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A System for Debugging Missing Is-a Structure in Networked Ontologies

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Data Integration in the Life Sciences (DILS 2010)

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

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Abstract

Ontologies are recognized as a key technology for semantics-based integration of the many available biomedical data sources. However, developing ontologies is not an easy task and the resulting ontologies may have defects affecting the results of ontology-based data integration and retrieval. In this paper we present a system for debugging ontologies regarding an important kind of modeling defects. Our system supports a domain expert to detect and repair missing is-a structure in ontologies in a semi-automatic way. The input for our system is a set of ontologies networked by correct mappings between their terms. Our tool uses the ontologies and mappings as domain knowledge to detect missing is-a relations in these ontologies. It also assists the user in repairing the ontologies by generating and recommending possible ways of repairing and executing the chosen repairing strategy. The detection and repairing phases can be interleaved. We present our approach, an implemented system as well as an experiment with two anatomy ontologies.

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References

  1. Bada, M., Hunter, L.: Identification of OBO nonalignments and its implication for OBO enrichment. Bioinformatics 24(12), 1448–1455 (2008)

    Article  Google Scholar 

  2. Cheung, K.-H., Smith, A., Yip, K., Baker, C., Gerstein, M.: Semantic web approach to database integration in the life sciences. In: Baker, Cheung (eds.) Semantic Web: revolutionizing knowledge discovery in the life sciences, pp. 11–30. Springer, Heidelberg (2007)

    Google Scholar 

  3. Cimiano, P., Staab, S.: Learning by googling. ACM SIGKDD Explorations Newsletter 6(2), 24–33 (2004)

    Article  Google Scholar 

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

    Article  Google Scholar 

  5. Conroy, C., Brennan, R., O’Sullivan, D., Lewis, D.: User evaluation study of a tagging approach to semantic mapping. In: Aroyo, L., Traverso, P., Ciravegna, F., Cimiano, P., Heath, T., Hyvönen, E., Mizoguchi, R., Oren, E., Sabou, M., Simperl, E. (eds.) ESWC 2009. LNCS, vol. 5554, pp. 623–637. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  6. Feneis, F., Dauber, W.: Pocket Atlas of Human Anatomy, 4th edn. Thieme Verlag (2000)

    Google Scholar 

  7. Hearst, M.A.: Automatic acquisition of hyponyms from large text corpora. In: 14th Int. Conf. on Computational Linguistics, pp. 539–545 (1992)

    Google Scholar 

  8. Jena, http://jena.sourceforge.net/

  9. Ji, Q., Haase, P., Qi, G., Hitzler, P., Stadtmuller, S.: RaDON - repair and diagnosis in ontology networks. In: Aroyo, L., et al. (eds.) ESWC 2009. LNCS, vol. 5554, pp. 863–867. Springer, Heidelberg (2009)

    Google Scholar 

  10. Kalyanpur, A., Parsia, B., Sirin, E., Hendler, J.: Debugging unsatisfiable classes in OWL ontologies. Journal of Web Semantics 3(4), 268–293 (2006)

    Google Scholar 

  11. Lacroix, Z., Critchlow, T.: Bioinformatics: managing scientific data. Morgan Kaufmann, San Francisco (2003)

    Google Scholar 

  12. Lambrix, P., Liu, Q.: Debugging the missing is-a structure within ontologies networked by partial reference alignments (forthcoming)

    Google Scholar 

  13. Lambrix, P., Liu, Q.: Using partial reference alignments to align ontologies. In: Aroyo, L., Traverso, P., Ciravegna, F., Cimiano, P., Heath, T., Hyvönen, E., Mizoguchi, R., Oren, E., Sabou, M., Simperl, E. (eds.) ESWC 2009. LNCS, vol. 5554, pp. 188–202. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  14. Lambrix, P., Liu, Q., Tan, H.: Repairing the missing is-a structure of ontologies. In: 4th Asian Semantic Web Conf., pp. 371–386 (2009)

    Google Scholar 

  15. Lambrix, P., Strömbäck, L., Tan, H.: Information integration in bioinformatics with ontologies and standards. In: Bry, Maluszynski (eds.) Semantic Techniques for the Web: The REWERSE perspective, pp. 343–376. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  16. MA. Adult mouse anatomical dictionary, http://www.informatics.jax.org/searches/AMA_form.shtml

  17. Maedche, A., Pekar, V., Staab, S.: Ontology learning part one - on discovering taxonomic relations from the web. In: Zhong, Liu, Yao (eds.) Web Intelligence, pp. 301–322. Springer, Heidelberg (2003)

    Google Scholar 

  18. Meilicke, C., Stuckenschmidt, H., Tamilin, A.: Repairing ontology mappings. In: 20th National Conf. on Artificial Intelligence, pp. 1408–1413 (2007)

    Google Scholar 

  19. MeSH. Medical subject headings, http://www.nlm.nih.gov/mesh/

  20. NCI-A. National cancer institute - anatomy, http://www.cancer.gov/cancerinfo/terminologyresources/

  21. Neches, R., Fikes, R., Finin, T., Gruber, T., Patil, R., Senator, T., Swartout, W.: Enabling technology for knowledge sharing. AI Magazine 12(3), 36–56 (1991)

    Google Scholar 

  22. Noy, N.F., Griffith, N., Musen, M.: Collecting community-based mappings in an ontology repository. In: 7th Int. Semantic Web Conf., pp. 371–386 (2008)

    Google Scholar 

  23. OBO. Open biological and biomedical ontologies, http://obo.sourceforge.net/

  24. PubMed, http://www.ncbi.nlm.nih.gov/pubmed/

  25. Schlobach, S.: Debugging and semantic clarification by pinpointing. In: Gómez-Pérez, A., Euzenat, J. (eds.) ESWC 2005. LNCS, vol. 3532, pp. 226–240. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  26. Schlobach, S., Cornet, R.: Non-standard reasoning services for the debugging of description logic terminologies. In: 18th Int. Joint Conf. on Artificial Intelligence, pp. 355–360 (2003)

    Google Scholar 

  27. UMLS. Unified medical language system, http://www.nlm.nih.gov/research/umls/about_umls.html

  28. van Hage, W.R., Katrenko, S., Schreiber, G.: A method to combine linguistic ontology-mapping techniques. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 732–744. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  29. Völker, J., Hitzler, P., Cimiano, P.: Acquisition of OWL DL axioms from lexical resources. In: Franconi, E., Kifer, M., May, W. (eds.) ESWC 2007. LNCS, vol. 4519, pp. 670–685. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  30. Wächter, T., Tan, H., Wobst, A., Lambrix, P., Schroeder, M.: A corpus-driven approach for design, evolution and alignment of ontologies. In: Winter Simulation Conf., pp. 1595–1602 (2006) (invited contribution)

    Google Scholar 

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

  32. Zavitsanos, E., Paliouras, G., Vouros, G.A., Petridis, S.: Discovering subsumption hierarchies of ontology concepts from text corpora. In: IEEE/WIC/ACM Int. Conf. on Web Intelligence, pp. 402–408 (2007)

    Google Scholar 

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Authors and Affiliations

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

    Qiang Liu & Patrick Lambrix

Authors
  1. Qiang Liu
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  2. Patrick Lambrix
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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

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Liu, Q., Lambrix, P. (2010). A System for Debugging Missing Is-a Structure in Networked Ontologies. 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_5

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  • DOI: https://doi.org/10.1007/978-3-642-15120-0_5

  • 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)

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