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Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience

Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis Marenco, Perry Miller, Gordon Shepherd, Kei-Hoi Cheung
2010 Artificial Intelligence in Medicine  
This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite  ...  The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources.  ...  We thank the members of the W3C Health Care and Life Science Interest Group, the Science Commons/Neurocommons project and the developers of the Basic Formal Ontology for their feedback and cooperation.  ... 
doi:10.1016/j.artmed.2009.11.003 pmid:20006477 pmcid:PMC3131218 fatcat:opz7xzq4e5emzfjqrn6neozvty

A journey to Semantic Web query federation in the life sciences

Kei-Hoi Cheung, H Robert Frost, M Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke
2009 BMC Bioinformatics  
As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing.  ...  We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets.  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 10, 2009: Semantic Web Applications and Tools for Life Sciences, 2008.  ... 
doi:10.1186/1471-2105-10-s10-s10 pmid:19796394 pmcid:PMC2755818 fatcat:ovbiczh3wnajbpqba5byn3f4fq

Introduction to semantic e-Science in biomedicine

Huajun Chen, Yimin Wang, Zhaohui Wu
2007 BMC Bioinformatics  
This special issue is intended to give an introduction of the state-of-the-art of Semantic Web technologies and describe how such technologies would be used to build the e-Science infrastructure for biomedical  ...  The Semantic Web technologies provide enhanced capabilities that allow data and the meaning of the data to be shared and reused across application, enterprise, and community boundaries, better enabling  ...  Acknowledgements We thank all of the program committee members of SeS2006 for their dedication and efforts to peer review the manuscripts submitted by the attendees.  ... 
doi:10.1186/1471-2105-8-s3-s1 fatcat:ajgvbuqndjb55hk7uw3bqq6jda

Life sciences on the Semantic Web: the Neurocommons and beyond

A. Ruttenberg, J. A. Rees, M. Samwald, M. S. Marshall
2009 Briefings in Bioinformatics  
In this article, we discuss the use of Semantic Web technology for assembling and querying biomedical knowledge from multiple sources and disciplines.  ...  as in the form of inference and distributable query, offers a social and technological basis for assembling, integrating and making available biomedical knowledge at Web scale.  ...  Acknowledgements The early development of the knowledge base was done with participation of a number of members of the W3C Semantic Web Health Care and Life Sciences (HCLS) Interest Group.  ... 
doi:10.1093/bib/bbp004 pmid:19282504 fatcat:urt7vus27vhj7mwuawet5qdy4q

Semantic Web meets Integrative Biology: a survey

H. Chen, T. Yu, J. Y. Chen
2012 Briefings in Bioinformatics  
We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB  ...  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  ...  The work of the authors is funded by China National Science Foundation (NSFC61070156), and China national 863 program China Cloud Initiative.  ... 
doi:10.1093/bib/bbs014 pmid:22492191 fatcat:n5xm5kbc75ethlnfwfmgwdtnhq

Advancing translational research with the Semantic Web

Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano (+11 others)
2007 BMC Bioinformatics  
Conclusion: Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision.  ...  Results: We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers.  ...  This article has been published as part of BMC Bioinformatics Volume 8 Supplement 3, 2007: Semantic e-Science in Biomedicine.  ... 
doi:10.1186/1471-2105-8-s3-s2 pmid:17493285 pmcid:PMC1892099 fatcat:sbsqc4hplba77fvazmrkeam2iy

The semantic web in translational medicine: current applications and future directions

C. M. Machado, D. Rebholz-Schuhmann, A. T. Freitas, F. M. Couto
2013 Briefings in Bioinformatics  
In this survey, we present the results of our analysis of translational medicine solutions that follow a semantic web approach.  ...  We assessed these solutions in terms of their target medical use case; the resources covered to achieve their objectives; and their use of existing semantic web resources for the purposes of data sharing  ...  Acknowledgements The authors would like to thank Miguel Gabriel for drawing the clinical practice illustration in Figure 1 , Doctor Daniel Faria for his assistance in revising the final manuscript and  ... 
doi:10.1093/bib/bbt079 pmid:24197933 pmcid:PMC4293377 fatcat:pjvgleeqnnc5hdnohuyw4kk2jq

AlzPharm: integration of neurodegeneration data using RDF

Hugo YK Lam, Luis Marenco, Tim Clark, Yong Gao, June Kinoshita, Gordon Shepherd, Perry Miller, Elizabeth Wu, Gwendolyn T Wong, Nian Liu, Chiquito Crasto, Thomas Morse (+2 others)
2007 BMC Bioinformatics  
Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in  ...  We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine).  ...  This article has been published as part of BMC Bioinformatics Volume 8 Supplement 3, 2007: Semantic e-Science in Biomedicine.  ... 
doi:10.1186/1471-2105-8-s3-s4 pmid:17493287 pmcid:PMC1892101 fatcat:iot4qgjhnfe4tidgz43b23wkja

A Medical Informatics Perspective on Health Informatics 3.0

P. Ruch
2011 IMIA Yearbook of Medical Informatics  
SummaryTo summarize current advances of the so-called Web 3.0 and emerging trends of the semantic web.We provide a synopsis of the articles selected for the IMIA Yearbook 2011, from which we attempt to  ...  While the most salient challenge and obsessional target of the semantic web remains its ambition to simply interconnect all available information, it is interesting to observe the developments of complementary  ...  Acknowledgement I greatly acknowledge the support of Martina Hutter and of the reviewers in the selection process of the IMIA Yearbook.  ... 
doi:10.1055/s-0038-1638733 fatcat:ctspv55l3zdhvd4mfkvva45w6m

Informatics in neuroscience

L. French, P. Pavlidis
2007 Briefings in Bioinformatics  
The application of informatics to neuroscience goes far beyond 'traditional' bioinformatics modalities such as DNA sequences.  ...  The continuing development of standards for data exchange and interoperability, together with increasing awareness and acceptance of the importance of data sharing, are among the key efforts required to  ...  Acknowledgements The authors thank Jesse Gillis for input on computational neuroscience, and Bill Bug for suggestions on the manuscript.  ... 
doi:10.1093/bib/bbm047 pmid:17932081 fatcat:2jeejrqeczhyzb7yzcv7cigncm

Linked Data in Neuroscience: Applications, Benefits, and Challenges [article]

B Nolan Nichols, Satrajit S Ghosh, Tibor Auer, Thomas J Grabowskith, Camille Maumet, David Keator, Kilian Pohl, Jean-Baptiste Poline
2016 bioRxiv   pre-print
The complexity of achieving this goal in neuroscience, and biomedicine in general, poses many technical and sociological challenges.  ...  The fundamental goal of neuroscience is to understand the nervous system at all levels of description, from molecular components to behavior.  ...  Acknowledgements We thank James Brinkley, Rosemary Fama, Stephanie Sassoon, Edith Sullivan for their insightful comments on early versions of this manuscript.  ... 
doi:10.1101/053934 fatcat:fodyripevbbuhct232bacd5sfq

Moby and Moby 2: Creatures of the Deep (Web)

B. P. Vandervalk, E. L. McCarthy, M. D. Wilkinson
2009 Briefings in Bioinformatics  
Here we examine 'The State of the Union' for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several  ...  Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare.  ...  The vision of the Semantic Web is to build a network of interconnected documents that can easily and unambiguously be processed by programs; this new web will be analogous to the network of human-readable  ... 
doi:10.1093/bib/bbn051 pmid:19151099 fatcat:giwou4xiurd6ratsqiqiczex7i

A practical approach for microscopy imaging data management (MIDM) in neuroscience

Shenglan Zhang, Xufei Qian, A. Gupta, M.E. Martone
15th International Conference on Scientific and Statistical Database Management, 2003.  
Current data management approaches can easily handle the relatively simple requirements for molecular biology research but not the more varied and sophisticated microscopy imaging data in neuroscience  ...  This paper describes the MIDM architecture and data mode in MIDM.  ...  the web access of MIDM.  ... 
doi:10.1109/ssdm.2003.1214986 dblp:conf/ssdbm/ZhangQGM03 fatcat:ah34xq77wbanjfr76udm4bufyy

Knowledge-based integration of neuroscience data sources

A. Gupta, B. Ludascher, M.E. Martone
Proceedings. 12th International Conference on Scientific and Statistica Database Management  
The need for information integration is paramount in many biological disciplines, because of the large heterogeneity in both the types of data involved and in the diversity of approaches (physiological  ...  The semantic integration of the disparate local data sources employs F-logic as a data and knowledge representation and reasoning formalism.  ...  semantics (or [LHL + 98] for a gentle introduction with a focus on the management of semistructured data and querying the Web).  ... 
doi:10.1109/ssdm.2000.869777 dblp:conf/ssdbm/GuptaLM00 fatcat:phmhayeodzbk5ab2ikcqekax2m

Acoustic source identification in an enclosed space using the inverse phased beam tracing at medium frequencies

Jeong‐Guon Ih, Cheol‐Ho Jeong
2008 Journal of the Acoustical Society of America  
identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate  ...  and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the  ...  The optimization is very easy using a web-based software. 6:20 2pAAc9. A systematic review on the influence of noise on patients' sleep in the Intensive Care Units.  ... 
doi:10.1121/1.2933749 fatcat:xiro7xkminfl5o3psp2ejziawq
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