HCLSIG/Project Ideas/VisualWebSemanticWeb

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Visual Web Meets Semantic Web

There is a growing community interest in applying Semantic Web and Web 2.0 technologies in health care and life sciences areas including the Health Care and Life Sciences Interest Group (HCLSIG ; http://www.w3.org/2001/sw/hcls/) and Medicine 2.0 (http://www.medicine20congress.com/). This has motivated us to explore how to intersect these two sets of technologies in the context of the HCLS Knowledge Base (KB). We have identified the following intersecting areas:

  • Wikinomics. As the Wiki technology has gained momentum in biosciences (e.g., Gene Wiki [1] and WikiProtein [2]), we plan to use Semantic Wiki technologies (e.g., DBPedia and Semantic MediaWiki) and the ontologies stored in the HCLS KB to create Wiki Neuron. This project leverages our previous effort of converting SenseLab databases into OWL ontologies (which are part of the HCLS KB). In addition, we have built a Web application called "Entrez Neuron" that provides a visual interface (built using Ajax) allowing the end-user to issue integrated queries against a collection of ontologies (including those in the HCLS KB) without the need to learn SPARQL or other RDF/OWL query languages. If Entrez Gene could be used to build Wiki Gene, we believe that our experience in building Entrez Neuron can help us create Wiki Neuron. We also plan to link Wiki Neuron to other bio-Wiki’s (e.g., WikiProtein and Wiki Gene).
  • 3D Web. We have begun exploring 3D Web technologies in the 3D visualization of ontologies. As a pilot study, we have tested and used Silverlight (http://silverlight.net/) in creating a prototype 3D ontology visualization using some of the ontologies accessed by Entrez Neuron. To expand this effort, we will apply 3D ontology visualization techniques to the HCLS KB.
  • Virtual World. In relation to 3D Web, 3D virtual worlds such as Second Life (http://secondlife.com/) and Twinity (http://www.twinity.com/) have emerged on the Web. There is a potential of 3D virtual worlds in medical and health education [3]. In one example, a virtual world such as Second Life has been used to simulate molecule docking (http://usefulchem.blogspot.com/2007/06/molecule-docking-in-second-life.html). In addition, there has been use of Second Life in displaying descriptions of individuals and classes from OWL DL ontologies [4]. We will explore the combination of virtual worlds and HCLS KB in HCLS research and education.


1. Huss JW 3rd, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI. (2008) A gene wiki for community annotation of gene function. PLoS Biol. 6(7):e175.

2. Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A. (2008). Calling on a million minds for community annotation in WikiProteins. Genome Biol. 2008;9(5):R89

3. Boulos MN, Hetherington L, Wheeler S. Second Life: an overview of the potential of 3-D virtual worlds in medical and health education. Health Info Libr J. 2007 Dec;24(4):233-45.

4. http://www.aueb.gr/users/ion/docs/ecai2008_naturalowl.pdf


  • Kei Cheung
  • Matthias Samwald
  • Huajun Chen
  • Maged N Kamel Boulos
  • Luis Marenco

Please add your name if you are interested. Suggestions are welcome.