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Building biomedical web communities using a semantically aware content management system

S. Das, L. Girard, T. Green, L. Weitzman, A. Lewis-Bowen, T. Clark
2009 Briefings in Bioinformatics  
At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web.  ...  Her research interests include design of interoperable bioinformatics systems and analysis of complex biomedical data using statistical and data-mining techniques.  ...  The SCF is software for building scientific web communities based on a semantically enabled distribution of the open-source content management system Drupal (  ... 
doi:10.1093/bib/bbn052 pmid:19060302 fatcat:3iw7evisn5d2rhzboioneofqlu

Federating Distributed Social Data to Build an Interlinked Online Information Society

Alexandre Passant, Matthias Samwald, John G. Breslin, Stefan Decker
2009 IEEE Intelligent Systems  
Content types. • When data produced by online communities and personal information management systems is represented using shared, lightweight schemas (notably SIOC, now in wide use as demonstrated by  ...  be instantiated in any online community that shares and collectively builds information on the Web.  ... 
doi:10.1109/mis.2009.113 fatcat:elove4zi7fdafn46qpy2pjhugm

Semantic mashup of biomedical data

Kei-Hoi Cheung, Vipul Kashyap, Joanne S. Luciano, Huajun Chen, Yimin Wang, Susie Stephens
2008 Journal of Biomedical Informatics  
[18] explore the combination of Semantic Web and Service technologies including Business Process Management and Service Oriented Architecture to build an adaptive medical workflow system.  ...  In addition, the authors demonstrate how the Semantic Web can be used to annotate Web content for enabling semantic mashup.  ... 
doi:10.1016/j.jbi.2008.08.003 pmid:18703163 pmcid:PMC3742004 fatcat:utdd2zyj6zfklh5etnhe4gbwwq

Sharing Biomedical Learning Knowledge for Social Ambient Intelligence

Sabah Mohammed, Jinan Fiaidhi, Osama Mohammed
2009 Journal of Computers  
In this paper, we describe a Bio-SAmI system, which is a Biomedical learning system that is context-aware and responsive to mobile learners sharing information on a social network.  ...  Bio-SAmI is a Web 2.0 enabled system which employees Social Ambient Intelligence techniques.  ...  Indeed, these problems will be solved only if the biomedical system and the learners use a common meaning for metadata values.  ... 
doi:10.4304/jcp.4.9.905-912 fatcat:yurmsrwt4vejhm4jajivnysf6i

A model-driven approach for representing clinical archetypes for Semantic Web environments

Catalina Martínez-Costa, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis, José Alberto Maldonado
2009 Journal of Biomedical Informatics  
In this work, Semantic Web technologies are used to specify clinical archetypes for advanced EHR architectures.  ...  Moreover, a solution combining Semantic Web and Model-driven Engineering technologies is proposed to transform ADL into OWL for the CEN EN13606 EHR architecture.  ...  In fact, the archetype community is aware of the usefulness of Semantic Web technologies for classification.  ... 
doi:10.1016/j.jbi.2008.05.005 pmid:18590985 fatcat:vpkn63udjvepjlros3gmsxxwse

LexGrid: A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime

J. Pathak, H. R. Solbrig, J. D. Buntrock, T. M. Johnson, C. G. Chute
2009 JAMIA Journal of the American Medical Informatics Association  
Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings.  ...  this gap using a common terminology model called the LexGrid model.  ...  Introduction Semantic interoperability among health information systems is a longstanding aspiration of the health care community Consensus-based information models and biomedical ontologies can address  ... 
doi:10.1197/jamia.m3006 pmid:19261933 pmcid:PMC2732233 fatcat:stxhyrsxbrehxbbusihr7i6z7e

Semantic Sensor Web

Amit Sheth, Cory Henson, Satya S. Sahoo
2008 IEEE Internet Computing  
Several ongoing initiatives are helping to build relevant ontologies within various communities, such as the US National Institute of Standards and Technology (www.nist. gov/), the W3C, and the OGC.  ...  Semantic Sensor Web The SSW is a framework for providing enhanced meaning for sensor observations so as to enable situation awareness.  ... 
doi:10.1109/mic.2008.87 fatcat:witzvxsnzjcull3sq6anknm2ky

Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

Pradeep Kumar Sreenivasaiah, Do Han Kim
2010 Frontiers in Physiology  
driven biomedical research.  ...  We will mention their roles in integration of biological data and investigate some of the emerging design concepts and computational technologies that are likely to have a key role in the future of systems  ...  However, software development using off-the-shelf tools pose several of its own problems than building a system from scratch or scaling a system by re-using components built internally in an organization  ... 
doi:10.3389/fphys.2010.00147 pmid:21423387 pmcid:PMC3059952 fatcat:3e72pyby35cidlaa6jr5llemuq

Biomedical Web, Collections and Meta-Analysis Literature Applications [chapter]

Layla Michan, Israel Munoz-Velasco, Eduardo Alvarez, Lyssania Macias
2011 Biomedical Engineering - From Theory to Applications  
Introduction Cause and effect of the digital revolution is the production of a lot and different kinds of web tools, applications and resources that permit optimization the retrieve, management and analysis  ...  The scientific communities recognize the value of the information, required it as a condition to perform fundamental research.  ...  a computer system.  ... 
doi:10.5772/18133 fatcat:cjogvh6gindgbabo3aqh6qetyu

Semantic Web meets Integrative Biology: a survey

H. Chen, T. Yu, J. Y. Chen
2012 Briefings in Bioinformatics  
We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies.The SW enables scientists to share content beyond the boundaries of applications and  ...  In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis.  ...  In this system, agents automatically generate semantic annotations for PubMed literature abstracts in terms of Gene Ontology (GO), and effectively transform textual contents into SW contents.  ... 
doi:10.1093/bib/bbs014 pmid:22492191 fatcat:n5xm5kbc75ethlnfwfmgwdtnhq

The OpenScienceLink architecture for novel services exploiting open access data in the biomedical domain

Efstathios Karanastasis, Vassiliki Andronikou, Efthymios Chondrogiannis, George Tsatsaronis, Daniel Eisinger, Alina Petrova
2014 Proceedings of the 18th Panhellenic Conference on Informatics - PCI '14  
introducing a web based Platform which offers efficient and intelligent added-value applications and services for exploiting open access scientific information in the biomedical domain.  ...  data, organizing data journals, as well as for improved tools and techniques for bibliographic analysis and management of scientometrics.  ...  The Content and Data Management Adaptor (CDMA) is responsible for the integration of the data management system of GoPubMed within the OpenScienceLink Platform.  ... 
doi:10.1145/2645791.2645811 dblp:conf/pci/KaranastasisACTEP14 fatcat:7gchbpxdezagjh4abdtuumtatu

User-centered semantic harmonization: A case study

Chunhua Weng, John H. Gennari, Douglas B. Fridsma
2007 Journal of Biomedical Informatics  
The authors also compare BRIDG with related efforts to achieve semantic interoperability in healthcare, including UMLS, InterMed, the Semantic Web, and the Ontology for Biomedical Investigations initiative  ...  Methods such as ontology alignment or use of metadata neither scale nor fundamentally alleviate semantic heterogeneity among information sources.  ...  developers are aware of them and would like to use them [32] .  ... 
doi:10.1016/j.jbi.2007.03.004 pmid:17452021 fatcat:toyojd6ggvgbbpl4zc3wgj2pwe

Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective

Jonathan P. Bona, Fred W. Prior, Meredith N. Zozus, Mathias Brochhausen
2019 IMIA Yearbook of Medical Informatics  
Our aim is to clarify the representational differences between traditional data management and semantic-web-based data management by providing use cases of clinical data and clinical research data re-representation  ...  Objectives: There exists a communication gap between the biomedical informatics community on one side and the computer science/artificial intelligence community on the other side regarding the meaning  ...  Under this contract, the University of Arkansas is funded by Leidos Biomedical Research subcontract 16X011. Funding was also provided by U24CA215109 and 3U24CA215109-02S1.  ... 
doi:10.1055/s-0039-1677912 pmid:31419826 pmcid:PMC6697506 fatcat:o5pk74rqebhsfhhmt5aems2z2q

A Semantic-Based Approach for Managing Healthcare Big Data: A Survey

Rafat Hammad, Malek Barhoush, Bilal H. Abed-alguni, Saverio Maietta
2020 Journal of Healthcare Engineering  
In the recent few years, a large number of organizations and companies have shown enthusiasm for using semantic web technologies with healthcare big data to convert data into knowledge and intelligence  ...  Based on our literature review, we will discuss how different techniques, standards, and points of view created by the semantic web community can participate in addressing the challenges related to healthcare  ...  Current study 2020 is study reviews the state of the art of semantic web technologies in healthcare management systems.  ... 
doi:10.1155/2020/8865808 pmid:33489061 pmcid:PMC7787845 fatcat:gorgipqn6famhkeffmqzr4tacq

A Semantic Web for bioinformatics: goals, tools, systems, applications

Nicola Cannata, Michael Schröder, Roberto Marangoni, Paolo Romano
2008 BMC Bioinformatics  
The paper includes a proposal for a generic infrastructure for knowledge management on the Semantic Web that is based on two interrelated ontologies: Ontology Metadata Vocabulary and Semantic Directory  ...  Even though a specific formal language able to describe all the properties of biological systems has not yet been designed, some properties of formal languages can be very useful to describe and manage  ... 
doi:10.1186/1471-2105-9-s4-s1 pmid:18460170 pmcid:PMC2367628 fatcat:axiel3c56vgo5ajdw4uv6riz6q
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