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Thematic series on biomedical ontologies in JBMS: challenges and new directions

Robert Hoehndorf, Melissa Haendel, Robert Stevens, Dietrich Rebholz-Schuhmann
2014 Journal of Biomedical Semantics  
The aim of the series is to disseminate the latest developments in research on biomedical ontologies and provide a venue for publishing newly developed ontologies, updates to existing ontologies as well  ...  Over the past 15 years, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, and to provide the corresponding infrastructure to maintain them  ...  Since they become an integral part of biological and biomedical research for the annotation of data -its integration, analysis, and visualization [1] -the demand for a place arises in which the scientific  ... 
doi:10.1186/2041-1480-5-15 pmid:24602198 pmcid:PMC4006457 fatcat:v5kignpyjrhxniirpbuxnylnsq

Evaluation of research in biomedical ontologies

R. Hoehndorf, M. Dumontier, G. V. Gkoutos
2012 Briefings in Bioinformatics  
To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated.  ...  We propose that results in applied ontology must be evaluated within their domain of application, based on some ontology-based task within the domain, and discuss quantitative measures which would facilitate  ...  integrative biomedical research.  ... 
doi:10.1093/bib/bbs053 pmid:22962340 pmcid:PMC3888109 fatcat:lyepy5en5vfpzgbq6uaaxr7aiu

Knowledge Representation and Ontologies [chapter]

Kin Wah Fung, Olivier Bodenreider
2012 Health Informatics Series  
The most popular ontology editor is Protégé, developed at the Stanford Center for Biomedical Informatics Research for two decades [18, 19].  ...  Ontologies have become important tools in biomedicine, supporting critical aspects of both health care and biomedical research, including clinical research [1] .  ...  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

Health-e-Child : An Integrated Biomedical Platform for Grid-Based Paediatric Applications [article]

Joerg Freund, Dorin Comaniciu, Yannis Ioannis, Peiya Liu, Richard McClatchey, Edwin Morley-Fletcher, Xavier Pennec, Giacomo Pongiglione, Xiang ZHOU
2006 arXiv   pre-print
The long-term goal of the project is to provide uninhibited access to universal biomedical knowledge repositories for personalised and preventive healthcare, large-scale information-based biomedical research  ...  There is a compelling demand for the integration and exploitation of heterogeneous biomedical information for improved clinical practice, medical research, and personalised healthcare across the EU.  ...  Acknowledgements The authors thank the European Commission and their institutes for support and particularly acknowledge the contribution to this paper of the following Health-e-Child consortium members  ... 
arXiv:cs/0603036v2 fatcat:2qbhyrzjwbg7xfdzmmynvtjya4

New Era of Developing and Using Ontologies for Microbiology Research and Diagnosis

Yu Lin
2012 Journal of Medical Microbiology & Diagnosis  
To facilitate integrative research in infectious diseases, a community-based Infectious Disease Ontology (IDO) has been developed [4] .  ...  The IDOBRU knowledge base is also integrated with other biomedical ontologies such as GO, IDO-core, and other specific IDO-core extensions.  ... 
doi:10.4172/2161-0703.1000e107 fatcat:redna4iutvac7hm65ihmaupx5e

Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
His research focuses on developing ontology-based approaches to integrate diverse information types for reasoning about biological systems.  ...  Shah is a research scientist at the Stanford Center for Biomedical Informatics group and member of the National Center for Biomedical Ontology.  ...  Acknowledgements This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1093/bib/bbm059 pmid:18077472 fatcat:z3orlk75yzherjf37i3nehqlmm

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

O. Bodenreider
2008 IMIA Yearbook of Medical Informatics  
Objectives To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support.  ...  Conclusions Ontologies play an important role in biomedical research through a variety of applications.  ...  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:10.1055/s-0038-1638585 fatcat:r7vz4bruq5fpxa5nhhgcxohd2e

Biomedical ontologies in action: role in knowledge management, data integration and decision support

O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support.  ...  Ontologies play an important role in biomedical research through a variety of applications.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
pmid:18660879 pmcid:PMC2592252 fatcat:axl74koixzbffmfi6m3txvlwqu

A Systems Approach to User Evaluation of Biomedical Ontologies

Maiga Gilbert, Ddembe Williams
2008 2008 First International Workshop on Ontologies in Interactive Systems  
The results indicate that it is sufficiently flexible for evaluating ontology based biomedical integrated systems, taking into account the conflicting needs of different users interested in accessing complex  ...  Biomedical ontologies integrate clinical and biological data so as to achieve interoperability between different sources [23] [16] [26] [18] [24].  ...  Ontology evaluation is a criterion based technical judgment for both the integrated and resulting ontologies [22] .  ... 
doi:10.1109/ontoract.2008.7 fatcat:nuhti36awbbozjcgq2b3q3yr5y

Selected papers from the 12th annual Bio-Ontologies meeting

Larisa N Soldatova, Phillip Lord, Susanna-Assunta Sansone, Susie M Stephens, Nigam H Shah
2010 Journal of Biomedical Semantics  
approach for semantic integration of heterogeneous data sources.  ...  Ontologies are used to annotate experimental data, to aid information retrieval, to enable integration of heterogeneous data sets, to drive literature mining, and to build electronic knowledge bases.  ...  This article has been published as part of Journal of Biomedical Semantics Volume 1 Supplement 1, 2010: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2009: Knowledge in Biology.  ... 
doi:10.1186/2041-1480-1-s1-i1 pmid:20626920 pmcid:PMC2903719 fatcat:rh62wecfifdnxgdrb2kx2v77xe

Accessing and integrating data and knowledge for biomedical research

A Burgun, O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
High-quality, integrated ontologies and knowledge bases serve as a source of prior knowledge used in combination with traditional data mining techniques and contribute to the development of more effective  ...  We analyzed the requirements for effective knowledge repositories and studied issues in the integration of biomedical knowledge.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
pmid:18660883 pmcid:PMC2553094 fatcat:buqnlvjixvfwdlblwug6hyajzy

Accessing and Integrating Data and Knowledge for Biomedical Research

O. Bodenreider, A. Burgun
2008 IMIA Yearbook of Medical Informatics  
High-quality, integrated ontologies and knowledge bases serve as a source of prior knowledge used in combination with traditional data mining techniques and contribute to the development of more effective  ...  We analyzed the requirements for effective knowledge repositories and studied issues in the integration of biomedical knowledge.  ...  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:10.1055/s-0038-1638588 fatcat:75nhlolnare4vfqehvoiowelqm

Building a European biomedical grid on cancer: the ACGT Integrated Project

M Tsiknakis, D Kafetzopoulos, G Potamias, A Analyti, K Marias, A Manganas
2006 Studies in Health Technology and Informatics  
The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and open source, enhanced by a set of interoperable  ...  This paper presents the needs and requirements that led to the formation of the ACGT (Advancing Clinico Genomic Trials) integrated project, its vision and methodological approaches of the project.  ...  Acknowledgements The authors wish to express their gratitude to the whole of the ACGT consortium for their contributions with various ideas on which the ACGT project was developed.  ... 
pmid:16823143 fatcat:y5z67zykjfeydiemgb6emr5oou

The open biomedical annotator

Clement Jonquet, Nigam H Shah, Mark A Musen
2009 Summit on translational bioinformatics  
Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval.  ...  This paper presents the Open Biomedical Annotator (OBA), an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata (www.bioontology.org  ...  Acknowledgments This work is supported by NIH grant U54 HG004028 in support of the National Center for Biomedical Ontology, one of the National Centers for Biomedical Computing.  ... 
pmid:21347171 pmcid:PMC3041576 fatcat:x67rj7ysrvd3dfrlagigsez5te

Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017)

Zhe He, Cui Tao, Jiang Bian, Rui Zhang, Jingshan Huang
2018 BMC Medical Informatics and Decision Making  
Acknowledgments The Guest Editors of this supplement would like to thank the authors and the reviewers for their scientific contribution and congratulate them on their high quality work.  ...  Ontology, semantic integration, and knowledge bases Ontologies are widely used in biological and biomedical research, where the past two decades have witnessed an explosion of ontology developments, from  ...  the development of the Gene Ontology (GO) in 1998 to national coordination efforts such as the Open Biomedical Ontologies (OBO) Foundry and the National Center for Biomedical Ontology.  ... 
doi:10.1186/s12911-018-0624-8 pmid:30066636 pmcid:PMC6069756 fatcat:qjkptie33fephlhestivneevg4
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