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Knowledge Representation and Ontologies [chapter]

Kin Wah Fung, Olivier Bodenreider
2012 Health Informatics Series  
Formalisms and tools for knowledge representation Many ontologies use description logics for their representation.  ...  ., for visualization, reasoning services, support for specific data formats) and the recently-developed web version of Protégé supports the collaborative development of ontologies.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1007/978-1-84882-448-5_14 fatcat:r7e2fbulcrcddpxh7jo6lu77wa

Ontology-based representation of simulation models of physiology

Daniel L Rubin, David Grossman, Maxwell Neal, Daniel L Cook, James B Bassingthwaighte, Mark A Musen
2006 AMIA Annual Symposium Proceedings  
The ontology also provided a framework to construct a graphical representation of the model, providing a simpler visualization than the large set of mathematical equations.  ...  The ontology provided an explicit representation of the model, both its mathematical and anatomic content, abstracting and hiding much of the mathematical complexity.  ...  In order to visualize the cardiovascular model as a set of linked instances, we use the Protégé Diagram Widget [5] , which provides a graphical paradigm for creating, linking, and visualizing instances  ... 
pmid:17238424 pmcid:PMC1839612 fatcat:zqkchvddfbhehfjuvly6rr4ryu

Motivation and Organizational Principles for Anatomical Knowledge Representation: The Digital Anatomist Symbolic Knowledge Base

C. Rosse, J. L. Mejino, B. R. Modayur, R. Jakobovits, K. P. Hinshaw, J. F. Brinkley
1998 JAMIA Journal of the American Medical Informatics Association  
Conceived from an anatomical viewpoint, the ontology can be generalized and mapped to other biomedical domains and problem solving tasks that require anatomical knowledge.  ...  Conclusions: The ontology formulated for the thorax is extendible to microscopic and cellular levels, as well as to other body parts, in that its classes subsume essentially all anatomical entities that  ...  McCray, National Library of Medicine, for her advice and support throughout this project and for reviewing an early draft of the manuscript; Kraig Eno and Jeff Prothero, for implementing the Knowledge  ... 
doi:10.1136/jamia.1998.0050017 pmid:9452983 pmcid:PMC61273 fatcat:253mdfrlfjgzbhyl32iryhcctu

Knowledge Cartography and Social Network Representation: Application to Collaborative Platforms in Scientific Area

Michel Plantie, P Riccio
2010 2010 Sixth International Conference on Signal-Image Technology and Internet Based Systems  
In our proposal we attempt to capture the individual information and then build social network representations to build a group representation of knowledge, attracting and encouraging people to participate  ...  Here, researchers from different domains interact and exchange information using our platforms as the common ground involving new concepts, methods and services to encourage collaborative work for their  ...  In this paper we discuss and highlight our methods used for information processing and integration to get a new visualising method for knowledge representation [5] and ontology construction [6] .  ... 
doi:10.1109/sitis.2010.45 dblp:conf/sitis/PlantieR10 fatcat:zyi5mudskzhmrm4nyekylkqyny

A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers

Andrew J. Buckler, David Paik, Matt Ouellette, Jovanna Danagoulian, Gary Wernsing, Baris E. Suzek
2013 Journal of digital imaging  
With the availability of tools for automatic ontology-based annotation of datasets, coupled with image archives, and a means for batch selection and processing of image and clinical data, imaging will  ...  Specifically, we describe the semantic components of our system, QI-Bench, that are used to specify and support experimental activities for statistical validation in quantitative imaging  ...  Use of OWL facilitates harmonization of different knowledge representations, namely UML and OWL, into one form, and further allows us to leverage its broader knowledge representation capability.  ... 
doi:10.1007/s10278-013-9598-3 pmid:23546775 pmcid:PMC3705009 fatcat:nkllru5k7fgbhb4bawn6zbllpq

National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge

Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Sima Misra, Monte Westerfield, Michael Ashburner, Ida Sim, Christopher G. Chute, Margaret-Anne Storey, Barry Smith, John Day-Richter, Natalya F. Noy (+1 others)
2006 Omics  
, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution  ...  develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form.  ...  We wish to acknowledge and thank Amelia Ireland of the Eu-RUBIN ET AL.  ... 
doi:10.1089/omi.2006.10.185 pmid:16901225 fatcat:s6m4gcw645fwrhnkc4zky7bav4

Experiment, Theory, Representation: Robert Hooke's Material Models [chapter]

Matthew C. Hunter
2010 Boston Studies in the Philosophy of Science  
In bristling detail, molds flower into putrid bloom, crystals protrude like warts from mineral skins and, for the first time in history, cells are brought to the eyes of a general viewership.  ...  A product of Oxford's lively scientific community of the 1650s and a protégé of the chemist Robert Boyle, he possessed intimate knowledge of the "new sciences" of the seventeenth century and a particular  ...  Acknowledgments Thanks to Moti Feingold, Tarja Knuuttila and, especially, to Roman Frigg for comments on previous drafts of this essay.  ... 
doi:10.1007/978-90-481-3851-7_9 fatcat:gyqnhdnh7zflxcpj3vct5zt5si

VINSIA: Visual Navigator for Surgical Information Access

Lingyun Luo, James Rowbottom, John Craker, Rong Xu, Guo-Qiang Zhang
2013 Military medicine  
Our development of a graphical, anatomy-driven navigator called Visual Navigator for Surgical Information Access (VINSIA) fulfills the goal for providing evidence-based clinical decision support, specifically  ...  guidelines, literature, and medical libraries; and (c) an administrative content management interface allowing only an accredited, expert-level curator to edit and update the clinical content to ensure  ...  ) component of the National Institutes of Health and NIH roadmap for Medical Research.  ... 
doi:10.7205/milmed-d-12-00406 pmid:23820348 pmcid:PMC6154499 fatcat:ty3yq4zxwncozkb3rhsizmy62y

Visualization of Pain Severity Events in Clinical Records Using Semantic Structures

Clare T. Grasso, Anupam Joshi, Eliot Siegel
2016 2016 IEEE Tenth International Conference on Semantic Computing (ICSC)  
This paper describes a prototype system that performs ontology-based semantic search through clinical text to extract pain severity events, and then presents them in a visualization to monitor the progression  ...  and its date and time in order to provide the proper context of the event.  ...  ACKNOWLEDGMENT This work was supported in part by NSF Grant IIS-0910838 and by the Department of Defense through a supplement to IIP-0934364.  ... 
doi:10.1109/icsc.2016.53 dblp:conf/semco/GrassoJS16 fatcat:wscr3nffwvchvlh3b45jop4m2e

Ontological Primitives for Visual Knowledge [chapter]

Alexandre Lorenzatti, Mara Abel, Sandro Rama Fiorini, Ariane Kravczyk Bernardes, Claiton Marion dos Santos Scherer
2010 Lecture Notes in Computer Science  
In the last few years, we have analyzed the best alternatives for acquiring and processing visual knowledge with the goal of supporting problem solving.  ...  In this paper, we describe a representational approach that helps geologists in capturing and applying this kind of knowledge, in order to support software development applied to interpretation tasks in  ...  We focus this paper on the needs of representation primitives for capturing content from images and scenes in order to build domain ontologies that provide support to storing, indexing and processing visual  ... 
doi:10.1007/978-3-642-16138-4_1 fatcat:pcvnv5fg4fatnpm7yflotkimte

Using explicit ontologies in KBS development

G. van Heijst, A.Th. Schreiber, B.J. Wielinga
1997 International Journal of Human-Computer Studies  
This application ontology is then exploited to organize the knowledge acquisition process and to support computational design .  ...  To facilitate this , the article presents some principles for organizing a library of reusable ontological theories which can be configured into an application ontology .  ...  This process is supported by graphical visualization and by dialogue structuring . The tool is able to perform simple completeness checks .  ... 
doi:10.1006/ijhc.1996.0090 fatcat:m2mhkerylnbkvgd62swzqpjyki

Knowledge-supported graphical illustration of texts

K. Hartmann, S. Schlechtweg, R. Helbing, Th. Strothotte
2002 Proceedings of the Working Conference on Advanced Visual Interfaces - AVI '02  
linguistic and visual realizations for entities within the formal domain representation.  ...  Part-whole relations are considered to assign visual representations to elements of the formal domain representation.  ...  The first author appreciate the constant support of the Agi 3 le project from Prof. D. Rösner and the members of knowledge-based systems and document processing group.  ... 
doi:10.1145/1556262.1556310 dblp:conf/avi/HartmannSHS02 fatcat:rr764wdzlnav5bqdgefr4nq4ru

Medical Vocabulary, Terminological Resources and Information Coding in the Health Domain [chapter]

C. Duclos, A. Burgun, J. B. Lamy, P. Landais, J. M. Rodrigues, L. Soualmia, P. Zweigenbaum
2013 Health Informatics Series  
Terminological resources are specific representations of medical language for dedicated use in particular health domains.  ...  We also provide examples of the dedicated use of terminological resources, such as disease coding, the indexing of biomedical publications, reasoning in decision support systems and data entry into electronic  ...  Formal Concept Representation Various knowledge representation tools are available to support compositional approaches to concept representation.  ... 
doi:10.1007/978-2-8178-0478-1_2 fatcat:eertyjzbmvblrojubtmrvhyw2e

Ontologies in Biological Data Visualization

Sheelagh Carpendale, Min Chen, Daniel Evanko, Nils Gehlenborg, Carsten Gorg, Larry Hunter, Francis Rowland, Margaret-Anne Storey, Hendrik Strobelt
2014 IEEE Computer Graphics and Applications  
Ontologies in Biological Data Visualization I n computer science, an ontology is essentially a graph-based knowledge representation in which each node corresponds to a concept and each edge specifi es  ...  We have two ultimate goals: ■ Support ontology developers, data curators, and data analysts with advanced visualization techniques. ■ Stimulate new research programs for developing knowledge-assisted visualization  ...  For more information, see the "Exploring On tologies in Biological Visualization" sidebar.  ... 
doi:10.1109/mcg.2014.33 pmid:24808195 fatcat:mkgfjlp4k5hodfbffq36hwjnsi

Creating and Curating a Terminology for Radiology: Ontology Modeling and Analysis

Daniel L. Rubin
2007 Journal of digital imaging  
In this work, we demonstrate that the RadLex terminology can be translated into an ontology, a representation of terminologies that is both human-browsable and machineprocessable.  ...  We believe that adopting an ontology representation of RadLex will permit more widespread use of the terminology and make it easier to collect feedback from the community that will ultimately lead to improving  ...  ACKNOWLEDGMENT We wish to thank Curtis P. Langlotz, MD, PhD, and Beverly Collins, PhD, for their assistance and support with RadLex and for their outstanding efforts in creating this rich resource.  ... 
doi:10.1007/s10278-007-9073-0 pmid:17874267 pmcid:PMC3043845 fatcat:rw3apkekobfkzh5ysikh7zhwua
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