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Semantic Disclosure in an e-Science Environment

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Semantic e-Science

Part of the book series: Annals of Information Systems ((AOIS,volume 11))

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Abstract

The Virtual Laboratory for e-Science (VL-e) project serves as a backdrop for the ideas described in this chapter. VL-e is a project with academic and industrial partners where e-science has been applied to several domains of scientific research. Adaptive Information Disclosure (AID), a subprogram within VL-e, is a multi-disciplinary group that concentrates expertise in information extraction, machine learning, and Semantic Web – a powerful combination of technologies that can be used to extract and store knowledge in a Semantic Web framework. In this chapter, the authors explain what “semantic disclosure” means and how it is essential to knowledge sharing in e-Science. The authors describe several Semantic Web applications and how they were built using components of the AIDA Toolkit (AID Application Toolkit). The lessons learned and the future of e-Science are also discussed.

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Notes

  1. 1.

    In the case of semantic disclosure, the subject could identify a data or service resource in order to disclose something about it, such as its dc:creator (“dc” from the Dublin Core standard, see http://dublincore.org/documents/dces/).

  2. 2.

    http://linkeddata.org/

  3. 3.

    David Shotton, University of Oxford.

  4. 4.

    http://www.w3.org/2001/sw/hcls/

  5. 5.

    http://www.w3.org/2004/07/swls-ws.html

  6. 6.

    http://www.vl-e.nl

  7. 7.

    http://adaptivedisclosure.org/

  8. 8.

    Sesame and related RDF software is available from http://openrdf.org

  9. 9.

    http://www.few.vu.nl/∼wrvhage/oaei2007/food.html

  10. 10.

    http://www.extjs.com/

  11. 11.

    http://www.atoapps.nl/foodinformatics/NewsItem.asp?NID=18

  12. 12.

    http://www.science.uva.nl/∼silvia/vlfmri

  13. 13.

    http://www.ncbi.nlm.nih.gov/pubmed/

  14. 14.

    http://www.mygrid.org.uk/tools/taverna/

  15. 15.

    http://www.myExperiment.org

  16. 16.

    Sesame supports RDF reasoning for RDF-Schema repositories, not for RDF repositories.

  17. 17.

    http://virtuoso.openlinksw.com/

  18. 18.

    The examples here are a simplified version of SeRQL; for complete SeRQL examples including namespaces, see http://www.adaptivedisclosure.org/aida/workflows/bioaid-serql-query-examples

  19. 19.

    http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=17540846

  20. 20.

    http://www.cs.vu.nl/das3/

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Acknowledgments

This work was carried out in the context of the Virtual Laboratory for e-Science project (http://www.vl-e.nl). This project is supported by a BSIK grant from the Dutch Ministry of Education, Culture, and Science (OC&W) and is part of the ICT innovation program of the Ministry of Economic Affairs (EZ). Special thanks go to Bob Herzberger, who made the VL-e project a reality and to Pieter Adriaans for creating and leading AID. We also thank Edgar Meij, Sophia Katrenko, Willem van Hage, Kostas Krommydas, Machiel Jansen, Marten de Rijke, Guus Schreiber, and Frank van Harmelen. Our VL-e Food Informatics partners: Jeen Broekstra, Fred van de Brug, Chide Groenouwe, Lars Hulzebos, Nicole Koenderink, Dirk Out, Hans Peters, Hajo Rijgersberg, Jan Top. Other VL-e colleagues: Piter de Boer, Silvia Olabarriaga, Adam Belloum, Spiros Koulouzis, Kasper van den Berg, Kamel Boulebiar, Tristan Glatard. Martijn Schuemie, Barend Mons, Erik van Mulligen (Erasmus University and Knew Co.). Simone Louisse for careful reading of this document. Thanks to Alan Ruttenberg and Jonathan Rees of Science Commons for supplying the Huntington’s corpus. We appreciate the support of many colleagues at NBIC, theW3C HCLS IG, myGrid, myExperiment, and OMII-UK.

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Authors and Affiliations

  1. Informatics Institute, University of Amsterdam, Kruislaan 403, Amsterdam, The Netherlands

    M. Scott Marshall

  2. Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands

    Marco Roos, Edgar Meij, Sophia Katrenko & Pieter W. Adriaans

  3. Business Informatics, Faculty of Sciences, Vrije Universiteit, Amsterdam, 1081HV, The Netherlands

    Willem Robert van Hage

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Correspondence to M. Scott Marshall .

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Editors and Affiliations

  1. College of Computer Science, Zhejiang University, Zheda Road 38, Hangzhou, 310058, China, People's Republic

    Huajun Chen

  2. Drug Discovery Pte Ltd., Lilly Singapore Centre for, Biomedical Grove 8A, Singapore, 138648, Singapore

    Yimin Wang

  3. Center for Medical Informatics, Yale University School of Medicine, Cedar St. 333, New Haven, 06520-8009, Connecticut, USA

    Kei-Hoi Cheung

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Marshall, M.S., Roos, M., Meij, E., Katrenko, S., van Hage, W.R., Adriaans, P.W. (2010). Semantic Disclosure in an e-Science Environment. In: Chen, H., Wang, Y., Cheung, KH. (eds) Semantic e-Science. Annals of Information Systems, vol 11. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-5908-9_2

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