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III Cambridge Semantic Web Gatherings

March 13, 2007 - Cambridge - Massachusetts - USA map it


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This has been the third chat about the SemanticWeb at MIT in Cambridge. The idea is to get together people in the local area who are interested in and/or working in the Semantic Web. A typical form will be a few presentations of recent work or recent problems discovered, some moderated discussion in the round, and a large amount of unmoderated chat.

Demos

At the meeting two demos have been presented :

SWAN (Semantic Web Applications in Neuromedicine)

Tim Clark presented the SWAN project that is the project I am working on (ontology and application development) here in Boston.

The SWAN project (Semantic Web Applications in Neuromedicine) aims to develop a practical, common, semantically-structured, framework for scientific discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN project is the result of a collaboration between the Alzheimer Research Forum (Alzforum) and informaticians at Harvard University, Massachusetts General Hospital and IBM. The initial concept has been proposed in a talk at the W3C Semantic Web in Life Sciences workshop, October 2004 [1]. SWAN has since been developed through a pilot application and is currently in the development stage of its first production-quality application [2,3,4]. The ability to use SWAN as an integrator of other semantic web ontologies for life science has begun to be shown in several collaborative demonstrator projects [5,6,7] and is an element of current use-case development work in the W3C Health Care and Life Science Task Force [8].

The SWAN project has built on Alzforum’s successful ten-year history as a scientific web community and strong social network[9,10] (currently with over 4,000 registered members) to construct a semantically-structured network of hypotheses, claims, dialogue, publications and digital repositories. Rather than attempting to construct a logically coherent model of the known facts about AD, SWAN sets itself the goal to model the scientific discourse about AD and its supporting evidence in a rich way that is compatible with functioning of the current social network as a technology-mediated ecosystem.

In many formal models of knowledge acquisition in science, research proceeds in a cycle – from hypothesis development; through experiment and data collection; to interpretation and drawing of conclusions; to communicating results to other scientists; to assimilating, criticizing and synthesizing the communications of colleagues. These practice-theory-practice cycles are socially interconnected in an extremely rich and complex way in what has been termed the “knowledge ecosystem” of science.

Theoretically this “ecosystemic” approach derives from work in industrial knowledge management [11.12] and is also inspired by third generation activity-theory approaches to human-computer interaction such as [13]. Practically it is based on many experiences in constructing information systems to support rapidly-evolving science, in which social factors and the social frame of the system were seen to strongly interact with the technology and content, critically influencing its ultimate success [14]. This approach is naturalistic and materialistic, in that it emphasizes emphasizes social factors, that is, what scientists actually do, in communicating knowledge of science.

SWAN References

  1. Clark T and Kinoshita J.
    A pilot KB of biological pathways important in Alzheimer’s Disease.
    W3C Workshop on Semantic Web for Life Sciences, Cambridge, MA, USA, October 2004.
  2. Gao Y, Kinoshita J, Wu E, et al.
    SWAN: A Distributed Knowledge Infrastructure for Alzheimer Disease Research.
    J Web Semantics, 2006, 4(3).
  3. Wong GT, Gao Y, Wu E, et al.
    Developing SWAN, a shared knowledge base for Alzheimer's disease research.
    Abstracts, Society for Neuroscience 2006, Atlanta, GA.
  4. Kinoshita J and Strobel S.
    Alzheimer Research Forum: A Knowledge Base and e-Community for AD Research. In Alzheimer: 100 Years and Beyond, Research and Perspectives in Alzheimer’s Disease.
    Ed. Jucker M, Beyreuther K, Haass C, Nitsch R, Christen Y. Springer, Berlin, Heidelberg, New York, 2006, pp. 457-463.
  5. Lam YK, Marenco L, Clark T, et al.
    Semantic Web Meets e-Neuroscience: An RDF Use Case.
    Proceedings of International Workshop on Semantic e-Science, ASWC 2006. Beijing, China: Jilin University Press, 2006, pp. 158-170.
  6. Cheung KH, Lam YK, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong G, Liu N, Crasto C, Morse T, Stephens S.
    AlzPharm: A Light-Weight RDF Warehouse for Integrating Neurodegenerative Data.
    ISWC 2006, Athens, Georgia.
  7. Lam YK, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong G, Liu N, Crasto C, Morse T, Stephens S, Cheung KH (2007)
    ‘Semantic Web Meets e-Neuroscience’,
    BMC BioInformatics (In press).
  8. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH (2007)
    Advancing translational research with the Semantic Web.
    BMC Bioinformatics (in press).
  9. Kinoshita J and Clark T,
    “Alzforum: Towards an e-Science for Alzheimer Disease”,
    in Crasto C (ed.) Neuroinformatics. Humana Press (in press).
  10. Clark T and Kinoshita J.
    Alzforum and SWAN: The Present and Future of Scientific Web Communities.
    (submitted for publication Feb 2007).
  11. Davenport T and Prusak L,
    Information Ecology: Mastering the Information and Knowledge Environment.
    Oxford University Press, 1997.
  12. Brown JS and Duguid P.
    The Social Life of Information.
    Cambridge: Harvard Business Review, 2002.
  13. Nardi BA.
    Activity Theory and Human-Computer Interaction,
    in Nardi, B. (ed.) Context and Consciousness: Activity Theory and Human-Computer Interaction. Cambridge: MIT Press,1996.
  14. Ficenec D, Osborne M, Pradines J, Richards D, Felciano R, Cho R, Chen R, Liefeld T, Owen JJ, Ruttenberg A, Reich C, Horvath J, and Clark T (2003)
    ‘Computational Knowledge Integration in Biopharmaceutical Research’.
    Briefings in Bioinformatics, VoL 4(3), pp 260-278.