Skip to main content
SpringerLink
Log in

Alignment of Biomedical Ontologies Using Life Science Literature

  • Conference paper
Knowledge Discovery in Life Science Literature (KDLL 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3886))

Abstract

In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned. In this paper we propose strategies for aligning ontologies based on life science literature. We propose a basic algorithm as well as extensions that take the structure of the ontologies into account. We evaluate the strategies and compare them with strategies implemented in the alignment system SAMBO. We also evaluate the combination of the proposed strategies and the SAMBO strategies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Collins, F., Green, E., Guttmacher, A., Guyer, M.: A vision for the future of genomics research. Nature 422, 835–847 (2003)

    Article  Google Scholar 

  2. Entrez, http://www.ncbi.nlm.nih.gov/Database/index.html

  3. Euzenat, J.: Introduction to the EON ontology alignment context. In: 3rd Int. Workshop on the Evaluation of Ontology-based Tools (2004)

    Google Scholar 

  4. The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genetics 25(1), 25–29 (2000), http://www.geneontology.org/

  5. Gómez-Pérez, A.: Ontological Engineering: A state of the Art. Expert Update 2(3), 33–43 (1999)

    Google Scholar 

  6. Jakoniene V., Lambrix P.: Ontology-based Integration for Bioinformatics. In: VLDB Workshop on Ontologies-based techniques for DataBases and Information Systems - ODBIS 2005, pp. 55-58 (2005)

    Google Scholar 

  7. Lambrix, P.: Ontologies in Bioinformatics and Systems Biology. In: Dubitzky, W., Azuaje, F. (eds.) Artificial Intelligence Methods and Tools for Systems Biology, ch. 8, vol. 8, pp. 129–146. Springer, Heidelberg (2004)

    Google Scholar 

  8. Lambrix, P.: Towards a Semantic Web for Bioinformatics using Ontology-based Annotation. In: 14th IEEE WET-ICE, Invited talk, pp. 3–7 (2005)

    Google Scholar 

  9. Lambrix, P., Edberg, A.: Evaluation of ontology merging tools in bioinformatics. Pacific Symposium on Biocomputing 8, 589–600 (2003)

    MATH  Google Scholar 

  10. Lambrix, P., Tan, H.: Merging DAML+OIL Ontologies. In: Barzdins, Caplinskas (eds.) Databases and Information Systems, pp. 249–258. IOS Press, Amsterdam (2005)

    Google Scholar 

  11. Lambrix, P., Tan, H.: A Framework for Aligning Ontologies. In: Fages, F., Soliman, S. (eds.) PPSWR 2005. LNCS, vol. 3703, pp. 17–31. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  12. Lambrix, P., Tan, H.: SAMBO - a System for Aligning and Merging Biomedical Ontologies (submitted, 2005)

    Google Scholar 

  13. MEDLINE, http://www.nlm.nih.gov/databases/databases_medline.html

  14. Mitchell, T.: Machine Learning. McGraw-Hill, New York (1997)

    MATH  Google Scholar 

  15. Mitra, P., Wiederhold, G.: Resolving terminological heterogeneity in ontologies. In: ECAI Workshop on Ontologies and Semantic Interoperability (2002)

    Google Scholar 

  16. Noy, N., Musen, M.: Anchor-PROMPT: Using Non-Local Context for Semantic Matching. In: IJCAI Workshop on Ontologies and Information Sharing, pp. 63–70 (2001)

    Google Scholar 

  17. Open Biomedical Ontologies, http://obo.sourceforge.net/

  18. OntoWeb Consortium: Deliverables 1.3 (A survey on ontology tools) and 1.4 (A survey on methodologies for developing, maintaining, evaluating and reengineering ontologies) (2002)

    Google Scholar 

  19. Protégé, http://protege.stanford.edu/index.html

  20. PubMed, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

  21. REWERSE, http://www.rewerse.net

  22. Stumme, G., Mädche, A.: FCA-Merge: Bottom-up merging of ontologies. In: 17th IJCAI, pp. 225–230 (2001)

    Google Scholar 

  23. Sayers E., Wheeler D.: Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils). NCBI Coursework

    Google Scholar 

  24. Sushama, S., Yun, P., Timothy, F.: Using Explicit Information To Map Between Two Ontologies. In: AAMAS Workshop on Ontologies in Agent Systems (2002)

    Google Scholar 

  25. Takai-Igarashi, T., Nadaoka, Y., Kaminuma, T.: A Database for Cell Signaling Networks. Journal of Computational Biology 5(4), 747–754 (1998)

    Article  Google Scholar 

  26. UMLS, http://www.nlm.nih.gov/research/umls/

  27. WordNet, http://wordnet.princeton.edu/

Download references

Author information

Authors and Affiliations

  1. Department of Computer and Information Science, Linköpings universitet, SE-581 83, Linköping, Sweden

    He Tan, Vaida Jakonienė, Patrick Lambrix, Johan Aberg & Nahid Shahmehri

Authors
  1. He Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vaida Jakonienė
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Patrick Lambrix
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Johan Aberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nahid Shahmehri
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Brain Tumor Research Program, Children’s Memorial Hospital, and Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

    Eric G. Bremer

  2. Computer Science Department, Knowledge Management in Bioinformatics, Humbold-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany

    Jörg Hakenberg

  3. iXmatch Inc., 5555 West 78th Street Suite E, 55439-2702, Minneapolis, MN, USA

    Eui-Hong (Sam) Han

  4. School of Biomedical Sciences, University of Ulster, Cromore Road,, BT52 1SA, Coleraine, Northern Ireland, UK

    Daniel Berrar

  5. School of Biomedial Sciences, Bioinformatics Research Group, University of Ulster, Cromore Road, BT52 1SA, Coleraine, Northern Ireland, UK

    Werner Dubitzky

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Tan, H., Jakonienė, V., Lambrix, P., Aberg, J., Shahmehri, N. (2006). Alignment of Biomedical Ontologies Using Life Science Literature. In: Bremer, E.G., Hakenberg, J., Han, EH.(., Berrar, D., Dubitzky, W. (eds) Knowledge Discovery in Life Science Literature. KDLL 2006. Lecture Notes in Computer Science(), vol 3886. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11683568_1

Download citation

  • DOI: https://doi.org/10.1007/11683568_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-32809-4

  • Online ISBN: 978-3-540-32810-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation