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Semantic web

Sujoy Roy, Brandon C Curry, Behrouz Madahian, Ramin Homayouni
BACKGROUND: The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs. RESULTS: For approximately 900 human miRNAs indexed in miRBase, text documents were created by concatenating titles and abstracts of MEDLINE citations which refer to the miRNAs...
October 6, 2016: BMC Bioinformatics
Arash Shaban-Nejad, Maxime Lavigne, Anya Okhmatovskaia, David L Buckeridge
Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e...
October 17, 2016: Annals of the New York Academy of Sciences
Nadine Tix, Paul Gießler, Ursula Ohnesorge-Radtke, Cord Spreckelsen
BACKGROUND: The Semantically Annotated Media (SAM) project aims to provide a flexible platform for searching, browsing, and indexing medical learning objects (MLOs) based on a semantic network derived from established classification systems. Primarily, SAM supports the Aachen emedia skills lab, but SAM is ready for indexing distributed content and the Simple Knowledge Organizing System standard provides a means for easily upgrading or even exchanging SAM's semantic network. There is a lack of research addressing the usability of MLO indexes or search portals like SAM and the user behavior with such platforms...
November 11, 2015: JMIR Med Educ
Guillermo Leale, Ariel Baya, Diego Milone, Pablo Granitto, Georgina Stegmayer
Characterizing genes with semantic information is an important process regarding the description of gene products. In spite that complete genomes of many organisms have been already sequenced, the biological functions of all of their genes are still unknown. Since experimentally studying the functions of those genes, one by one, would be unfeasible, new computational methods for gene functions inference are needed. We present here a novel computational approach for inferring biological function for a set of genes with previously unknown function, given a set of genes with well-known information...
October 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Wei Chen, Xiayu Xia, Nan Song, Ying Wang, Hua Zhu, Wei Deng, Qi Kong, Xianmin Pan, Chuan Qin
BACKGROUND: Mouse has been extensively used as a tool for investigating the onset and development of human neurological disorders. As a first step to construct a transgenic mouse model of human brain lesions, it is of fundamental importance to clarify the similarity and divergence of genetic background between non-diseased human and mouse brain tissues. METHODS: We systematically compared, based on large scale integrated microarray data, the transcriptomes of three anatomically distinct brain regions; prefrontal cortex (PFC), hippocampus (HIP) and striatum (STR), across human and mouse...
2016: PloS One
Litao Yu, Yang Yang, Zi Huang, Peng Wang, Jingkuan Song, Heng Tao 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 analyze 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 large-granular events and carry limited textual information...
December 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel Peitsch, Juliane Fluck
Network-based approaches have become extremely important in systems biology to achieve a better understanding of biological mechanisms. For network representation, the Biological Expression Language (BEL) is well designed to collate findings from the scientific literature into biological network models. To facilitate encoding and biocuration of such findings in BEL, a BEL Information Extraction Workflow (BELIEF) was developed. BELIEF provides a web-based curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks...
2016: Database: the Journal of Biological Databases and Curation
Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E Lewis, Mark P Schildhauer, Ramona L Walls, Christopher J Mungall
BACKGROUND: The Environment Ontology (ENVO; ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description...
2016: Journal of Biomedical Semantics
Guiguang Ding, Yuchen Guo, Jile Zhou, Yue Gao
By transforming data into binary representation, i.e., Hashing, we can perform high-speed search with low storage cost, and thus Hashing has collected increasing research interest in the recent years. Recently, how to generate Hashcode for multimodal data (e.g., images with textual tags, documents with photos, etc) for large-scale cross-modality search (e.g., searching semantically related images in database for a document query) is an important research issue because of the fast growth of multimodal data in the Web...
September 8, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Michel Dumontier, Alasdair J G Gray, M Scott Marshall, Vladimir Alexiev, Peter Ansell, Gary Bader, Joachim Baran, Jerven T Bolleman, Alison Callahan, José Cruz-Toledo, Pascale Gaudet, Erich A Gombocz, Alejandra N Gonzalez-Beltran, Paul Groth, Melissa Haendel, Maori Ito, Simon Jupp, Nick Juty, Toshiaki Katayama, Norio Kobayashi, Kalpana Krishnaswami, Camille Laibe, Nicolas Le Novère, Simon Lin, James Malone, Michael Miller, Christopher J Mungall, Laurens Rietveld, Sarala M Wimalaratne, Atsuko Yamaguchi
Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets...
2016: PeerJ
Jiajie Peng, Hongxiang Li, Yongzhuang Liu, Liran Juan, Qinghua Jiang, Yadong Wang, Jin Chen
BACKGROUND: The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs...
2016: BMC Genomics
Marco Schweitzer, Alexander Hoerbst
Electronic Health Records (EHRs) play a crucial role in healthcare today. Considering a data-centric view, EHRs are very advanced as they provide and share healthcare data in a cross-institutional and patient-centered way adhering to high syntactic and semantic interoperability. However, the EHR functionalities available for the end users are rare and hence often limited to basic document query functions. Future EHR use necessitates the ability to let the users define their needed data according to a certain situation and how this data should be processed...
2016: Studies in Health Technology and Informatics
Samina Raza Abidi, Jafna Cox, Ashraf Abusharekh, Nima Hashemian, Syed Sibte Raza Abidi
Atrial Fibrillation (AF) is the most common cardiac arrhythmia. Generally, the therapeutic options for managing AF include the use of anticoagulant drugs that prevent the coagulation of blood. New Oral Anticoagulants (NOACs) are not optimally prescribed to patients, despite their efficacy. In Canada, NOAC medications are not directly available to patients who belong to provincial benefits programs, rather a NOAC special authorization process establishes the eligibility of a patient to receive a NOAC and be paid by the provincial Pharmacare program...
2016: Studies in Health Technology and Informatics
Yassine Lassoued, Léa Deleris
In this paper we describe a semantic approach for grouping medical terms into a hierarchy of concepts based on the UMLS meta-thesaurus. The context of this work is Medical Recap, a Web system that automatically extracts risk information from PubMed abstracts, and then aggregates this knowledge into dependence graphs or Bayesian networks.
2016: Studies in Health Technology and Informatics
Wasif Baig, Samina Abidi, Syed Sibte Raza Abidi
Behavior change approaches aim to assist patients in achieving self-efficacy in managing their condition. Social cognitive theory (SCT) stipulates self-efficacy as a central element to behavior change and provides constructs to achieve self-efficacy guided by person-specific action plans. In our work, to administer behaviour change in patient with chronic conditions, our approach entails the computerization of SCT-based self-efficacy constructs in order to generate personalized action plans that are suitable to an individual's current care scenario...
2016: Studies in Health Technology and Informatics
Nelia Lasierra, Marco Schweitzer, Thilo Gorfer, Ioan Toma, Alexander Hoerbst
In order to facilitate and increase the usability of Electronic Health Records (EHRs) for healthcare professional's daily work, we have designed a system that enables functional and flexible EHR access, based on the execution of clinical workflows and the composition of Semantic Web Services (SWS). The backbone of this system is based on an ontology. In this paper we present the strategy that we have followed for its design, and an overview of the resulting model. The designed ontology enables to model patient-centred clinical EHR workflows, the involved sequence of tasks and its associated functionality and managed clinical data...
2016: Studies in Health Technology and Informatics
Gaoussou Camara, Al Hassim Diallo, Moussa Lo, Jacques-Noël Tendeng, Seynabou Lo
In Senegal, great amounts of data are daily generated by medical activities such as consultation, hospitalization, blood test, x-ray, birth, death, etc. These data are still recorded in register, printed images, audios and movies which are manually processed. However, some medical organizations have their own software for non-standardized patient record management, appointment, wages, etc. without any possibility of sharing these data or communicating with other medical structures. This leads to lots of limitations in reusing or sharing these data because of their possible structural and semantic heterogeneity...
2016: Studies in Health Technology and Informatics
Chen Liang, Jingchun Sun, Cui Tao
Despite ongoing progress towards treating mental illness, there remain significant difficulties in selecting probable candidate drugs from the existing database. We describe an ontology - oriented approach aims to represent the nexus between genes, drugs, phenotypes, symptoms, and diseases from multiple information sources. Along with this approach, we report a case study in which we attempted to explore the candidate drugs that effective for both bipolar disorder and epilepsy. We constructed an ontology that incorporates the knowledge between the two diseases and performed semantic reasoning task on the ontology...
2016: AMIA Summits on Translational Science Proceedings
Afef Samet Ellouze, Rafik Bouaziz, Hanen Ghorbel
PURPOSE: Integrating semantic dimension into clinical archetypes is necessary once modeling medical records. First, it enables semantic interoperability and, it offers applying semantic activities on clinical data and provides a higher design quality of Electronic Medical Record (EMR) systems. However, to obtain these advantages, designers need to use archetypes that cover semantic features of clinical concepts involved in their specific applications. In fact, most of archetypes filed within open repositories are expressed in the Archetype Definition Language (ALD) which allows defining only the syntactic structure of clinical concepts weakening semantic activities on the EMR content in the semantic web environment...
August 24, 2016: Journal of Biomedical Informatics
Colin Bird, Simon J Coles, Jeremy G Frey
In this paper we take a historical view of e-Science and e-Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21(st) Century. We cover our research on aspects of the representation of chemical information in the context of the world wide web (WWW) and its semantic enhancement (the Semantic Web) and illustrate this with the example of the representation of quantities and units within the Semantic Web...
September 2015: Molecular Informatics
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