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This article is part of the supplement: Semantic e-Science in Biomedicine

Open Access Highly Accessed Methodology

Advancing translational research with the Semantic Web

Alan Ruttenberg1, Tim Clark2, William Bug3, Matthias Samwald4, Olivier Bodenreider5, Helen Chen6, Donald Doherty7, Kerstin Forsberg8, Yong Gao9, Vipul Kashyap10, June Kinoshita11, Joanne Luciano12, M Scott Marshall13, Chimezie Ogbuji14, Jonathan Rees15, Susie Stephens16, Gwendolyn T Wong11, Elizabeth Wu11, Davide Zaccagnini17, Tonya Hongsermeier10, Eric Neumann18, Ivan Herman19 and Kei-Hoi Cheung20*

Author Affiliations

1 Millennium Pharmaceuticals, Cambridge, MA, USA

2 Initiative in Innovative Computing, Harvard University, Cambridge, MA, USA

3 Laboratory for Bioimaging and Anatomical Informatics, Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA

4 Section on Medical Expert and Knowledge-Based Systems, Medical University of Vienna, Vienna, Austria

5 National Library of Medicine, Bethesda, MD, USA

6 Agfa Healthcare, Waterloo, Ontario, Canada

7 Brainstage Research, Pittsburgh, PA, USA

8 AstraZeneca, Mölndal, Sweden

9 MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA

10 Partners HealthCare System, Wellesley, MA, USA

11 Alzheimer Research Forum, Boston, MA, USA

12 Harvard Medical School, Boston, MA, USA

13 Integrative Bioinformatics Unit, University of Amsterdam, Amsterdam, The Netherlands

14 Cleveland Clinic Foundation, Cleveland, OH, USA

15 Science Commons, Cambridge, MA, USA

16 Oracle, Burlington, MA, USA

17 Language & Computing, Reston, VA, USA

18 Teranode Corporation, Seattle, WA, USA

19 World Wide Web Consortium (W3C)

20 Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA

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BMC Bioinformatics 2007, 8(Suppl 3):S2  doi:10.1186/1471-2105-8-S3-S2

Published: 9 May 2007

Abstract

Background

A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature.

Results

We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine.

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. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.