
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
https://www.readbyqxmd.com/read/29214177/linked-registries-connecting-rare-diseases-patient-registries-through-a-semantic-web-layer
#10
Pedro Sernadela, Lorena González-Castro, Claudio Carta, Eelke van der Horst, Pedro Lopes, Rajaram Kaliyaperumal, Mark Thompson, Rachel Thompson, Núria Queralt-Rosinach, Estrella Lopez, Libby Wood, Agata Robertson, Claudia Lamanna, Mette Gilling, Michael Orth, Roxana Merino-Martinez, Manuel Posada, Domenica Taruscio, Hanns Lochmüller, Peter Robinson, Marco Roos, José Luís Oliveira
Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine. However, the growing number of disease-specific patient registries brings also new technical challenges. Usually, these systems are developed as closed data silos, with independent formats and models, lacking comprehensive mechanisms to enable data sharing. To tackle these challenges, we developed a Semantic Web based solution that allows connecting distributed and heterogeneous registries, enabling the federation of knowledge between multiple independent environments...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29202137/non-visual-web-browsing-beyond-web-accessibility
#11
I V Ramakrishnan, Vikas Ashok, Syed Masum Billah
People with vision impairments typically use screen readers to browse the Web. To facilitate non-visual browsing, web sites must be made accessible to screen readers, i.e., all the visible elements in the web site must be readable by the screen reader. But even if web sites are accessible, screen-reader users may not find them easy to use and/or easy to navigate. For example, they may not be able to locate the desired information without having to listen to a lot of irrelevant contents. These issues go beyond web accessibility and directly impact web usability...
July 2017: Universal Access in Human-Computer Interaction: Designing Novel Interactions: 11th International Conference, UAHCI 2017, Held As Part of HCI International 2017, Vancouver, BC, Canada, July 9-14, 2017, Proceedings. Part II
https://www.readbyqxmd.com/read/29186322/sapp-functional-genome-annotation-and-analysis-through-a-semantic-framework-using-fair-principles
#12
Jasper J Koehorst, Jesse C J van Dam, Edoardo Saccenti, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Summary: To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyse existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29186292/satori-a-system-for-ontology-guided-visual-exploration-of-biomedical-data-repositories
#13
Fritz Lekschas, Nils Gehlenborg
Motivation: The ever-increasing number of biomedical data sets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating data sets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find data sets of interest. Results: We developed SATORI -an integrative search and visual exploration interface for the exploration of biomedical data repositories...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29175431/a-cloud-based-framework-for-large-scale-traditional-chinese-medical-record-retrieval
#14
Lijun Liu, Li Liu, Xiaodong Fu, Qingsong Huang, Xianwen Zhang, Yin Zhang
INTRODUCTION: Electronic medical records are increasingly common in medical practice. The secondary use of medical records has become increasingly important. It relies on the ability to retrieve the complete information about desired patient populations. How to effectively and accurately retrieve relevant medical records from large- scale medical big data is becoming a big challenge. Therefore, we propose an efficient and robust framework based on cloud for large-scale Traditional Chinese Medical Records (TCMRs) retrieval...
November 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29111222/ssel-ade-a-semi-supervised-ensemble-learning-framework-for-extracting-adverse-drug-events-from-social-media
#15
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
#16
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
#17
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
#18
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
#19
(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
#20
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
keyword
keyword
59717
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"