Skip to main content
SpringerLink
Log in

On Matching Large Life Science Ontologies in Parallel

  • Conference paper
Data Integration in the Life Sciences (DILS 2010)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6254))

Included in the following conference series:

Abstract

Matching life science ontologies to determine ontology mappings has recently become an active field of research. The large size of existing ontologies and the application of complex match strategies for obtaining high quality mappings makes ontology matching a resource- and time-intensive process. To improve performance we investigate different approaches for parallel matching on multiple compute nodes. In particular, we consider inter-matcher and intra-matcher parallelism as well as the parallel execution of element- and structure-level matching. We implemented a distributed infrastructure for parallel ontology matching and evaluate different approaches for parallel matching of large life science ontologies in the field of anatomy and molecular biology.

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. Aumueller, D., Do, H.H., Massmann, S., Rahm, E.: Schema and ontology matching with COMA++. In: Proc. of ACM SIGMOD Intl. Conference on Management of Data, pp. 906–908 (2005)

    Google Scholar 

  2. Bastian, F., Parmentier, G., Roux, J., et al.: Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds.) DILS 2008. LNCS (LNBI), vol. 5109, pp. 124–131. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  3. Bernstein, P.A., Melnik, S., Petropoulos, M., Quix, C.: Industrial Strength Schema Matching. ACM SIGMOD Record 33(4), 38–43 (2004)

    Article  Google Scholar 

  4. Bodenreider, O., Burgun, A.: Linking the Gene Ontology to other biological ontologies. In: Proc. of 8th ISMB Meeting on Bio-Ontologies, pp. 17–18 (2005)

    Google Scholar 

  5. Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Briefings in Bioinformatics 7(3), 256–274 (2006)

    Article  Google Scholar 

  6. Do, H.H., Rahm, E.: COMA – A System for Flexible Combination of Schema Matching Approaches. In: Proc. of the 28th Intl. Conference on Very Large Databases (VLDB), pp. 610–621 (2002)

    Google Scholar 

  7. Do, H.H., Rahm, E.: Matching large schemas: Approaches and evaluation. Information Systems 32(6), 857–885 (2007)

    Article  Google Scholar 

  8. Ehrig, M., Staab, S.: QOM – Quick Ontology Mapping. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 683–697. Springer, Heidelberg (2004)

    Google Scholar 

  9. Euzenat, J., Shvaiko, P.: Ontology Matching. Springer, Heidelberg (2007)

    MATH  Google Scholar 

  10. The Gene Ontology Consortium: The Gene Ontology project in 2008. Nucleic Acids Research 36(Database issue), D440–D444 (2008)

    Google Scholar 

  11. Gross, A., Hartung, M., Kirsten, T., Rahm, E.: Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes. In: Paton, N.W., Missier, P., Hedeler, C. (eds.) DILS 2009. LNCS (LNBI), vol. 5647, pp. 71–87. Springer, Heidelberg (2009)

    Google Scholar 

  12. Hartung, M., Kirsten, T., Rahm, E.: Analyzing the Evolution of Life Science Ontologies and Mappings. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds.) DILS 2008. LNCS (LNBI), vol. 5109, pp. 11–27. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  13. Hayamizu, T.F., Mangan, M., Corradi, J.P., Kadin, J.A., Ringwald, M.: The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biology 6(3), R29 (2005)

    Article  Google Scholar 

  14. Hu, W., Qu, Y., Cheng, G.: Matching large ontologies: A divide-and-conquer approach. Data & Knowledge Engineering 67(1), 140–160 (2008)

    Article  Google Scholar 

  15. Jakoniene, V., Lambrix, P.: Ontology-based integration for bioinformatics. In: Proc. VLDB Workshop on Ontologies-based techniques for Databases and Information Systems (ODBIS), pp. 55–58 (2005)

    Google Scholar 

  16. Kirsten, T., Hartung, M., Gross, A., Rahm, E.: Efficient Management of Biomedical Ontology Versions. In: Meersman, R., Herrero, P., Dillon, T.S. (eds.): On the Move to Meaningful Internet Systems Workshops. Proceedings. LNCS, vol. 4544, pp. 172-187. Springer, Heidelberg (2007)

    Google Scholar 

  17. Kirsten, T., Thor, A., Rahm, E.: Instance-based matching of large life science ontologies. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds.) DILS 2008. LNCS (LNBI), vol. 5109, pp. 11–27. Springer, Heidelberg (2008)

    Google Scholar 

  18. Lambrix, P., Edberg, A.: Evaluation of ontology merging tools in bioinformatics. In: Proc. of the 8th Pacific Symposium on Biocomputing, pp. 589–600 (2003)

    Google Scholar 

  19. Lambrix, P., Tan, H., Jakoniene, V., Strömbäck, L.: Biological Ontologies. In: Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, pp. 85–99 (2007)

    Google Scholar 

  20. Ontology Alignment Evaluation Initiative, http://20.ontologymatching.org/

  21. Melnik, S., Garcia-Molina, H., Rahm, E.: Similarity Flooding: A Versatile Graph Matching Algorithm and Its Application to Schema Matching. In: Proc. of the 18th Intl. Conference on Data Engineering (ICDE), pp. 117–128 (2002)

    Google Scholar 

  22. Mork, P., Bernstein, P.A.: Adapting a Generic Match Algorithm to Align Ontologies of Human Anatomy. In: Proc. of the 20th Intl. Conference on Data Engineering (ICDE), pp. 787–790 (2004)

    Google Scholar 

  23. Peukert, E., Berthold, H., Rahm, E.: Rewrite Techniques for performance Optimization of Schema Matching Processes. In: Proc. 13th Intl. Conference on Extending Database Technology (EDBT), pp. 453–464 (2010)

    Google Scholar 

  24. Rahm, E., Bernstein, P.A.: A survey of approaches to automatic schema matching. VLDB Journal 10(4), 334–350 (2001)

    Article  MATH  Google Scholar 

  25. Rahm, E., Do, H.H., Massmann, S.: Matching large XML schemas. ACM SIGMOD Record 33(4), 26–31 (2004)

    Article  Google Scholar 

  26. Rance, B., Gibrat, J.F., Froidevaux, C.: An Adaptive Combination of Matchers: Application to the Mapping of Biological Ontologies for Genome Annotation. In: Paton, N.W., Missier, P., Hedeler, C. (eds.) DILS 2009. LNCS (LNBI), vol. 5647, pp. 113–126. Springer, Heidelberg (2009)

    Google Scholar 

  27. Saleem, K., Bellahsene, Z., Hunt, E.: PORSCHE: Performance ORiented SCHEma mediation. Information Systems 33(7-8), 637–657 (2008)

    Article  Google Scholar 

  28. Seddiqui, H., Aono, M.: An efficient and scalable algorithm for segmented alignment of ontologies of arbitrary size. Web Semantics: Science, Services and Agents on the World Wide Web 7(4), 344–356 (2009)

    Article  Google Scholar 

  29. Shvaiko, P., Euzenat, J.: Ten challenges for ontology matching. In: Proc. of on the Move to Meaningful Internet Systems (OTM), pp. 1164–1182 (2008)

    Google Scholar 

  30. Sioutos, N., de Coronado, S., Haber, M.W., et al.: NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics 40(1), 30–43 (2007)

    Article  Google Scholar 

  31. Smith, B., Ashburner, M., Rosse, C., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25(11), 1251–1255 (2007)

    Article  Google Scholar 

  32. Thor, A., Hartung, M., Gross, A., Kirsten, T., Rahm, E.: An evolution-based approach for assessing ontology mappings - A case study in the life sciences. In: Proc. Conference of the Business, Technology and Web (BTW), pp. 277–286 (2009)

    Google Scholar 

  33. Zhang, S., Bodenreider, O.: Aligning Representations of Anatomy using Lexical and Structural Methods. In: Proc. of AMIA Annual Symposium, pp. 753–757 (2003)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, University of Leipzig,  

    Anika Gross, Michael Hartung & Erhard Rahm

  2. Interdisciplinary Centre for Bioinformatics, University of Leipzig,  

    Anika Gross, Michael Hartung, Toralf Kirsten & Erhard Rahm

  3. Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig,  

    Toralf Kirsten

Authors
  1. Anika Gross
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael Hartung
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Toralf Kirsten
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Erhard Rahm
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

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

    Patrick Lambrix

  2. Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, 412 96, Gothenburg,, Sweden

    Graham Kemp

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Gross, A., Hartung, M., Kirsten, T., Rahm, E. (2010). On Matching Large Life Science Ontologies in Parallel. In: Lambrix, P., Kemp, G. (eds) Data Integration in the Life Sciences. DILS 2010. Lecture Notes in Computer Science(), vol 6254. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15120-0_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-15120-0_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15119-4

  • Online ISBN: 978-3-642-15120-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation