Advertisement

Extracting Justifications from BioPortal Ontologies

  • Matthew Horridge
  • Bijan Parsia
  • Ulrike Sattler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7650)

Abstract

This paper presents an evaluation of state of the art black box justification finding algorithms on the NCBO BioPortal ontology corpus. This corpus represents a set of naturally occurring ontologies that vary greatly in size and expressivity. The results paint a picture of the performance that can be expected when finding all justifications for entailments using black box justification finding techniques. The results also show that many naturally occurring ontologies exhibit a rich justificatory structure, with some ontologies having extremely high numbers of justifications per entailment.

Keywords

Biomedical Ontology Model Base Diagnosis Cell Line Ontology Entailment Check Ontology Document 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Readings in Model Based Diagnosis. Morgan Kaufmann Publishers Inc. (1992)Google Scholar
  2. 2.
    Baader, F., Peñaloza, R.: Axiom pinpointing in general tableaux. Journal of Logic Computation 20(1), 5–34 (2010)zbMATHCrossRefGoogle Scholar
  3. 3.
    Cuenca Grau, B., Halaschek-Wiener, C., Kazakov, Y.: History Matters: Incremental Ontology Reasoning Using Modules. In: Aberer, K., Choi, K.-S., Noy, N., Allemang, D., Lee, K.-I., Nixon, L.J.B., Golbeck, J., Mika, P., Maynard, D., Mizoguchi, R., Schreiber, G., Cudré-Mauroux, P. (eds.) ASWC 2007 and ISWC 2007. LNCS, vol. 4825, pp. 183–196. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  4. 4.
    Dolby, J., Fokoue, A., Kalyanpur, A., Kershenbaum, A., Schonberg, E., Srinivas, K., Ma, L.: Scalable semantic retrieval through summarization and refinement. In: AAAI 2007 (2007)Google Scholar
  5. 5.
    Glimm, B., Rudolph, S., Völker, J.: Integrated Metamodeling and Diagnosis in OWL 2. In: Patel-Schneider, P.F., Pan, Y., Hitzler, P., Mika, P., Zhang, L., Pan, J.Z., Horrocks, I., Glimm, B. (eds.) ISWC 2010, Part I. LNCS, vol. 6496, pp. 257–272. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  6. 6.
    Golbreich, C., Horrocks, I.: The OBO to OWL mapping, GO to OWL 1.1! In: OWLED 2007 (2007)Google Scholar
  7. 7.
    Grimm, S., Wissmann, J.: Elimination of Redundancy in Ontologies. In: Antoniou, G., Grobelnik, M., Simperl, E., Parsia, B., Plexousakis, D., De Leenheer, P., Pan, J. (eds.) ESWC 2011, Part I. LNCS, vol. 6643, pp. 260–274. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  8. 8.
    Grove, M.: OWLSight (October 2009), http://pellet.owldl.com/ontology-browser
  9. 9.
    Halaschek-Wiener, C., Katz, Y., Parsia, B.: Belief base revision for expressive description logics. In: OWLED 2006 (2006)Google Scholar
  10. 10.
    Horridge, M.: Justification Based Explanation in Ontologies. Ph.D. thesis, School of Computer Science, The University of Manchester (2011)Google Scholar
  11. 11.
    Horridge, M., Bechhofer, S.: The OWL API: A Java API for OWL ontologies. Semantic Web 2(1), 11–21 (2011)Google Scholar
  12. 12.
    Horridge, M., Parsia, B., Sattler, U.: Explanation of OWL entailments in Protégé-4. Poster and Demo Track, ISWC 2008 (2008)Google Scholar
  13. 13.
    Horridge, M., Parsia, B., Sattler, U.: Laconic and Precise Justifications in OWL. In: Sheth, A.P., Staab, S., Dean, M., Paolucci, M., Maynard, D., Finin, T., Thirunarayan, K. (eds.) ISWC 2008. LNCS, vol. 5318, pp. 323–338. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  14. 14.
    Ji, Q., Haase, P., Qi, G., Hitzler, P., Stadtmüller, S.: RaDON — Repair and Diagnosis in Ontology Networks. 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. 863–867. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  15. 15.
    Ji, Q., Qi, G., Haase, P.: A Relevance-Directed Algorithm for Finding Justifications of DL Entailments. In: Gómez-Pérez, A., Yu, Y., Ding, Y. (eds.) ASWC 2009. LNCS, vol. 5926, pp. 306–320. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  16. 16.
    Kalyanpur, A.: Debugging and Repair of OWL Ontologies. Ph.D. thesis, The Graduate School of the University of Maryland (2006)Google Scholar
  17. 17.
    Kalyanpur, A., Parsia, B., Hendler, J.: A tool for working with web ontologies. International Journal on Semantic Web and Information Systems 1 (2005)Google Scholar
  18. 18.
    Kalyanpur, A., Parsia, B., Horridge, M., Sirin, E.: Finding All Justifications of OWL DL Entailments. In: Aberer, K., Choi, K.-S., Noy, N., Allemang, D., Lee, K.-I., Nixon, L.J.B., Golbeck, J., Mika, P., Maynard, D., Mizoguchi, R., Schreiber, G., Cudré-Mauroux, P. (eds.) ASWC 2007 and ISWC 2007. LNCS, vol. 4825, pp. 267–280. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  19. 19.
    Knublauch, H.: Composing the semantic web: Explaining inferences, http://composing-the-semantic-web.blogspot.com/2007/08/explanining-inferences.html
  20. 20.
    Meyer, T., Lee, K., Booth, R., Pan, J.Z.: Finding maximally satisfiable terminologies for the description logic \(\mathcal{ALC}\). In: AAAI 2006 (2006)Google Scholar
  21. 21.
    Mungall, C.: OBO Flat File Format 1.4 syntax and semantics (February 2011), ftp://ftp.geneontology.org/pub/go/www/obo-syntax.html
  22. 22.
    Noy, N.F.: BioPortal: Ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37 (May 2009)Google Scholar
  23. 23.
    Reiter, R.: A theory of diagnosis from first principles. Artificial Intelligence 32, 57–95 (1987)MathSciNetzbMATHCrossRefGoogle Scholar
  24. 24.
    Scharrenbach, T., d’Amato, C., Fanizzi, N., Grütter, R., Waldvogel, B., Bernstein, A.: Default Logics for Plausible Reasoning with Controversial Axioms. In: Bobillo, F. (ed.) URSW 2010 (2010)Google Scholar
  25. 25.
    Schlobach, S., Cornet, R.: Non-standard reasoning services for the debugging of description logic terminologies. In: IJCAI 2003 (2003)Google Scholar
  26. 26.
    Schlobach, S., Huang, Z., Cornet, R., van Harmelen, F.: Debugging incoherent terminologies. Journal of Automated Reasoning 39, 317–349 (2007)MathSciNetzbMATHCrossRefGoogle Scholar
  27. 27.
    Shchekotykhin, K., Friedrich, G., Jannach, D.: On computing minimal conflicts for ontology debugging. In: ECAI 2008 (2008)Google Scholar
  28. 28.
    Smith, B.: The OBO Foundary: Coordinated evolution of ontology to support biomedical data integration. Nature BiotechnologyGoogle Scholar
  29. 29.
    Stuckenschmidt, H.: Debugging OWL ontologies - a reality check. In: EON-SWSC 2008 (2008)Google Scholar
  30. 30.
    Suntisrivaraporn, B.: Polynomial-Time Reasoning Support for Design and Maintenance of Large-Scale Biomedical Ontologies. Ph.D. thesis, Technical University of Dresden (2009)Google Scholar
  31. 31.
    Suntisrivaraporn, B., Qi, G., Ji, Q., Haase, P.: A Modularization-Based Approach to Finding All Justifications for OWL DL Entailments. In: Domingue, J., Anutariya, C. (eds.) ASWC 2008. LNCS, vol. 5367, pp. 1–15. Springer, Heidelberg (2008)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Matthew Horridge
    • 1
  • Bijan Parsia
    • 2
  • Ulrike Sattler
    • 2
  1. 1.Stanford UniversityUSA
  2. 2.The University of ManchesterManchesterUK

Personalised recommendations